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SwedishEpigeneticsandChromatinMeetingEpiChrom2017
November30–December1,2017Rudbecksalen
DagHammarskjöldsväg20Uppsala
Artworkkindlyprovidedby:Dr.MhairiTowler-UniversityofDundee/Vivomotion(www.vivomotion.co.uk),LinkLiandDr.PaulHarrison-UniversityofDundee
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Day1
8:00 Registrationandcoffee8:30 Welcomeaddress8:40 SessionI:UnderstandingEpigeneticsI8:40 UnderstandingthenexusbetweenlncRNAsandchromatin-levelgeneexpression
ChandrasekharKanduri,UniversityofGothenburg9:20 AmicroarrayscreenidentifiesnovelTGFbeta-regulatedlongnon-codingRNAs
PanagiotisPapoutsoglou,UppsalaUniversity9:40 TheChromatinremodelingcomplexB-WICHisrequiredforDNAPolItranscriptionactivationby
glucosestimulationYuanGuo,StockholmUniversity
10:00 Coffeeandsandwiches10:30 SessionII:Epigeneticsinsolidtumors10:30 Tissue-typespecificfunctionalannotationoftranscriptionfactormotifsforprioritizationofnoncoding
variantsHusenUmer,UppsalaUniversity
10:50 ExosomesreleasedbypediatricgliomastemcellsinducegeneexpressionchangesinneuralcellsAgotaTuzesi,UniversityofGothenburg
11:10 OrthotopictransplantationofpediatricgliomastemcellsinmicemirrorstheclinicalcourseofthepatientAnnaWenger,UniversityofGothenburg
11:30 Coffeebreak11:50 SessionIII:Epigeneticsinhematologicalmalignancies11:50 Adistinctgeneregulatorynetwork,establishedindependentofcodingmutations,underpinstheCLL
phenotypeAylaDePaepe,KarolinskaInstitutet
12:10 DiscoveryofnewmolecularsubgroupsinpediatricALLusingDNAmethylationclassificationandRNA-sequencingYanaraMarincevic-Zuniga,UppsalaUniversity
12:30 Genome-wideDNAmethylationprofilinginchroniclymphocyticleukemiapatientscarryingstereotypedB-cellreceptorsLarryMansouri,UppsalaUniversity
12:50 Epigeneticco-regulationasapotentialtherapeutictargetinmultiplemyelomaAlbaAtienzaPárraga,UppsalaUniversity
13:10 Lunchandposters14:15 Immunememory
HenkStunnenberg,RadboudInstituteforMolecularLifeSciences(RIMLS),Nijmegen,TheNetherlands
15:15 Coffeeandsweets15:50 SessionIV:Epigeneticsandimmunity15:50 ReactivationpotentialofHIV-1inprimaryCD4Tcellsdependonthechromatinmicroenvironment
PeterSvensson,KarolinskaInstitutet16:10 MajortranscriptionalchangesobservedintheFulani,anethnicgrouplesssusceptibletomalaria
JaclynQuin,StockholmUniversity16:30 EnhancerregulationbyGPS2modulatesmacrophageinflammation
ZhiqiangHuang,KarolinskaInstitutet16:50
UtilizingepigenomicstounderstandneurodegenerationinMultipleSclerosis:whataretheneuronstellingus?LaraKular,KarolinskaInstitutet
17:10 Mingle
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Day 2
8:30 SessionV:UnderstandingEpigeneticsII8:30 DecipheringthecooperativityofPolycombrepression
YuriSchwartz,UmeåUniversity9:10 TargetingPolycombrepressivecomplexesthroughevolutionaryconservedDNAelements
JuanIgnacioBarrasaLopez,UmeåUniversity9:30 DevelopmentalpatterningandgeneregulationbytheBEN-solofamily
QiDai,StockholmUniversity9:50 ThefutureofepigeneticsatSciLifeLab?SimonElsässer,KarolinskaInstitutet10:10 Coffeeandsandwiches10:40 SessionVI:Epigeneticsacrossspecies10:40 EctopicapplicationofH3K9me2establishespostzygoticreproductiveisolationinArabidopsis
HuaJiang,SwedishUniversityofAgriculturalSciences11:00 ImprintedgeneregulationbythepaternallyexpressedgenePHERES1inArabidopsis
RitaBatista,SwedishUniversityofAgriculturalSciences11:20 GeneticdissectionofDrosophilaHDAC3function
MinTang,StockholmUniversity11:40 C12D8.1:AnegativeregulatorofRNAiinheritanceinCaenorhabditiselegans
BenjaminHolmgren,UppsalaUniversity12:00 Lunchandposters13:00 ComputationalEpigenomicApproachesforDecipheringtheNon-codingHumanGenome
JasonErnst,UniversityofCalifornia,LosAngeles(UCLA),USA14:00 Coffeebreak14:20 SessionVII:Epigenomics14:20 MechanisticInsightsintoAutoinhibitionoftheOncogenicChromatinRemodelerALC1
SebastianDeindl,UppsalaUniversity14:40 Identificationofoligodendrocytelineagestateswithsingle-cellATAC-seq
EneritzAgirre,KarolinskaInstitutet15:00 Protein-codingsequenceexclusionbyalternativetranscriptionstartsiteusageacrossthehumanbody
WenboDong,KarolinskaInstitutet15:20 Nascenttranscriptionplasticityinmouseembryonicstemcells
RuiShao,KarolinskaInstitutet15:40 Coffeeandsweets16:10 SessionVIII:Epitools16:10 Chromatrap®;Amoreefficient,sensitive&robustmethodofchromatinimmunoprecipitation
(commercial)LindsayParkes
16:25 ActiveMotif,enableschromatinandgeneregulationresearch(commercial)SarantisChlamydas
16:40 Anovelmethodologyforidentifyinggenome-wideRNA-chromatininteractionsAlessandroBonetti,KarolinskaInstitutet
17:00 ModellingthedynamicsofepigeneticmemoryLudvigLizana,UmeåUniversity
17:20 Closingremarks
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Posters EpiChrom 2017 Day 1 1
SingleCRISPR-Cas9knockoutofEMT-relatedtranscriptionfactorsfailstoinduceepithelialreversionofmesenchymalbreastcancercellsVarunMaturi,UppsalaUniversity
2 IdentificationoflncRNAassociatedwithoutcomeinacutemyeloidleukemia(AML)AnneNeddermeyer,UppsalaUniversity
3 MechanisticcharacterizationofHDACimediatedKITdownregulationinsystemicmastocytosisHaniAbdulkadirAli,KarolinskaInstitutet
4 Functionalevaluationofnon-codingmutationinChronicLymphocyticLeukemiaLuciaPenaPerez,KarolinskaInstitutet
5 Fromcellstodatain24hours-High-ThroughputChIPmentationonultra-lowcellnumbersCharlotteGustafsson,KarolinskaInstitutet
6 RROSETTA:atoolkitforcreatingroughsetmodelsMateuszGarbulowski,UppsalaUniversity
Posters EpiChrom 2017 Day 2
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AlternativesplicingandSWI/SNFchromatinremodelingcomplexAntoniGanezZapater,StockholmUniversity
2 DissectionofGPS2-PPARapathwaysgoverninghepaticlipidmetabolismNingLiang,KarolinskaInstitutet
3 InvestigatingthefunctionofBEN-solotranscriptionfactorsinthedevelopingDrosophilaCNSMalinUeberschär,StockholmUniversity
4 SPlintedLigationAdapterTagging(SPLAT),anovellibrarypreparationmethodforwholegenomebisulphitesequencingAmandaRaine,UppsalaUniversity
5 MonitoringoftheepigeneticstateinlivecellsCeciliaBergqvist,StockholmUniversity
6 Improvedtreatmentsofpediatricbraintumorsusingepigeneticdrugs?SusannaLarsson,SahlgrenskaCancerCenter/UniversityofGothenburg
7 LSD1modulationbyallostericligandsJohanWinquist,Beactica
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Thursday, November 30th 2017
Session I: Understanding Epigenetics I Chair:HelenaJernberg-Wiklund
Invitedspeaker:
ChandrasekharKanduri
Dr.ChandraKanduriisaProfessorattheDepartmentofMedicalBiochemistryand Cell Biology, Institute of Biomedicine, University of Gothenburg,Gothenburg. He holds a doctoral degree from the Banaras Hindu University,India and did his postdoctoral work at the Department of Development andGenetics, Uppsala University. He is a MHF1-Vetenskapsrådet-Medicin panelmember and a reviewer for AICR, ESF, EURYI (European Young InvestigatorAward), The Netherlands organization for Scientific Research (NWO), FRMFrance,INSERMFranceandSwissNationalFoundation.
Hisworkexploresthefunctionoflong-noncodingRNAsintheepigeneticregulationoftranscriptionduring development and disease, and aims at developing lncRNA-based therapeutics in thetreatmentofcancer.
Understanding the nexus between lncRNAs and chromatin-level gene expression
Chromatin is organized into active and inactive compartments with distinct epigenetics codes.These active and inactive chromatin-specific histone modifications are defined by regulatoryinteractions between DNA sequences and chromatin remodelers in a tissue and developmentalstage dependent manner. However, it is not clear how chromatin remodelers are targeted tospecificchromatinregionsacrossthegenome.RecentevidencessuggestthatlncRNAsconstituteanimportant feature in the targeting of chromatin remodelers across the genome. Thus there is agrowinginteresttoaddressthefunctionalcontributionoflncRNAsinthesub-compartmentalizationof the eukaryotic genome. Characterization of chromatin-associated lncRNAs in functionallydemarcatedchromatincompartmentsmayhelpusbetterunderstandthefunctionalnexusbetweenlncRNAs and epigenetic states of the chromatin. Towards this broader aim, we have optimizedchromatinRNAimmunoprecipitation(ChRIP),toprofilechromatinassociatedRNAtranscriptsfromdifferentchromatincompartmentsacrossthegenome.ByusingChRIPtechnique,wecharacterizedlncRNAsthatarefunctionallyassociatedwithactive(enrichedwithahistonemodificationH3K4me2andachromatinreaderandH3K4-specificmethyltransferaseWDR5)andinactive(enrichedwithahistone modification H3K27me3 and H3K27-specific methyltransferase EZH2) chromatincompartments.ByperformingmechanisticinvestigationsonahandfulofselectedcandidatesfromtheactiveandinactivechromatinassociatedlncRNAs,wehavecharacterizedmechanismsbywhichtheyinfluencetargetgeneexpressionincisortransviatargetingchromatinremodelers.
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A microarray screen identifies novel TGFβ-regulated long non-coding RNAs
PanagiotisPapoutsoglou1,YutaroTsubakihara1,Carl-HenrikHeldin1andAristidisMoustakas11DepartmentofMedicalBiochemistryandMicrobiology,ScienceforLifeLaboratory,UppsalaUniversity,Uppsala,Sweden
The transforming growth factor beta (TGFβ) signaling pathway plays crucial roles in embryonicdevelopment, cellular homeostasis and tumor progression. TGFβ signals via the activation ofeffectorSmadproteins,Smad2andSmad3,whicharephosphorylatedbythetypeITGFβreceptor.Smad2/3formcomplexwiththecommonSmad(Smad4)andtranslocateintothenucleus,engagingintheregulationofgeneexpression.Longnon-codingRNAs(lncRNAs)aretranscripts, longerthan200nucleotides, lacking inproteincodingpotential.Theymainlyparticipate in themodulationofgene expression at the transcriptional or post-transcriptional level by interacting with genomicregions,RNAmoleculesorproteins.AlthoughthebiologyoflncRNAshasbeenextensivelystudiedoverthelastyears,theirmechanismsoffunction,aswellastheirinvolvementinTGFβsignalingarenot fully understood. In this study, we aimed to elucidate novel lncRNAs, whose expression isregulatedbyTGFβsignaling.OurmicroarrayexperimentrevealedseveralTGFβ-targetlncRNAsandamongthem,wefocusedonthegeneadjacenttotheTGFB2locus,namedasTGFB2antisenseRNA1 (TGFB2-AS1),which is induced by TGFβ. Both Smad and protein kinase signaling pathways areimportantfortheinductionofTGFB2-AS1expression.UsingRNAinsituhybridizationweobservedapredominant nuclear localizationof the TGFB2-AS1 transcript.Depletionof TGFB2-AS1 enhancedthe TGFβ/Smad-mediated transcriptional responses, aswell as theexpressionof the TGFβ-targetgenes fibronectin, SMAD7 and PAI-1. On the other hand, cells stably over-expressing TGFB2-AS1showed reduced fibronectin and SMAD7expression levels.Moreover, TGFB2-AS1 attenuated theTGFβ-inducedcellgrowtharrestinhumanimmortalizedkeratinocytes.Collectively,weidentifiedanovelTGFβ-targetlncRNAwithaninhibitoryroleonTGFβsignalingoutput,suggestingthatTGFB2-AS1isapartofanauto-regulatorynegativefeedbackloopthatbalancesTGFβ-mediatedresponses.
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The Chromatin remodeling complex B-WICH is required for DNA Pol I transcription activation by glucose stimulation
Anna Rolicka1, Yuan Guo1, Antoni Zapater Ganez1, Jaclyn Quin1, Anna Vintermist1,FatemehSadeghifar1,MarieHenriksson2andAnn-KristinÖstlundFarrants11DepartmentofMolecularBiosciences,TheWenner-GrenInstitute,StockholmUniversity2DepartmentofMicrobiology,TumorandCellBiology,KarolinskaInstitute
The Chromatin remodeling complex B-WICHwith its core sub-units SNF2h, theWilliamSyndrome Transcription Factor (WSTF) and nuclear myosin (NM1), is involved intranscription of ribosomal genes and associates with the RNA pol I machinery in thenucleolus.InRNApolItranscription,B-WICHremodelschromatinlocallyatthepromoterregion andwhich leads to an increasedhistoneH3acetylation.Our recent results haveshown that B-WICH sub-unit WSTF plays an important role in glucose regulated rDNAtranscription. We have observed increased chromatin accessibility upon glucosestimulationwhichisnotobservableinabsenceofWSTF.Furthermore,wehaveobservedincreasedpresenceofthePolImachinery,H3HATSandc-MYCatrDNApromoterregion.Theunderlyingmechanismof the“closed”chromatinstate isnotknown.TheATPase inthesilencingcomplexNuRD(CHD4)whichrepressesrRNAtranscriptionwasstillpresentatthepromoteruponglucosestimulationinWSTFKDcells.
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Session II: Epigenetics in solid tumors Chair:AntoniaKalushkova
Gene regulatory defects in a pan-cancer cohort of 2,515 samples
HusenM.Umer1,JanKomorowski1,2,ClaesWadelius31ScienceforLifeLaboratory,DepartmentofCellandMolecularBiology,UppsalaUniversity,Uppsala,Sweden2InstituteofComputerScience,PolishAcademyofSciences,Warsaw,Poland3ScienceforLifeLaboratory,DepartmentofImmunology,GeneticsandPathology,UppsalaUniversity,Uppsala,Sweden
Thenoncodinggenomecontains thevastmajorityof somaticmutations identified froma cancergenome. While very few of the mutations are expected to be cancer drivers, those affectingregulatoryelementshavethepotentialtohavedownstreameffectsongenederegulationthatmaycontributetocancerprogression.Toidentifypotentialregulatorymutations,wescreenedsomaticmutations in a pan-cancer cohort of 2,515 cancerwhole genome sequences.We found a highlysignificant positive selection for regulatorymutations in transcription factor motifs across manycancer types. Overall, 10,806 mutated functional regulatory elements were identified in 2,263tumorsamplescontaining25,454candidatefunctionalregulatorymutations(CFRMs).409elementswerehighlyenrichedforsomaticmutations.OuranalysisindicatedsixorfewerCFRMspertumorin50%ofthesamplesandanaverageofelevenCFRMspertumor.Ourresultsprovideadetailedviewoftheroleofregulatorymutationsincancergenomes.
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Exosomes released by paediatric glioma stem cells induce gene expression changes in neural cells
ÁgotaTűzesi1,TeresiaKling1,AnnaWenger1,TaralRLunavat2,SuChulJang2,BertilRydenhag3,JanLötvall2,StevenM.Pollard4,AnnaDanielsson5andHelenaCarén11Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy,UniversityofGothenburg,Gothenburg,Sweden2KreftingResearchCenter,DepartmentofInternalMedicineandClinicalNutrition,UniversityofGothenburg,Gothenburg,Sweden3Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University ofGothenburg,Gothenburg,Sweden4MRCCentreforRegenerativeMedicine,UniversityofEdinburgh,EdinburghbioQuarter,5LittleFranceDrive,Edinburgh,UK5Sahlgrenska Cancer Center, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University ofGothenburg,Gothenburg,Sweden
Background:Most cells, including cancer stem cells, release different-sized vesicles that containgeneticmaterialandhavean importantrole incell–to-cellcommunication.Themoststudiedandsmallest in size of these extracellular vesicles are the exosomes.MicroRNAs (miRNAs) are smallnon-codingRNAs(19-25nucleotideslong)withmRNAsilencingfunction.MiRNAscanbeenclosedinextracellularvesiclesandtransferredfromcelltocell.A driving force behind pediatric high grade gliomas (HGG) is thought to be cancer stem cells.Epigeneticchanges,suchasthoseinducedbymiRNAs,haveanimportantroleinthegenerationandmaintenance of cancer stem cells. However, we have limited knowledge of the involvement ofexosomalmiRNAsreleasedbypediatricgliomastemcells(GSC) intothetumormicroenvironmentandtherebyinfluencingthepropertiesofneighboringcells.
Methods: We explored the expression of miRNAs in GSC and in exosomes derived therefrom,compared to normal neural stem cells (NSC) and corresponding exosomes, using miRNAmicroarrays. Further,we studied theGSC exosomalmiRNAs effect onNSCwith gene expressionanalysisusingTaqManLowDensityArray(TLDA)cards.
Results:Whereas cellular miRNAs were similar in normal and tumor cells, the exosomal miRNAprofiles differed, and our study identified several differentially expressed miRNAs. Of particularinterestismiR-1290andmiR-1246,whichhavepreviouslybeenlinkedto‘stemness’andinvasioninother cancers. We demonstrate that GSC-secreted exosomes influence the gene expression ofreceivingNSCs,particularlytargetinggeneswitharoleincellfateandtumorigenesis.
Conclusions:ThisstudyshowsthatGSCexosomescouldinfluencemalignantfeaturesofHGG.
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Orthotopic transplantation of pediatric glioma stem cells in mice mirrors the clinical course of the patient
AnnaWenger1,SusannaLarsson1,SandorDósa2,TeresiaKling1,HelenaCarén11Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy,UniversityofGothenburg2DepartmentofPathology,SahlgrenskaUniversityHospital
Background: The leading cause of cancer-related mortality among children is brain tumors andglioblastomamultiforme(GBM)hastheworstprognosis.Epigeneticderegulationisbelievedtobeadriver as these patients have few mutations compared to adults. New treatments are urgentlyneededbutfewpre-clinicalinvivomodelsexist.Oneapproachofgeneratingtheseistotransplanttumor tissue intomice, but it yields highly variable results and requires serial passaging inmice,which is time-consuming, expensive and ethically questionable.Wehave therefore established acellline-basedorthotopicmousemodelrepresentativeofthepatienttumor’smethylome.
Methods: Patient-derived cancer stem cell (CSC) lines from pediatric GBM were orthotopicallytransplanted into immunodeficient mice. The xenograft tumors were evaluated by histology forgliomafeatures.Genome-wideDNAmethylationanalysiswasperformedontheCSC,xenograftandpatienttumors.
Results:AllCSC lines initiated tumorsand thesurvivalof themicecorrelatedwith thesurvivaloftheirrespectivepatient.ThexenografttumorshadkeygliomafeaturesandwereclassifiedasGBMby histology andmethylation profiling. Themethylation profile of the xenograft tumor clusteredtogetherwith thepatient tumor (<3%ofCpG sites changedmethylation status) and the injectedCSCline.
Conclusions:Wehaveestablisheda robust and reproducible xenograftmodel forGBMbasedonprimaryCSClines.Thexenografttumorsaccuratelyreflectedthepatienttumorsandmirroredtheclinicalcourseofthepatient.Thismodelisthereforeidealforelucidatingthemethylome’sroleintumorsandaccuratelypredictingpatientresponseinpre-clinicalstudies.
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Session III: Epigenetics in hematological malignancies Chair:AndreasLennartsson
A distinct gene regulatory network, established independent of coding mutations, underpins the CLL phenotype
AleksandraKrstic1*,AylaDePaepe1*,CharlotteGustafsson1,KristinaSonnevi2,XaozeLi1,ShabnamKharazi1, Minna Taipale3, Minna Suomela1,2, Kenian Chen4, Malin Larsson5, Dag Ahrén6, RuthClifford7,EvaHellqvist1,EvaKimby1,2,YinLin4,AnnaSchuh8andRobertMånsson1,2*Theseauthorscontributedequallytothiswork1CenterforHematologyandRegenerativeMedicine,KarolinskaInstitutet,Stockholm,Sweden2HematologyCenter,KarolinskaUniversityHospital,Stockholm,Sweden3DepartmentofMedicalBiochemistryandBiophysics,KarolinskaInstitutet,Stockholm,Sweden4BaylorInstituteforImmunologyResearch,BaylorScott&WhiteResearchInstitute,Dallas5NBIS,LinköpingUniversity,Linköping,Sweden6NBIS,LundUniversity,Lund,Sweden7HaematologyDepartment,UniversityHospitalLimerick,Limerick,Ireland8DepartmentofOncology,UniversityofOxford,Oxford,UnitedKingdom
Chroniclymphocyticleukemia(CLL)patientspresentawiderangeofchromosomalaberrationsandmutations;still theyarepresentedwithaCLLphonotype.Hereweshowthat,despitethe lackofgeneticconsistency,wefoundaconsistentepigeneticsignatureforCLLusingChIP-seqandATAC-seq.Weidentifiedbothpromoter-proximalanddistalregulatoryelementswithhistoneChIP-seqforfreshlysortedperipheralbloodB-cells fromCLLpatientsandhealthycontrols.ToavoiddetectingnormalB-cellvariation,weuseduptofivedifferenthealthymatureB-cellpopulationstocontrastwith CLL. In this way we detected a set of CLL specific regulatory elements showing consistentchange between CLLs and our selection of normal B-cell populations. Linking these epigeneticchangeswiththeindividualsowngeneexpressiondeterminedbyRNA-seq,resultedinasetofCLLaberrant genes potentially deregulated by epigenetic changes. Based on ATAC-seq guidedmotifprediction in distal regulatory elementswith deviating activity in CLL,we generated networks ofpredictedchangesintranscriptionfactorusageandthegenesthesearepotentiallyderegulatinginCLL.Inaddition,ourdatacanalsodistinguishbetweentheusageofregulatoryelementsinthetwomajorCLLsubgroups,showingsignaturesspecificforIGHVmutatedandunmutatedCLL.Theresultis an exploration of regulatory elements in CLL and the proposed links these have to geneexpressionandtranscriptionfactorusage.
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Discovery of new molecular subgroups in pediatric ALL using DNA methylation classification and RNA-sequencing
YanaraMarincevic-Zuniga1,SaraNystedt1,SaraNilsson1,JohanDahlberg1,TrondFlaegstad2,MatsHeyman3, Kjeld Schmiegelow4, Kim Vettenranta5, Erik Forestier6, Gudmar Lönnerholm7, Ann-ChristineSyvänen1andJessicaNordlund11Dept.ofMedicalSciences,UppsalaUniversity2Dept.ofPediatrics,TromsøUniversityandUniversityHospital3ChildhoodCancerResearchUnit,KarolinskaInstitutet,AstridLindgrenChildren’sHospital,KarolinskaUniversityHospital4PediatricsandAdolescentMedicine,Rigshospitalet,and theMedicalFaculty, InstituteofClinicalMedicine,UniversityofCopenhagen5DivisionofHematology-OncologyandStemCellTransplantation,Children'sHospital,UniversityofHelsinki6Dept.ofMedicalBiosciences,UniversityofUmeå,7Dept.ofWomen’sandChildren’sHealth,UppsalaUniversity
Pediatricacutelymphoblasticleukemia(ALL)iscytogeneticallysub-groupedbasedonthepresenceoflarge-scalegenomicrearrangementssuchastranslocationsgivingrisetofusionsornon-randomgain/loss of chromosomes. Many of these alterations are recurrent in ALL and associated withsubtype-specific DNAmethylation (DNAm) profiles.We designedDNAm classifiers to predict thecytogeneticsubtypeofALLsamplesthatcomprisesevenofthecommonALLsubtypes1.
Herein, we evaluate the performance of the classifiers in an independent cohort of ALL patientsamples.Theclassifiersaccuratelypredictedsubtype-membershipof89%ofthesamples,achievingameansensitivityof0.91andspecificityof0.99.Wealsousedtheclassifierstoscreenforsubtype-membershipof116additionalALLpatientswithundefined/otherkaryotypesatdiagnosis(denotedBCP-other).Over60%ofthesecaseswerere-classifiedintoaknownsubtypebasedon“subtype-like” DNAm patterns. In depth analysis of “subtype-like” samples is currently on-going byintegrating theDNAmpredictionwith copynumberanalysis andRNA-sequencing.Moreover, thenewemergingsubgroupsinBCP-othercharacterizedbyfusionsinvolvingDUX4andZNF384arealsoassociatedwithdistinctDNAmprofiles2.WearedesigningandimplementingnewDNAmclassifierstoscreenforthesetwosubgroupsinBCP-otherpatients.
Together,ourDNAm-basedclassificationprovidesimproveddelineationoftheheterogeneousBCP-othergroup.Preliminary results fromtheclassifiers confirm thatDNAm isa robustandpowerfulepigeneticmarkerthatcouldserveasacomplementtocurrentdiagnosticmethods.TheclassifiercouldpotentiallybeusedasatooltodiscovernovelmolecularALLsubtypes.
1. NordlundJetal.,Clin.Epigenetics,20152. Marincevic-Zunigaetal.,J.Hematol.Oncol.,2017
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Genome-wide DNA methylation profiling in chronic lymphocytic leukemia patients carrying stereotyped B-cell receptors
Larry Mansouri1*, Sujata Bhoi1*, Giancarlo Castellano2, Lesley-Ann Sutton1, NikosPapakonstantinou3, Ana Queirós4, Panagiotis Baliakas1, Sara Ek5, Venera Kuci Emruli5, KarlaPlevova6,7, Stavroula Ntoufa3, Zadie Davis8, Emma Young1, Hanna Göransson-Kultima9, AndersIsaksson9, Karin E. Smedby10, Gianluca Gaidano11, Anton W. Langerak12, Frederic Davi13, DavideRossi14,DavidOscier8,SarkaPospisilova6,7,PaoloGhia15,EliasCampo2,KostasStamatopoulos3,José-IgnacioMartín-Subero4**andRichardRosenquist1,16**Contributedequally1DepartmentofImmunology,GeneticsandPathology,ScienceforLifeLaboratory,UppsalaUniversity,Sweden2HematopathologyUnit, Hospital Clinic, Institut d'Investigacions BiomèdiquesAugust Pi i Sunyer (IDIBAPS),University ofBarcelona,Barcelona,Spain3InstituteofAppliedBiosciences,CentreforResearchandTechnology-Hellas,Thessaloniki,Greece4Biomedical Epigenomics Group, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), University ofBarcelona,Barcelona,Spain5DepartmentofImmunotechnology,LundUniversity,Sweden6DepartmentofInternalMedicine–HematologyandOncology,UniversityHospitalBrnoandFacultyofMedicine,MasarykUniversity,Brno,CzechRepublic7Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, CzechRepublic8DepartmentofMolecularPathology,RoyalBournemouthHospital,UK9DepartmentofMedicalSciences,CancerPharmacologyandComputationalMedicine,UppsalaUniversity,Sweden10DepartmentofMedicine,ClinicalEpidemiologyUnit,KarolinskaInstitutet,Stockholm,Sweden11DivisionofHematology,DepartmentofTranslationalMedicine,UniversityofEasternPiedmont,Novara,Italy12DepartmentofImmunology,ErasmusMC,UniversityMedicalCenterRotterdam,theNetherlands13Pitie-SalpetriereandUniversityPierreandMarieCurie,Paris,France14Hematology Department, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona,Switzerland15DivisionofExperimentalOncology,UniversitàVita-SaluteSanRaffaeleandIRCCSSanRaffaeleScientificInstitute,Milan,Italy16DepartmentofMolecularMedicineandSurgery,KarolinskaInstitutet,Stockholm,Sweden.
Inrecentyears,subsetsofchroniclymphocyticleukemia(CLL)patientscarryingstereotypedB-cellreceptors(BcRs)havebeenidentifiedthatshareclinicobiologicalfeaturesandoutcome.Using450Kmicroarrays, we investigated 176 CLL cases assigned to 8 major subsets including the clinicallyaggressive IGHV-unmutated(U-CLL)subsets#1,#3,#5,#6,#7and#8,the indolent IGHV-mutated(M-CLL) subset #4, as well as subset #2, which displays mixed IGHV mutation status and pooroutcome. In addition, we included non-subset CLL (n=325), subgrouped based on the recentlyproposedepigeneticclassificationofCLL,i.e.naïve-likeCLL(n-CLL),memory-likeCLL(m-CLL),andathird intermediate CLL subgroup (i-CLL), as well as sorted normal B-cell populations at differentstages of differentiation. Overall, unsupervised analysis revealed that all U-CLL subsets clusteredwith n-CLL, subset #4 clustered with m-CLL, while subset #2 clustered separately with i-CLL.Accordingly, supervised analysis revealed a limited number of CpG sites that were differentiallymethylated when comparing each U-CLL or M-CLL subset versus non-subset cases. In contrast,almost all subset #2 cases clustered separately from i-CLL, indicating that this subset mightrepresent a distinct subgroup of i-CLL. Additionally, we observed significant differences inepigenetic‘burden’insubset#1and#2vs.non-subsetcases,inlinewiththeirverypooroutcome.Inconclusion,whileU-CLLandM-CLLsubsetsgenerallyclusteredwithn-CLLandm-CLLcategories,respectively,implyingcommoncellularorigins,subset#2emergedasthefirstdefinedmemberofi-CLL,whichalludestoadistinctcellularoriginforthissubgroupofpatients.
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Epigenetic co-regulation as a potential therapeutic target in multiple myeloma
AlbaAtienzaPárraga1,KlevDiamanti2,AronSkaftason1,LoganLaurent1,MohammadAlzrigat1,AnqiMa3,JianJin3,JoséIgnacioMartín-Subero4,AndreasLennartsson5,JanKomorowski2,FredrikÖberg1,HelenaJernberg-Wiklund1*andAntoniaKalushkova1**Indicateslastco-authors1Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratoriet, UppsalaUniversity,Uppsala,Sweden2Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala Biomedicinska Centrum, UppsalaUniversity,Uppsala,Sweden3DepartmentsofPharmacologicalSciencesandOncologicalSciences, IcahnSchoolofMedicineatMountSinai,NewYork,NY,USA4Department of Pathology, Hematopathology Section, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi iSunyer(IDIBAPS),UniversityofBarcelona,Barcelona,Spain5DepartmentofBiosciencesandNutrition,KarolinskaInstitutet,Stockholm,Sweden.
Although multiple myeloma (MM) is a largely heterogeneous malignancy, we found anunderexpressed gene profile enriched in H3K27me3 targets as a common denominator amongpatients.WehavethereforeevaluatedtheimpactofH3K27me3genesilencinginMM,aswellasitsmoleculartargetsandtheroleofotherpotentialepigeneticcollaborators.RemovalofH3K27me3viaEZH2 inhibition led toapoptosis inMMcells.Among the reactivated targets,we foundgeneswithaknowntumorsuppressorfunctioninMMaswellasmiRNAsshowntobeunderexpressedinMM.InsilicopredictionidentifiedtheIRF4,BLIMP1andXBP1genes,withoncogenicrolesinMM,as targets of the reactivated miR-125a-3p and miR-320c. Strikingly, integrative analysis of theH3K27me3 targets and gene expression data showed that only bivalent genes (i.e. marked byH3K27me3 and H3K4me3) became active upon EZH2 inhibition, pointing towards additionalsilencingmechanisms.DNAmethylationandH3K27me3co-localizedatB-cellenhancers,suggestinga role of these two machineries at regulatory regions in MM. Combined treatment with DNAdemethylating agents and an EZH2 inhibitor synergistically reduced MM proliferation. Our datahighlightthemultifacetedroleofH3K27me3,aloneorincollaborationwithotherepigeneticmarks,ingeneregulationinMM
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KEYNOTE SPEAKER
HenkStunnenberg
Henk Stunnenberg is full professor at the Science andMedical facultyand head of theDepartment ofMolecular Biology andDirector of theRadboud Institute forMolecular Life Sciences of the Science faculty atRadboudUniversity,Nijmegen.HeismemberofEMBO,wasthechairofScientific Steering Committee of the International Human EpigenomeConsortium(IHEC),heisamemberoftheCouncilofScientistsofHumanFrontier Science Program Organization (HFSPO), Program Committeemember for the International Cancer Genome Consortium (ICGC) and
memberoftheOrganizingCommitteeoftheHumanCellAtlas.
Hisresearchaimsatunravelingthemolecularbasisofdevelopmentanddifferentiationemanatingfromthegenomeandepigenomeinthecontextofhealthanddiseasewithemphasisoncancerandmostrecentlyonimmunedisease.State-of-the-arttechnologicaldevelopmentsareappliedrangingfrom single molecule studies through to genome wide elucidation of genetic and epigeneticpathwaysandmechanisms.Heaimstodefinethequantitativeframeworkaroundthedynamicsoftheepigenomeanditsdeterminantsandtheirtranslationintoregulatorymodelsofdiseases.
Immune memory
Innate immunememory is thephenomenonwhereby innate immunecells suchasmonocytesormacrophagesundergofunctionalreprogrammingafterexposuretomicrobialcomponentssuchasLPS.Weappliedanintegratedepigenomicapproachtocharacterizethemoleculareventsinvolvedin LPS-induced tolerance in a time dependent manner. Our hypothesis-free analyses identifiedspecificpathwaysdysregulatedinnaïvemacrophagesandsuchderivedfrommonocytesexposedtoLPS. Transcriptional inactivity in response to a second LPS exposure in tolerizedmacrophages isaccompaniedwith failure todepositactivehistonemarksatpromotersof tolerizedgenes.Takentogether,weunveiledthatinnateimmunememoryinmonocytesandmacrophagesiswrittenintheepigenome.
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Session IV: Epigenetics and immunity Chair:GoncaloCastelo-Branco
Reactivation potential of HIV-1 in primary CD4 T cells depend on the chromatin microenvironment
J.PeterSvensson11DepartmentofBiosciencesandNutrition,KarolinskaInstitutet
OnceHuman ImmunodeficiencyVirus-1 (HIV-1) infectsa cell, theviral genomecan integrate inahostchromosome.Upon integration, theviral sequence ispackaged intochromatin,and insomecells, the proviral chromatin then becomes silenced.When the viral proteins are degraded, thelatentcell is indistinguishable fromanuninfectedcellandescapes the immunesystemaswellascurrent drugs. However, using host factors, at any time can the provirus reactivate andsubsequentlyre-infectneighboringcells.ThisreservoiroflatentlyinfectedcellsisthemainobstacletoacureforHIV/AIDS.
Wehavedetermined that theepigeneticmicroenvironmentprovidesapredictor for viral latencyreversal. Using primary CD4+ T lymphocytes infected with a reporter virus, we are able todistinguish between productive, reactivatable latent and truly latent cell populations. We havefollowed the maturation of proviral chromatin during the months following infection anddetermined how it affects the reactivation potential of the provirus. We also identified HIV-1integrationsitesbysequencingtheflankinghostregionsandfoundthatthethreepopulationsarefoundindistinctchromatinsettings.Whereasthetruly latentprovirusesare integratedinregionsmarked by several heterochromatic marks, the reactivatable portion is integrated in sites moreoftenassociatedwithactivechromatinmarks.
These results are important in that theyprovide clues to improve therapyofoneof the globallymostdevastatinghuman infections today. Insteadof focusingoneliminating theentire reservoir,focus may instead be shifted to finding drugs targeting the distinct cell population with areactivatableprovirus.
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Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria
JaclynQuin1*,IoanaBujila1*,MariamaChérif2,3,GuillaumeS.Sanou2,YingQu4,ManijehVafa5,AnnaRolicka1¤,SodiomonB.Sirima2,MaryA.O’Connell6,AndreasLennartsson4,MaritaTroye-Blomberg1,IssaNébié2andAnn-KristinÖstlundFarrants1*Theseauthorscontributedequallytothiswork.1DepartmentofMolecularBiosciences,TheWenner-GrenInstitute,StockholmUniversity2CentreNationaldeRechercheetdeFormationsurlePaludisme,BurkinaFaso3UniversitéPolytechniquedeBoboDioulasso,BurkinaFaso4DepartmentofBiosciencesandNutrition,KarolinskaInstitute5InfectiousDiseasesUnit,DepartmentofMedicine,KarolinskaInstitute6CentralEuropeanInstituteofTechnology,CzechRepublic
The Fulani ethnic grouphas relatively better protection fromPlasmodium falciparummalaria, asreflectedbyfewersymptomaticcasesofmalaria,lowerinfectionrates,andlowerparasitedensitiescomparedtosympatricethnicgroups.However,thebasisforthislowersusceptibilitytomalariabytheFulaniisunknown.TheincidenceofclassicmalariaresistancegenesarelowerintheFulanithaninothersympatricethnicpopulations,andtargetedSNPanalysesofothercandidategenesinvolvedinthe immuneresponsetomalariahavenotbeenabletoaccount fortheobserveddifference inthe Fulani susceptibility toP.falciparum. Therefore,wehaveperformedapilot study to examineglobaltranscriptionandDNAmethylationpatternsinspecificimmunecellpopulationsintheFulanitoelucidatethemechanismsthatconferthelowersusceptibilitytoP.falciparummalaria.Whenwecompared uninfected and infected Fulani individuals, in contrast to uninfected and infectedindividuals from the sympatric ethnic group Mossi, we observed a key difference: a strongtranscriptionalresponsewasonlydetectedinthemonocytefractionoftheFulani,whereover1000genesweresignificantlydifferentiallyexpresseduponP.falciparuminfection.
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Enhancer regulation by GPS2 modulates macrophage inflammation
ZhiqiangHuang1,SaioaGoñi1,MinnaU.Kaikkonen2,RongrongFan1,AnastasiosDamdimopoulos1,TomasJakobsson1,CliveD’Santos3,JasonCarroll3,NicolasVenteclef4,EckardtTreuter11Department of Biosciences and Nutrition, Center for Innovative Medicine (CIMED), Karolinska Institutet, CampusFlemingsberg,14157Huddinge,Sweden2A.I.VirtanenInstitute,UniversityofEasternFinland,70211Kuopio,Finland3CancerResearchUKCambridgeInstitute,UniversityofCambridge,CB20RE,UK4SorbonneUniversités.UniversitéPierreetMarie-Curie,INSERM,Paris,France
Transcriptionfactorsandco-regulatorscoordinatemacrophageinflammation.Ourrecentworkhasidentified a key role of a GPS2-containing co-repressor complex in suppressingmetabolic stress-induced macrophage inflammation via epigenomic mechanisms1. In the current study, wesystemically investigated the role of enhancers in GPS2-mediated repression with a particularemphasisonCcl2(Mcp-1).ChIP-seqandmicroarraydataindicatethatGPS2isrecruitedtoenhancerlociofmostup-regulatedgenesinGPS2KOmacrophages.GPS2wasreleasedupontreatmentwithLPS (a TLR4 agonist) at those enhancers. GPS2 ablationwas correlatedwith increased enhanceractivity, as judged by measuring H3K27 acetylation (by ChIP-seq) and enhancer RNA (eRNA)expression (by GRO-seq). We further identified the functionally important GPS2-regulatedenhancers at theCcl2 locusbydepleting specific enhancersusingCRISPR/Cas9.DepletionofonedistalenhancerledtoreducedH3K27acetylationatallotherCcl2enhancers,alongwithdecreasedeRNA expression, suggesting interaction of these enhancers. Intriguingly, inhibition of oneenhancer-derived eRNA (by antisense LNA GapmeR) significantly abolished LPS-induced Ccl2transcriptionandhadamajor impacton theGPS2KOeffectsat theCcl2 locus.Overall,ourdatasuggesttheinvolvementofeRNAsinmodulatingpro-inflammatorygeneresponsesinmacrophageswith a specific role of the GPS2 co-repressor complex in regulating eRNA expression at keyenhancers.
1. Fan,R.,Toubal,A.,Goni,S.,Drareni,K.,Huang,Z.,Alzaid,F.,Ballaire,R.,Ancel,P.,Liang,N.,Damdimopoulos,A.,et al. (2016). Lossof the co-repressorGPS2 sensitizesmacrophageactivationuponmetabolic stress inducedbyobesityandtype2diabetes.NatMed22,780-791.
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Utilizing epigenomics to understand neurodegeneration in Multiple Sclerosis: what are the neurons telling us?
Lara Kular1, Maria Needhamsen1, Milena Z Adzemovic1, Tatiana Kramarova1, David Gomez-Cabrero2,EwoudEwing1,JesperTegnér2,FredrikPiehl1,LouBrundin1andMajaJagodic11DepartmentofClinicalNeuroscience,CenterforMolecularMedicine,KarolinskaInstitutet,Stockholm,Sweden2Department ofMedicine, Unit of ComputationalMedicine, Center forMolecularMedicine, Karolinska Institutet, Solna,Sweden.
MultipleSclerosis(MS)isachronicinflammatorydiseasecharacterizedbyautoimmunedestructionofmyelin andneurons in the central nervous system. Today,MS is oneof the leading causesofneurologicaldisabilityinyoungadults.Currenttreatmentsactbroadlyontheimmunesystemandtheyareeffective incontrolling the inflammatorystageofdiseasewhile thereareno treatmentsthatprevent sustainedneuronal lossanddiseaseprogression.Although thecauseofMSremainsunknown,vastepidemiologicaldataestablishMSasacomplexdisease influencedbygeneticandenvironmentalfactors.Epigeneticmechanisms,suchasDNAmethylation,orchestrateactivityofthegenome in response to environmental cues and may provide better understanding of diseasepathogenesis.OneofthemainchallengeswithstudyingdiseasessuchasMSisthelimitedaccesstothe target tissue - the brain. Recent progress in development of methods to survey epigeneticmodifications,and fromthem infergenomeactivity,openeduppossibilities to studybrain tissueandmechanismsthatunderlieneuronallossinMSpatients.
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Friday, December 1st 2017
Session V: Understanding Epigenetics II Chair:SebastianDeindl
Invitedspeaker:
YuriB.Schwartz
Dr. Yuri Schwartz is associate professor of genetics at the Department ofMolecular Biology, Umeå University. He produced one of the best high-resolutiongenome-widemapsofPolycombregulationinDrosophilaandmadeimportantcontributionstounderstandcross-talkbetweendifferentPolycombcomponents in flies and human cells. He co-founded the EpiCoN initiative(Epigenetic Cooperation Norrland, www.epicon.nu), which aims to fostergroundbreakingepigeneticsresearchinNorthernSweden.
Deciphering the cooperativity of Polycomb repression
TatyanaG.Kahn,SarinaR.Cameron, Juan I.Barrasa,EshaghDorafshan, JanaŠmigová,AlexanderGlotovandYuriB.SchwartzDepartmentofMolecularBiology,UmeåUniversity,Sweden
Polycombproteins are epigenetic repressors that regulatemanyof the same keydevelopmentalgenes in insectsandvertebrates.Polycombproteinsact inconcertas largecomplexesofthetwotypes: PRC1 and PRC2. The lattermethylate Lysine 27 of histoneH3 (H3K27) and tri-methylatedH3K27transmitsepigeneticmemoryoftherepressedstatewhencellsdivide.HowthepresenceofH3K27me3translatesintoadvantagefortherepressionisnotveryclear.WorkingwithDrosophilamodel,wefindthatH3K27me3isnotessentialtotargetPRCcomplexestospecificgenes.InsteadithelpsPRCcomplexesanchoredatPolycombResponseElements(PREs)tointeractwithsurroundingchromatin.WealsofindthatPRC1canbindPREsintheabsenceofPRC2but,atmostPREs,PRC2requiresPRC1tobetargeted.OurstudiesonhumanculturedcellsfurthersuggestthattargetingofPRC1bycompactDNAelements isanevolutionarilyold featureofPolycombrepression.We findthatcoordinatedrecruitmentofmammalianPRC1andPRC2complexesinvolvesacombinationofaspecialized PRC1 targeting element (PTE) and an adjacent CpG-island, which together act asmammalianPolycombResponseElements.
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Targeting Polycomb repressive complexes through evolutionary conserved DNA elements
BarrasaJI1,KahnTG1,CameronSR1,RusseilJ1,DeplanckeB1,SchwartzYB11DepartmentofMolecularBiology,UmeåUniversity,Sweden
Polycomb group proteins are transcriptional repressors with a key role in the development ofmulticellular organisms.Miss-expression of Polycomb proteins is known to cause developmentalabnormalities and is also linked to several types of cancer. Polycombproteins formmultiproteincomplexes to repress transcriptionat specific targetgenes,but themechanisms involved in theirrecruitmentinmammalsarepoorlyunderstood.First,andincontrasttothewell-knownDrosophilaPolycomb Response Elements (PREs), no specific DNA elements have been identified to recruitmammalian Polycomb complexes. And second, considering that is unclear whether Polycombproteins can themselvesbindDNA,noDNAbindingpartnershavebeenunambiguously linked tothetargetingofPolycombcomplexes.ThehistonemodificationsdepositedbyPolycombRepressiveComplexes1and2(PRC1andPRC2),H2AK119UbandH3K27me3respectively,areassociatedwithtranscriptionalrepressionbutneitherofthemissufficienttorecruitPRCcomplexestotheirtargetgenes.
WehaverecentlyestablishedtheCyclinD2(CCND2)oncogeneasamodeltounravelsomeofthesequestions1.Wehaveidentifieda1kbDNAelementupstreamofthehumanCCND2genepromoterthat autonomously recruits PRC1 but very little PRC2. This PRC1 targeting element (PTE), incollaborationwithaproximalCpG islandspecialized inPRC2 recruitment, resembles the functionand modular structure ofDrosophila PREs. Here we demonstrate that these DNA elements areevolutionary conserved inmouse anduse this system to identify potentialDNAbindingpartnersinvolvedintherecruitmentofPRCcomplexestotheirtargetgenes.
1. Cameron SR,Nandi S, Kahn TG, Barrasa JI, Stenberg P, Schwartz YB. 2017.PTE, a novelmodule ofmammalianPolycombResponseElements.bioRxivdoi:https://doi.org/10.1101/177097
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Developmental patterning and gene regulation by the BEN-solo family
JiayuWen1,MalinUeberschär3,BrianJoseph1,TsutomuAoki2,PaulSchedl2,EricLai1,QiDai31ProgrammeofDevelopmentalBiology,MemorialSloanKetteringInstitute2DepartmentofMolecularBiology,PrincetonUniversity3DepartmentofMolecularBioscience,theWenner-GrenInstitute,StockholmUniversity
Background:Geneexpression is regulatedbythe interplaybetweenchromatin factors,sequence-specifictranscriptionfactors(TFs)andgeneraltranscriptionmachinery.Westudyanovelfamilyofproteins, the BEN-solo family that can not only act as TFs but also as insulator proteins. The flygenome encodes three BEN-solo proteins, namely Insensitive (Insv), Bsg25A (Elba1) and CG9883(Elba2).InsvpromotessensoryorgandevelopmentthroughinteractingwithNotchsignaling,anditcanbind toa specificpalindromicDNAsequence tomediate transcriptional repression.AlthoughElba1andElba2areabletobindthesameInsvmotif,theyalsoheterotrimerizewiththeirobligateadaptorElba3torecognizeasimilarbutasymmetricmotifintheFab-7insulator.
Results: Using genome-wide approaches, we found that the binding regions of the three Elbaproteins overlap throughout the genome. Different from Insv binding loci that represent classicenhancer-type, Elba-bound regions are enriched for active histone marks at promoters and +1nucleosomes.As+1nucleosomewasshowntoregulateRNApolymeraseIIpausing,wecomparedElba-occupied regionswith paused promoters, and found high correlation between Elba bindingandpausing.CandidatetargetgenesboundbyElbabecameup-regulatedinelbamutants.
Conclusions:We separated the functionalities between Insv and the Elba type of BEN proteins,Elba1andElba2.Unexpectedly,wefoundthattheElbacomplexmayinteractwith+1nucleosomestoregulatetranscription(and/ortofunctionas insulators).WespeculatethatbindingbytheElbaproteins may be a novel type of mechanisms that regulates Pol II activities (e.g., pausing) intranscription.
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Session VI: Epigenetics across species Chair:Ann-KristinÖstlundFarrants
Ectopic application of H3K9me2 establishes postzygotic reproductive isolation in Aradibopsis
HuaJiang1,JordiMoreno-Romero1,JuanSantos-González1andClaudiaKöhler11DepartmentofPlantBiology,UppsalaBioCenter,SwedishUniversityofAgriculturalSciencesandLinneanCenterforPlantBiology,Uppsala,Sweden
Understanding themechanisms bywhich populations become reproductively isolated is amajorgoal of evolutionary biology. Postzygotic reproductive isolation in response to hybridizations ofplants thatdiffer inploidy (interploidyhybridizations) is amajorpath for sympatric speciation inplants. This mechanism is manifested in the endosperm, a dosage sensitive tissue supportingembryogrowth.Deregulatedexpressionofapaternally-expressedimprintedgene(PEG),ADMETOS(ADM), underpin the interploidy hybridization barrier in the endosperm inArabidopsis thaliana1.Moreover,threeadditionalPEGs,SUVH7,PEG2,andPEG9werealsofoundtoestablishinterploidyhybridizationbarriersintheendosperm2,revealingthatPEGsplayamajorroleasspeciationgenesin plants. However, themechanisms of their action remained unknown. Here, I will discuss ourlatestfindingthatADMinteractswithanAT-richDNAbindingproteinandectopicallyrecruitstheheterochromatic mark H3K9me2 to AT-rich transposable elements (TEs), causing deregulatedexpressionofneighboringgenes3.OurdatasuggeststhatreproductiveisolationasaconsequenceofepigeneticregulationofTEsisaconservedfeatureinanimalsandplants.
1. KradolferD,WolffP,JiangH,SiretskiyA,KöhlerC.(2013).AnimprintedgeneunderliespostzygoticreproductiveisolationinArabidopsisthaliana.DevCell.26:525-535.
2. Wolff P, Jiang H,Wang G, Santos-Gonzàlez J, Köhler C (2015). Paternally expressed imprinted genes establishpostzygotichybridizationbarriersinArabidopsisthaliana.eLife.10074.
3. JiangH,Moreno-RomeroJ,Santos-GonzálezJ,DeJaegerG,GevaertK,VanDeSlijkeE,KöhlerC. (2017).Ectopicapplication of the repressive histone modification H3K9me2 establishes post-zygotic reproductive isolation inArabidopsisthaliana.Genes&Dev.31:1272-1287.
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Imprinted gene regulation by the paternally expressed gene PHERES1 in Arabidopsis thaliana
Rita A. Batista1, DuarteD. Figueiredo1, JordiMoreno-Romero1, Charlotte Siemons1, Juan Santos-González1andClaudiaKöhler11DepartmentofPlantBiology,UppsalaBioCenter,SwedishUniversityofAgriculturalSciencesandLinneanCenterforPlantBiology,Uppsala,Sweden
In flowering plants, seed development is initiated by the fertilization of the maternal egg andcentral cells by two paternal sperm cells, leading to the formation of the embryo and theendosperm,respectively.Theendospermisaproliferatingtissuethatnourishestheembryoduringits development, thus being functionally analogous to the mammalian placenta. Contrary tomammals,genomicimprintinginfloweringplantsseemstoberestrictedtotheendospermanditsdisruption is correlated with failure of endosperm development, which consequently leads toembryoarrest.Therefore,it is importanttounderstandindetailthemechanismsestablishingandregulatinggenomicimprinting.
In this work we found that dysregulation of PHERES1, a MADS-box transcription factor and apaternallyexpressedgene(PEG),iscorrelatedwithendospermfailureandthereforewesetouttocharacterize the functions of this PEG. We found that PHE1 controls the expression of otherimprintedgenes,especiallyPEGs,providinganexampleofimprintedtrans-regulationofimprintedgenes. In the particular case of PEG targets, we observe that the binding of PHERES1 occurs innarrow regions devoid of DNA methylation and repressive histone marks in the otherwiseepigeneticallyrepressedmaternalallele.WealsoobservethatPHERES1bindingsitesarefrequentlycontained in transposable elements, specifically in RC/Helitrons, which have been previouslyimplicated in imprinting establishment. Thus, this work provides evidence for moleculardomestication of transposable elements, and adds a layer of complexity in imprinted generegulation.
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Genetic dissection of Drosophila HDAC3 function
MinTang1,OlgaShilkova1andMattiasMannervik11DepartmentofMolecularBiosciences,TheWenner-GrenInstitute,StockholmUniveristy
Controloftranscriptionestablishesthegeneexpressionprogramsthatdefineacellanddirectscelldifferentiation. Histone deacetylases (HDACs) influence transcriptional regulation by catalyzingdeacetylationofhistones.Here,wetakeadvantageofDrosophilaasanexcellentmodeltostudythebiological function of HDAC3 in early embryo patterning and in brain development. The histonedeacetylaseHDAC3isbelievedtoregulategenetranscriptionbyitscatalyticactivityandbyformingacomplexwiththeco-repressorNCoR/SMRT.Usingtransgenicknock-downofHDAC3inthefemalegermline, we showed that depletion of maternal HDAC3 caused a failure in embryo hatching,various cuticle defects, and de-repression of sog gene expression in the mesoderm where it isnormally silenced by the Snail repressor. The phenotypes were partially rescued by a miRNA-resistantwttransgene.Site-directedmutagenesisofHDAC3wasperformedtodistinguishbetweena catalytic function and complex formation with the co-repressor NCoR/SMRT. Three differentmutations have been introduced based on mammalian HDAC3. A Y303F mutation renders theenzymeinactive,butdoesnotaffecttheinteractionbetweenHDAC3andthedeacetylaseactivationdomain (DAD) inNCoR/SMRT.TheK26Amutationandacombinationofmutations (HEBI)disruptthe interaction with DAD to different extents, and also impair deacetylase activity. These site-directedmutantmiRNAresistanttransgenesrescuedtheHDAC3phenotypetodifferentlevels.WealsogeneratedaHDAC3nullmutantaswellassite-directedknock-inmutants,andcharacterizedanopticlobephenotypeinthird-instarlarvalbrainsfromthedifferentmutants.Together,ourresultsshow thatHDAC3 function is not redundantwith other histonedeacetylases, but is essential forspecificdevelopmentalprocesses,andpartiallyindependentofcatalyticactivity.
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C12D8.1: A negative regulator of RNAi inheritance in Caenorhabditis elegans
BenjaminHolmgren1,LinneaBäckström1,YaniZhao1,andAndreaHinas11DepartmentofCellandMolecularBiology,UppsalaUniversity
InthenematodeCaenorhabditiselegans,RNAinterference(RNAi),sequence-specificgenesilencingmediatedbysmallRNAs,canbepassedonfromparenttooffspring.InheritanceofexogenousRNAiis limited, leading to progressivelyweaker silencing and restoration of target gene expression topre-silencing levels within a few generations. This loss of silencing has been suggested to beimportant forkeepinggeneexpressionplasticity,enablinganimals toquicklyadapt tochanges inthe environment. However, very little is known about the underlyingmechanisms that regulatepersistence of inheritance. In this study, we initially used bacteria-mediated (feeding) RNAi tosilenceasetofsevengenesidentifiedinayeasttwo-hybridscreenusingtheRNAtransportproteinSID-5 as bait. Target gene knockdown was followed by feeding RNAi against body wall muscle-expressed GFP, where three out of seven tested genes displayed reduced GFP RNAi efficiencycomparedtocontrolanimals.Oneofthesegenes,C12D8.1,waschosenforfurtherstudies.C12D8.1encodes a putative RNA- binding protein of the conserved Far upstream binding protein (FBP)family, which affects transcription and RNA metabolism in mammals. We found that aC12D8.1::mCherrytranslationalfusionproteincanlocalizetoboththenucleusandtocytoplasmic,oftenperinuclear,foci.Uponfurther investigationoftheeffectofC12D8.1onRNAiefficiency,wediscovered that twostrainscarryingdifferentputative lossof functionC12D8.1mutationsdonotphenocopytheC12D8.1RNAiknockdown,but insteaddisplayenhancedRNAi.Aseriesof feedingRNAiexperimentsindicatethatC12D8.1mutantshavestrongerinheritanceofexogenousRNAithanwildtypeworms.However,C12D8.1mutantswithinheritedRNAiwillmountaweakerresponsetoasecondroundofRNAiagainstadifferenttargetgene.Takentogether,thissuggeststhatC12D8.1negatively regulates inheritance of RNAi, thereby facilitating a dynamic epigenetic response tochangesintheenvironment.
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KEYNOTE SPEAKER
JasonErnst
Jason Ernst joined the faculty atUCLA in theDepartment of BiologicalChemistry, the Computer Science Department, and the BioinformaticsProgramin2012.Priortothat,hewasapostdoctoralfellowinManolisKellis' Computational Biology Group in the Computer Science andArtificial Intelligence Laboratory at MIT and affiliated with the BroadInstitute. In 2008, Jason completed a PhD advised by Ziv Bar-Josephwhere he was part of the Systems Biology Group, Machine LearningDepartment, and School of Computer Science at Carnegie Mellon
University.HeisamemberoftheeditorialboardatGenomeResearchandhasbeenaprogramco-chair for the ISMB Regulatory Genomics Special Interest Group (RegGenSIG) meeting. He is arecipientofaSloanFellowship,NIH-AvenirAward,NSFCareerAward,NSFPostdoctoralFellowship,aSiebelScholarship,andaGoldwaterScholarship.
Computational Epigenomic Approaches for Deciphering the Non-coding Human Genome Understanding the human genome sequence and in particular the vast non-coding regions is acentralchallengeformodernmolecularbiologywithprofoundimplicationstowardsunderstandingthegeneticbasisofdisease.WhileunderstandingthegenomebydirectlyreadingtheprimaryDNAsequenceisextremelychallenging,thepresenceofepigeneticmarksontopofthesequenceholdsgreatpromisetoaidourunderstandingofthegenome.Technologicaladvancesinsequencinghasmadeitpossibleinasingleexperimenttogeneratetensofmillionsofdatapointsonthelocationofaepigeneticmarkacrossthegenomeinaspecificcelltype,whichraisesanumberofcomputationalchallengesandopportunities.InthistalkIwillfirstdescribeamethodthatIpreviouslydeveloped,ChromHMM, that learns de novo combinatorial and spatial patterns from maps of multipleepigeneticmarksusingamultivariatehiddenMarkovmodel.Thesepatternscorrespondtodifferentclassesofgenomicelements,which Ihavethenusedtoprovideacell typespecificannotationofthe human genome. I will then describe a combined computational modeling and experimentalapproach,Sharpr-MPRA,that inhigh-throughputcantestputativeregulatoryelementsof interestidentified based on epigenomics patterns and identify within them at high resolution basesactivatingorrepressinggeneexpression.Finally,Iwilldescribeamethod,ChromImpute,toimputemapsofepigeneticmarksthatIhaveappliedinthecontextoftheRoadmapEpigenomicsprojecttocomputationally predict over 4000 epigenomic datasets vastly accelerating the coverage of thehuman epigenome while providing overall more robust maps than have been obtainedexperimentally.
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Session VII: Epigenomics Chair:JanKomorowski
Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1 MolecularCell,inpress
LauraC.Lehmann1,3,GraemeHewitt2,3,ShintaroAibara4,AlexanderLeitner5,EmilMarklund1,SarahL.Maslen6,VarunMaturi7,YangChen1,DavidvanderSpoel8,J.MarkSkehel6,AristidisMoustakas7,SimonJ.Boulton2,*,andSebastianDeindl1,9,*1DepartmentofCellandMolecularBiology,ScienceforLifeLaboratory,UppsalaUniversity,75124Uppsala,Sweden2TheFrancisCrickInstitute,1MidlandRoad,LondonNW11AT,UK3Theseauthorscontributedequally4DepartmentofBiochemistryandBiophysics,ScienceforLifeLaboratoryandStockholmUniversity,10691Stockholmand17121Solna,Sweden5Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zürich,Switzerland6MRCLaboratoryofMolecularBiology,FrancisCrickAvenue,CambridgeBiomedicalCampus,CambridgeCB20QH,UK7Department of Medical Biochemistry and Microbiology, and Ludwig Institute for Cancer Research, Science for LifeLaboratory,UppsalaUniversity,75123Uppsala,Sweden8DepartmentofCellandMolecularBiology,ComputationalBiologyandBioinformatics,UppsalaUniversity,75124Uppsala,Sweden9LeadContact
HumanALC1isanoncogene-encodedchromatin-remodelingenzymerequiredforDNArepairthatpossessesapoly(ADP-ribose)(PAR)-bindingmacrodomain. ItsengagementwithPARylatedPARP1activatesALC1atsitesofDNAdamage,buttheunderlyingmechanismremainsunclear.Here,weestablishadualroleforthemacrodomaininauto-inhibitionofALC1ATPaseactivityandcouplingto nucleosome mobilization. In the absence of DNA damage, an inactive conformation of theATPase ismaintainedby juxtapositionofthemacrodomainagainstpredominantlytheC-terminalATPase lobethroughconservedelectrostatic interactions.Mutationswithinthis interfacedisplacethemacrodomain,constitutivelyactivatetheALC1ATPaseindependentofPARylatedPARP1,andalter the dynamics of ALC1 recruitment at DNA damage sites. Upon DNA damage, binding ofPARylated PARP1 by the macro domain induces a conformational change that relieves auto-inhibitory interactionswith theATPasemotor,which selectively activatesALC1 remodeling uponrecruitmenttositesofDNAdamage.
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Identification of oligodendrocyte lineage states with single-cell ATAC-seq
EneritzAgirre1,MandyMeijer1,XingqiChen2,HowardYChang2andGonçaloCastelo-Branco11LaboratoryofMolecularNeurobiology,DepartmentMedicalBiochemistryandBiophysics,KarolinskaInstitutet,Stockholm,Sweden2Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine,Stanford,CA94305,USA
Oligodendrocyteprecursorcells(OPCs)constitute5to8%ofthetotalnumberofcellsintheadultcentral nervous system (CNS) being the main population that generates oligodendrocytes (OLs)duringCNSdevelopmentandremyelinationevents[1].OLsproducemyelin,alipid-richmembranethatinsulatesneuronalaxons.TheunderstandingoftranscriptionalandepigeneticregulationoftheOLlineagehasbeenlimitedtothebulkstudyofcellpopulations.Theadventofsingle-cellgenomicsallowedagreatercellularheterogeneity.Forinstance,ourgrouphaspreviouslyshownbysingle-cellRNA-seq that OPCs and OLs are more heterogeneous at transcriptional level than previouslythought,wheredifferentsubpopulationsarerelatedtodifferentstates[2].DuringOPCproliferationtheinterplaybetweentranscriptionfactorsandepigeneticmodifiersisessentialfortheacquisitionofspecificcellstates/fates.Thedisruptionofthesecellstatesithasbeenfoundtobecharacteristicofthedecreasedabilitytorepairmyelininspecificdiseases,suchasMultipleSclerosis.
InordertocharacterizeOLlineageepigeneticstatesweperformedscATAC-seq[5],formeasuringthe chromatin accessibility at single cell level. Single cells were FACS sorted and marked withspecificmatureOLandOPCmarkers.Asaresult,werecoveredOPCs,maturedOLsandacombinedpopulation of newly formed OLs. Although scATAC-seq corresponds to a highly sparse data,preliminary results showed a high correlation between single cell and bulk ATAC-seq.Implementation of scATAC-seq showed significant chromatin accessibility variability for specifictranscription factors in the different OL lineage populations. Applying dimensionality reductionmethods, such as t-SNE, single cells from different populations were clustered based on thechromatinaccessibilityofspecificregulators.Bycombiningresultsfromchromatinaccessibilityandtranscriptomics,weplantodefinespecificstatesclueforOPCdifferentiationtolaterlinkthemtospecificdiseases,suchasMultipleSclerosis.
1. Levine JM,ReynoldsR, Fawcett JW. Theoligodendrocyteprecursor cell inhealth anddisease. TrendsNeurosci.2001;24(1):39-47.2.
2. MarquesS,ZeiselA,CodeluppiS,vanBruggenD,FalcãoAM,XiaoL,etal.Oligodendrocyteheterogeneity inthemousejuvenileandadultcentralnervoussystem.Science.2016;352(6291):1326-9.
3. Castelo-BrancoG,LiljaT,WallenborgK,FalcaoAM,MarquesSC,GraciasA,etal.Neuralstemcelldifferentiationisdictated by distinct actions of nuclear receptor corepressors and histone deacetylases. Stem Cell Reports.2014;3(3):502-15.
4. YuY,ChenY,KimB,WangH,ZhaoC,HeX,etal.Olig2TargetsChromatinRemodelersToEnhancersTo InitiateOligodendrocyteDifferentiation.Cell.2013;152(1-2):248-61.
5. BuenrostroJD,WuB,ChangHY,GreenleafWJ.ATAC-seq:AMethodforAssayingChromatinAccessibilityGenome-Wide.CurrProtocMolBiol.2015;109:2191-9.
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Protein-coding sequence exclusion by alternative transcription start site usage across the human body
Wenbo Dong2* , Berit Lilje1*, Farzaneh Shahin Varnoosfaderani2, Erik Arner3, The FANTOMconsortium,AlbinSandelin1#,AndreasLennartsson2#*Sharedfirstauthor#Sharedcorrespondingauthor1The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre (BRIC), University ofCopenhagen,OleMaaloesVej5,DK2200Copenhagen,Denmark2DepartmentofBiosciencesandNutrition,KarolinskaInstitutet,Hälsovägen7-9,SE-14183Huddinge,Sweden3RIKENCenterforLifeScienceTechnologies,DivisionofGenomicTechnologies,Yokohama,Kanagawa,230-0045Japan
Gene transcription start sites (TSSs) and associated core promoters are focal points fortranscriptional regulation. .Withina single gene, alternativeusageof TSSs can lead to truncatedRNAs excluding protein-coding exons, with functional consequences. The FANTOM5 promoterexpression atlas enables comprehensive analyses of alternative TSS usage over a wide range ofprimarycellsacrossthehumanbody.Weanalysedthefantom5data,andfoundthat fractionofusedannotatedandnovelTSSswithingenebodiesisstrikinglyuniformacrossmostcelltypes.Over1.700 annotated TSSs lead to exclusion of protein-coding exons within ~1.000 genes, includingseveral epigenetic regulators. The truncated isoforms caused by alternative TSSs usage could becanonical,anditisacommonfeatureinmostcelltypes,butespeciallyinbloodcells.WealsofoundmultiplecasesofalternativeTSSswitchingbetweencelltypesleadingtoproteindomainexclusion,andconsequentlypotentialcelltypespecificfunction.
32
Nascent transcription plasticity in mouse embryonic stem cells
RuiShao1,MichaelLiedschreiber2,KatjaLiedschreiber2,PatrickCramer2,SimonElsässer11DepartmentofDepartmentofMedicalBiochemistryandBiophysics,KarolinskaInstitutet2DepartmentofBiosciencesandNutrition,KarolinskaInstitutet
Transcriptional regulation is one of the primary steps in gene expression control. It is nowappreciated that a large of the genome is transcribed, suggesting many roles of transcriptionbeyond the production of protein-coding mRNA and other functional RNAs. A recent methoddevelopedby theCramer lab for transient transcriptome sequencingTT-Seqallows sensitive andunbiased profiling of total transcriptional activity. We established the TT-Seq method in mouseembryonic stemcells tounderstand the transcriptionalplasticityofpluripotent stemcells. Inourpreliminarydata,wefound>70%nascenttranscriptsarenon-codingRNAs,inwhichnearlyhalfareintergenic RNAs. TT-Seq in combination with total RNA-Seq also allows to estimate synthesizingratesandstabilitiesofeachRNAspecies.Weaimtofurtherfunctionallyannotatenewregulatorytranscription units by intersecting transcriptomic and epigenomic data, as well as using geneticmanipulationtoperturbtranscriptiondynamics.
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Session VIII: Epitools Chair:KlevDiamanti
CommercialsponsorChromatrap®; A more efficient, sensitive & robust method of chromatin immunoprecipitation
LindsayParkes11Chromatrap,PorvairSciences,Wrexham,UK
Chromatrap® is a life science companyenabling theadvancementofepigenetic research throughit’srevolutionarysolid-statesystemforchromatinimmunoprecipitation(ChIP).Featuringauniquepatented filtration platform, Chromatrap® offers significant advantages in both handling andsensitivityoverconventionalbeadbasedChIPmethods.Chromatrap®’sadvancesinhighthroughputChIPandnextgeneration sequencingarepaving theway forglobalgeneexpressionanalysisandexamination of the epigenetic landscape. Validated on a wide range of cell types the novelChromatrap® ChIP kits eliminate the laborious use of beads, allowing researchers to investigatespecific protein-DNA interactions in a faster, easier and more sensitive platform to reveal theunderlyingmolecularmechanismsofgeneregulation.
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CommercialsponsorActive Motif, enables chromatin and gene regulation research
SarantisChlamydas11ActiveMotif
Active Motif is the industry leader in developing and delivering innovative tools to enableepigenetics and gene regulation research. We are committed to providing the highest qualityproductsalongwithsuperiorservice&supporttothelifescience,clinicalandpharmaceutical/drugdiscovery communities. Whether you are an expert in the field of epigenetics or a researcherinterested in integrating epigenetics research into your studies, our comprehensive portfolio ofexpertswillenableyoutotackleyourmostdifficultscientificchallenges.
Weprovide:
• InnovativeproductsforChromatinImmunoprecipitationandDNAMethylation• EpigeneticServices• AntibodiesforChIPandChIP-Seq• RecombinantProteinsandsubstrates• MultiplexHistonePTMQuantitationproductsandservices• LuciferaseReporterAssays
NewAdvancesinChromatinRelatedexperimentsActiveMotifhasdevelopedavarietyoftoolsandservicestoovercomemanyofcurrentchallengesin the field of Epigenetics and Transcription Regulation. Apart of our rigorously validated kits,antibodies and recombinantproteins,weareoffering a seriesof EpigeneticResearch Services tobetter studyChromatinbased interactions,HistoneModifications andDNAmethylation.A list ofhighimpactfactorpapersfromourcustomerssupportsourcapabilitiesineveryresearcharea.
Chromatin Immunoprecipitation or ChIP has provided many important insights into a variety ofbiologicalprocessesanddiseases.Ourexpertisecanprovideinsightsforchallengingsamples,suchaslowcellnumberandFormalin-FixedParaffinEmbedded(FFPE)samples,inamostaccurateandquantitativeway.
Ourlistofcapabilitiesforrareanddifficultsamplesinclude:LowCellNumberChIP-seq,FFPEChIP-Seq,ATAC-Seq,ReducedRepresentationBisulfite-Seq(RRBS),high-throughputscreeningofhistonemodification levels of clinical or compound-treated samples but also ChromatinImmunoprecipitation followed by Mass Spectrometry (RIME) to identify potential chromatinproteincomplexes.
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A novel methodology for identifying genome-wide RNA-chromatin interactions
AlessandroBonetti1andGoncaloCastelo-Branco1DepartmentofMedicalBiochemistryandBiophysics(MBB),KarolinskaInstitutet
Mammalian genomes are pervasively transcribed with the most abundant fraction beingrepresented by non-protein-coding RNAs. More recently long noncoding RNAs have gained anincreased appreciation for their functional importance. Most noncoding transcripts exhibit anuclear localization and several have shown to play a role in the regulation of gene expression.Although some methodologies to specifically identify RNA-chromatin interactions have beendeveloped, technologies to massively map the genomic binding sites of multiple transcripts arelacking.Here,toaddressthesechallenges,wehavedevelopedRNAandDNAinteractingcomplexesligatedand sequenced (RADICL-seq), anovel technology thatmaps genome-wideRNA-chromatininteractions. RADICL-seq is a proximity ligation based methodology that broadly identifies thegenomicbindingsitesofcodingandnoncodingRNAs,uncoveringanunderappreciatedcomplexityfortheRNA-DNAinteractome.
36
Modeling the dynamics of epigenetic memory
LudvigLizana1andYuriB.Schwartz21DepartmentofPhysics,IntegratedScienceLab,UmeåUniversity2DepartmentofMolecularBiology,UmeåUniversity.
HerewepresentourprogresstowardsarealisticcomputationalmodelofepigeneticrepressionbyDrosophilaPolycombGroupproteins.Severalfeaturesmakethissystemattractiveformodeling.Itisevolutionaryconserved,extensivelystudiedinbothmammalsandsimplermodelorganisms,andclinicallyrelevant.
Tomakeamodel,wepartitionthegenomeintonucleosome-sized“boxes”. Inthefinalversionofthemodel theseboxeswill representeitheractivegenes,high-affinitybindingsites forPolycombcomplexes(socalledPolycombResponseElements,PREs)ortherestofthegenome.Torepresentchromatin, we will arrange the histone-sized boxes into a linear array that has the samearrangement of genes, PRE’s etc. as real Drosophila chromosomes. The epigenetic memory ofPolycombrepressionis“recorded”viamethylationofLysine27ofhistoneH3(H3K27).Torepresentall four possiblemethylation states of H3K27, themodel’s boxesmay also switch between fourstatesaccordingtocertainrates.Importantly,theseratesarenotconstant.Theydependonseveralfactors suchaspreviousmethylation states,methylation statesofneighboringnucleosomes, andconcentrationsofPolycombcomplexes.Someoftheserelationshipshavebeenmappedoutbefore,but their importance for the establishment and maintenance of the epigenetic memory onchromosomal level is not clear and is something that we explore. To visualize how changes ofparameters affect the methylation states during simulation, we employ a Java script-basedgraphicaluserinterface.
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Listofparticipants:Firstname Familyname EmailAddress Organization/University/Company
Agota Tuzesi [email protected] SahlgrenskaCancerCenter /UniversityofGothenburg
Aida Hoshiar [email protected] UppsalaUniversity
Alba Atienza-Parraga [email protected] UppsalaUniversity
Alejandra DuqueJaramillo [email protected] UppsalaUniversity
Alessandro Bonetti [email protected] KarolinskaInstitutet
Alisa Alekseenko [email protected] KarolinskaInstitutet
Amanda Raine [email protected] UppsalaUniversity
Anders Kämpe [email protected] KarolinskaInstitutet
Anders Isaksson [email protected] UppsalaUniversity
Andre Fontes [email protected] UppsalaUniversity
Andrea Hinas [email protected] UppsalaUniversity
Andreas Lennartsson [email protected] KarolinskaInstitutet
Angeliki Pournara [email protected] UppsalaUniversity
Angelo Salazar [email protected] KarolinskaInstitutet
Anna Wenger [email protected] UniversityofGothenburg
Anna PalaudeMiguel [email protected] KarolinskaInstitutet
Anna-Maria Katsori [email protected] KarolinskaInstitutet
Ann-Christine Syvänen [email protected] UppsalaUniversity
Anne Neddermeyer [email protected] UppsalaUniversity
Annika Scheynius [email protected] KarolinskaInstitutet
Ann-Kristin ÖstlundFarrants [email protected] StockholmUniversity
Antoni GanezZapater [email protected] StockholmUniversity
Antonia Kalushkova [email protected] UppsalaUniversity
Arshad NoorulAin [email protected] KarolinskaInstitutet
Asimina Zisi [email protected] KarolinskaInstitutet
Ayla DePaepe [email protected] KarolinskaInstitutet
Banushree Kumar [email protected] KarolinskaInstitutet
Behrooz Torabi [email protected] UppsalaUniversity
Benjamin Holmgren [email protected] UppsalaUniversity
Bo Segerman [email protected] National Veterinary Institute / UppsalaUniversity
Cecilia Bergqvist [email protected] StockholmUniversity
Chandrasekhar Kanduri [email protected] UniversityofGothenburg
Charlotta Sandberg [email protected] UppsalaUniversity
Charlotte Otema [email protected] NordicBiolabsAB
Charlotte Gustafsson [email protected] KarolinskaInstitutet
Claudia Kutter [email protected] KarolinskaInstitutet
Daniel Käll [email protected] NordicDiagnostica
Dorte Schlesinger [email protected] KarolinskaInstitutet
Eckardt Treuter [email protected] KarolinskaInstitutet
Elham Barazeghi [email protected] UppsalaUniversity
38
Enen Guo [email protected] StockholmUniversity
Eneritz Agirre [email protected] KarolinskaInstitutet
Erik Gudmunds [email protected] UppsalaUniversity
Estelle SuaudLefebvre [email protected] ActiveMotif,Europe
Eva DvorakTomastikova [email protected] SwedishUniversityofAgriculturalSciences
Eva Sverremark-Ekström [email protected] StockholmUniversity
Farzaneh ShahinVarnoosfaderani [email protected] KarolinskaInstitutet
Francesco Marabita [email protected] KarolinskaInstitutet
Frida Niss [email protected] StockholmUniversity
George Kostallas [email protected] BioNordikaSweden
Gintare Lasaviciute [email protected] StockholmUniversity
Goncalo Castelo-Branco [email protected] KarolinskaInstitutet
Hani AbdulkadirAli [email protected] KarolinskaInstitutet
Helena Carén [email protected] UniversityofGothenburg
Helena JernbergWiklund [email protected] UppsalaUniversity
Helene Lindegren [email protected] Merck
Henk Stunnenberg [email protected] Radboud Institute for Molecular LifeSciences(RIMLS)
Hua Jiang [email protected] SwedishUniversityofAgriculturalSciences
HusenM. Umer [email protected] UppsalaUniversity
Huthayfa Mujahed [email protected] KarolinskaInstitutet
Isabel Regadas [email protected] StockholmUniversity
Jaclyn Quin [email protected] StockholmUniversity
Jakub OrzechowskiWestholm [email protected] StocholmUniversity
Jan Komorowski [email protected] UppsalaUniversity
Jarmila Nahalkova [email protected] private
Jason Ernst [email protected] UniversityofCalifornia,LosAngeles
Jessica Nordlund [email protected] UppsalaUniversity / SNP-SEQ TechnologyPlatform
Joaquin CustodioRojo [email protected] KarolinskaInstitutet
Johan Winquist [email protected] Beactica
Jordi Planells [email protected] StockholmUniversity
JoseRamon Barcenas-Walls [email protected] UppsalaUniversity
Juan Inda [email protected] UppsalaUniversity
JuanIgnacio BarrasaLopez [email protected] UmeåUniversity
Juliana Imgenberg-Kreuz [email protected] UppsalaUniversity
Karolina Smolinska [email protected] UppsalaUniversity
Katarina Lyberg [email protected] KarolinskaInstitutet
Klev Diamanti [email protected] UppsalaUniversity
Koji Ando [email protected] UppsalaUniversity
Kwangchol Mun [email protected] UppsalaUniversity
Kyle Kimler [email protected] SciLifeLab
39
Lara Kular [email protected] KarolinskaInstitutet
Larry Mansouri [email protected] UppsalaUniversity
Laura Rojas [email protected] UppsalaUniversity
Laura Eme [email protected] UppsalaUniversity
Leif Karlsson [email protected] KarolinskaInstitutet
Lejon Kralemann [email protected] SwedishUniversityofAgriculturalSciences
Li He [email protected] StockholmUniversity
Lindsay Parkes [email protected] Chromatrap
Ling Shen [email protected] UppsalaUniversity
Lluis MillanArino [email protected] KarolinskaInstitutet
Lucia Pena-Perez [email protected] KarolinskaInstitutet
Ludvig Lizana [email protected] UmeåUniversity
Malin Ueberschär [email protected] StockholmUniversity
Marek Bartosovic [email protected] KarolinskaInstitutet
Marina Wiklander [email protected] Merck
Marina Zelenina [email protected] KTHRoyalInstituteofTechnology
Marko Sankala [email protected] Merck
Mateusz Garbulowski [email protected] UppsalaUniversity
Matilda Kjellander [email protected] KarolinskaInstitutet
Mattias Mannervik [email protected] StockholmUniversity
Mattias Alenius [email protected] UmeåUniversity
Melika Hajkazemian [email protected] StockholmUniversity
Min Tang [email protected] StockholmUniversity
Miyuki Nakamura [email protected] SwedishUniversityofAgriculturalSciences
Mohsen KarimiArzenani [email protected] KarolinskaInstitutet
My Bjöklund [email protected] UppsalaUniversity/
Naveed Jhamat [email protected] SwedishUniversityofAgriculturalSciences
Nicholas Baltzer [email protected] UppsalaUniversity
Ning Liang [email protected] KarolinskaInstitutetP NavaneethKrishna Menon [email protected] UppsalaUniversity
Panagiotis Papoutsoglou [email protected] UppsalaUniversity
Paraskevi Heldin [email protected] Uppsalauniversity
Patricia Stoll [email protected] UppsalaUniversity
Patricia RomansFuertes [email protected] StockholmUniversity
Pelin Sahlen [email protected] KTHRoyalInstituteofTechnology
Peter Svensson [email protected] KarolinskaInstitutet
Philippe Cronet [email protected] Diagenode
Qi Dai [email protected] StockholmUniversity
Rita Batista [email protected] SwedishUniversityofAgriculturalSciences
Robert Månsson [email protected] KarolinskaInstitutet
Rongrong Fan [email protected] KarolinskaInstitutet
Roshan Vaid [email protected] StockholmUniversity
40
Rui Shao [email protected] KarolinskaInstitutet
Samudhra Sabari [email protected] UppsalaUniversity
Samudyata Samudyata [email protected] KarolinskaInstitutet
Sara Yones [email protected] UppsalaUniversity
Sarantis Chlamydas [email protected] ActiveMotif
Sarbashis Das [email protected] UppsalaUniversity
Sascha Krakovka [email protected] UppsalaUniversity
Sebastian Deindl [email protected] UppsalaUniversity
Sergey Belikov [email protected] Stockholmuniversity
Shadi Jafari [email protected] LinköpingUniversity/NewYorkUniversity
Shujing Liu [email protected] SwedishUniversityofAgriculturalSciences
Simon Elsässer [email protected] KarolinskaInstitutet
Sujata Bhoi [email protected] UppsalaUniversity
Susanna Larsson [email protected] SahlgrenskaCancerCenter /UniversityofGothenburg
Susanne Kerje [email protected] UppsalaUniversity
Sylvain Mareschal [email protected] KarolinskaInstitutet/UppsalaUniversity
Valentina Peona [email protected] UppsalaUniversity
Varshni Rajagopal [email protected] UppsalaUniversity
Varun Maturi [email protected] UppsalaUniversity
VelinMarita Sequeira [email protected] UppsalaUniversity
Wenbo Dong [email protected] KarolinskaInstitutet
Vicent Pelechano [email protected] KarolinskaInstitutet
Vidhur Seshadri [email protected] UppsalaUniversity
Xiaoyan Qian [email protected] StockholmUniversity
Xiushan Yin [email protected] KarolinskaInstitutet
Yanara Marincevic [email protected] UppsalaUniversity
Yerma ParejaSanchez [email protected] KarolinskaInstitutet
Ying Qu [email protected] KarolinskaInstitutet
Yuan Guo [email protected] StockholmUniversity
Yuri Schwartz [email protected] UmeåUniversity
Zeeshan Khaliq [email protected] UppsalaUniversity
Zhiqiang Huang [email protected] KarolinskaInstitutet
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