Keystone Symposia in Whistler Long Noncoding RNAs

Joint with the conference on RNA-Protein Interactions

Scientific Organizers: Saba Valadkhan, Case Western Reserve University, USA Piero Carninci, RIKEN Center for Life Science Technologies, Japan

Although emerging evidence points to the critical importance of the long noncoding transcriptome in human physiology and pathology, the clinical potential of long noncoding RNAs (lncRNAs) as therapeutic and prognostic targets remain largely unexplored. The increasing availability of high-throughput technologies and newly developed computational methodologies is rapidly making it possible to address this gap in our knowledge. However, optimal use of these new capabilities and recognition of their power in transforming the field of lncRNA research requires the formation of new collaborative and training efforts. This conference specifically aims to: 1) Communicate the latest available technologies and developing methodologies for lncRNA functional genetics to the lncRNA community; 2) Promote collaborations and new research directions that will bridge the already thriving lncRNA mechanistic and basic research to the clinical need for novel, effective diagnostic, prognostic and therapeutic targets; 3) Contribute to attracting the attention of biotech and pharmaceutical industry and clinically-oriented funding agencies to the lncRNA field; and 4) Integrate lncRNA research into other biological fields through the joint pairing with the conference on “RNA-Protein Interactions.”

Session Topics: • Functional RNA Elements in Mammalian Genomes (Joint) • lncRNAs, Transposons and Evolution of the Genome • Coding and Noncoding RNAs on Chromatin (Joint) • Regulation of Differentiation and Development by lncRNAs • lncRNAs in Disease: Tools for Discovery • Novel Insights into Functional Mechanism of lncRNAs• lncRNAs: Diversity in Form and Function • RNA and RBP in Disease (Joint) plus two workshops

a 501(c)(3) nonprofit educational organization

Keystone Symposia in WhistlerLong Noncoding RNAs: From Molecular Mechanisms to Functional Genetics

Scholarship/Discounted Abstract Deadline: Oct 25, 2018; Abstract Deadline: Nov 29, 2018; Discounted Registration Deadline: Jan 10, 2019

Visit www.keystonesymposia.org/19X2 for more details.

Whistler Conference Centre | Whistler, British Columbia, Canada | February 24–28, 2019

SUNDAY, FEBRUARY 24Arrival and Registration

MONDAY, FEBRUARY 25Welcome and Keynote Session (Joint) *Douglas L. Black, University of California, Los Angeles, USA*Anne Ephrussi, European Molecular Biology Laboratory, Germany*Saba Valadkhan, Case Western Reserve University, USA*Piero Carninci, RIKEN Center for Integrative Medical Sciences,JapanJennifer A. Doudna, HHMI/University of California, Berkeley, USANew Genome Editors and Inhibitors from the CRISPR Family TreeJohn S. Mattick, University of Oxford, UKThe New World of RNA Biology

Functional RNA Elements in Mammalian Genomes (Joint) *Danesh Moazed, Harvard Medical School, USA*Howard Y. Chang, Stanford University, USAXiang-Dong Fu, University of California, San Diego, USABroad Roles of RNA-Binding Proteins in Regulated Gene ExpressionThomas R. Cech, HHMI/University of Colorado, USARNA-Protein Interactions Regulate Epigenetic SilencingChris B. Burge, Massachusetts Institute of Technology, USAPatterns in the Recognition of RNAs by RBPsMaiwen Caudron-Herger, German Cancer Research Center,GermanyShort Talk: Proteome-Wide and Quantitative Identification ofRNA-Dependent Protein ComplexesMario A. Flores, NCBI, National Institutes of Health, USAShort Talk: Dissecting the Characteristics and Functions ofTranscribed EnhancersYoav Lubelsky, Weizmann Institute of Science, IsraelShort Talk: Elucidating the Crosstalk between hnRNPK Binding andNuclear Retention of Long RNAsYoko Matsuno, Niigata University, JapanShort Talk: Characteristic Convergent Variation in LINE-1 NucleotidesCan Benefit Redundantly Forming Triplexes with lncRNA inMammalian X-Chromosome Inactivation

Workshop 1: lncRNAs: Diversity of Function (X2)*Ling-Ling Chen, Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences, China*Susan B. Carpenter, University of California, Santa Cruz, USAThomas C. Brodnicki, St Vincent's Institute, AustraliaA Long Noncoding RNA Attenuates Dendritic Cell Function andDecreases Autoimmune Disease Susceptibility

Ousman Tamgue, University of Douala, Cameroon and University ofCape Town, IDM, South AfricaLong Non-Coding RNA-26 Promotes Intracellular Mycobacteriumtuberculosis Growth through Inhibition of Pro-Inflammatory GenesExpression and Macrophage Activation Fabio Desideri, Sapienza University of Rome, ItalyCharme Long Noncoding RNA Shapes the 3D Nuclear Structure byits Close Cooperation with ChromatinMarine Gautier, Centre National de la Recherche Scientifique, FranceFunctional Characterization of Hypoxia-Regulated lncRNAs inNon-Small Cell Lung CarcinomasParas Sehgal, Institute of Genomics and Integrative Biology, IndiaRegulation of Diacyl Glycerol-Mediated Protein Kinase C-BetaActivation by Vascular Endothelial -Associated Long Noncoding RNA2 Modulates Endothelial PermeabilityRoberto Vendramin, VIB-KU Leuven, BelgiumSAMMSON Fosters Cancer Cell Fitness by Concertedly EnhancingMitochondrial and Cytosolic TranslationTan Phat Pham, Amsterdam University Medical Center, NetherlandsThe Age and Shear Regulated Long Non-Coding RNA AerrieControls Endothelial Cell FunctionLaura Stanicek, Amsterdam University Medical Center, NetherlandsThe Shear Stress-Induced Long Non-Coding RNA LASSIE as aRegulator of Endothelial Cell Junctions

Workshop 1: New RNA Technologies (X1)Daniel Benhalevy, NIAMS, National Institutes of Health, USAProximity-CLIP Provides a Snapshot of Protein-Occupied RNAElements in Sub-Cellular Compartments*Kevin Drew, University of Texas at Austin, USASystematic Discovery of Endogenous Human RibonucleoproteinComplexesHong Han, University of Toronto, CanadaAn Integrated High-Throughput Chemical Screening Platform for RNASplicing ModulatorsSudhakar Jha, National University of Singapore, SingaporeUtilization of a Novel Technique to Identify RNA-Binding ProteinsJakob Trendel, European Molecular Biology Laboratory, GermanyProtein Half-Lives on RNA Reveal Human Ribosome MaintenanceIndependent of Ribosome BiogenesisMarta Gabryelska, University of Edinburgh, UKProbing Ribosome Assembly Dynamics with CLASH*Alena Shkumatava, Institut Curie-Centre de Recherche, FranceSystematic Identification and Quantitative Measurement ofRNA-Protein Interactions by incPRINT

* Session Chair † Invited but not yet accepted Program current as of November 21, 2021. Meal formats are based on meeting venue. For the most up-to-date details, visit https://www.keystonesymposia.org.

KEYSTONE SYMPOSIAon Molecular and Cellular Biology

Long Noncoding RNAs: From Molecular Mechanism to Functional Genetics (X2)Scientific Organizers: Saba Valadkhan and Piero Carninci

Sponsored by Cell Research and Ionis Pharmaceuticals, Inc.

RNA-Protein Interactions (X1)Scientific Organizers: Xiang-Dong Fu, Anne Ephrussi and Douglas L. BlackFebruary 24-28, 2019 • Whistler Conference Centre • Whistler, BC, Canada

Sponsored by Cell ResearchDiscounted Abstract & Scholarship Deadline: October 25, 2018 / Abstract Deadline: November 29, 2018 / Discounted Registration Deadline: January 10, 2019

lncRNAs, Transposons and Evolution of the Genome (X2)*John L. Rinn, University of Colorado Boulder, USAIgor Ulitsky, Weizmann Institute of Science, IsraelFunctions, Modes of Action and Localization of Long NoncodingRNAs in Mammalian CellsLynne E. Maquat, University of Rochester Medical Center, USARole of Retrotransposon Elements within Cellular RNAsPaulo P. Amaral, University of Cambridge, UKDefining the Landscape of Covalent Modifications in ConservedNoncoding RNAs using Direct-RNA SequencingPiero Carninci, RIKEN Center for Integrative Medical Sciences, JapanFunctional Genomics of lncRNAsPaolo Gandellini, Fondazione IRCCS Istituto Nazionale dei Tumori,ItalyShort Talk: LEADeR Role of miR-205 Host Gene as Long Non-CodingRNA in Prostate Basal Cell DifferentiationGiovanni Pascarella, RIKEN Yokohama Institute, JapanShort Talk: Somatic Retrotransoposons-Associated Structural Variantsin Health and Neurodegeneration

RNP in Phase Transition (X1)*Kristen W. Lynch, University of Pennsylvania, USAKathrin Plath, University of California, Los Angeles, USAA New Mode of Xist ActionRoy R. Parker, HHMI/University of Colorado, USARNP Granules in Health and DiseaseKimberly L. Mowry, Brown University, USALarge RNP Transport Granules Drive mRNA LocalizationJoseph Lobel, University of California, San Francisco, USAShort Talk: Pat1 Activates Late Steps in mRNA Decay by MultipleMechanismsXiong Ji, Peking University, ChinaShort Talk: RNAPII Condensates Connect Genome Organization andGene Regulation

Poster Session 1

TUESDAY, FEBRUARY 26Coding and Noncoding RNAs on Chromatin (Joint) *Kathrin Plath, University of California, Los Angeles, USA*Igor Ulitsky, Weizmann Institute of Science, IsraelDanesh Moazed, Harvard Medical School, USARNAi in Chromatin RemodelingYijun Ruan, The Jackson Laboratory for Genomic Medicine, USAProtein-RNA-Chromatin Interactions

Jeannie T. Lee, Massachusetts General Hospital / Harvard MedicalSchool, USAXist RNA Antagonizes the Chromatin Remodeler, BRG1, on theInactive X Chromosome Valerio Orlando, King Abdullah University of Science andTechnology, Saudi ArabiaRNAi Component Ago1 Interacts with lncRNAs to Regulate NuclearArchitecture and Cell DifferentiationRyan A.. Flynn, Boston Children’s Hospital, USAShort Talk: DNA-PK Leverages Non-Coding RNA Binding to RegulateNucleolar FunctionsRiki Kurokawa, Saitama Medical University, JapanShort Talk: Arginine Methylation of RNA Binding Protein TLS InhibitsBinding to Long Noncoding RNA, Repressing the HistoneAcetyltransferase ActivitySaigopal Somasundaram, Case Western Reserve University, USAShort Talk: The DNMT1-Associated lincRNA DACOR1 ReprogramsGenome-Wide DNA Methylation in Colon CancerEric James de Bony de Lavergne, Ghent University, BelgiumShort Talk: NESPR Long Non-Coding RNA, a NewNeuroblastoma-Specific Oncogene

Regulation of Differentiation and Development by lncRNAs (X2)*Lynne E. Maquat, University of Rochester Medical Center, USASaba Valadkhan, Case Western Reserve University, USARegulation of Cellular Quiescence by lncRNAsJoshua T. Mendell, University of Texas Southwestern MedicalCenter, USAlncRNAs in Mammalian Physiology and DiseaseSusan B. Carpenter, University of California, Santa Cruz, USAGenetic Models Reveal cis and trans Immune-Regulatory Activitiesfor lincRNA-Cox2 Gaultier Hericher, Université Laval – CRCHU de Québec, CanadaShort Talk: Novel Tuna Isoforms Define the Pluripotent Stem Cell State

Dissecting RNP Functions in vivo (X1)*V. Narry Kim, Institute for Basic Science, South KoreaJoan A. Steitz, Yale University, USATarget-Directed miRNA Decay: Yet Another Function of Ago ProteinsSusan L. Ackerman, University of California, San Diego, USAtRNAs and Neuron FunctionKristen W. Lynch, University of Pennsylvania, USACELF2 Regulation of Splicing and Polyadenylation in Activated T Cells







Danielle Widner, Yale University, USAShort Talk: RNA-Protein Complex Formation in a Mysterious LargencRNAQingqing Wang, University of California, Berkeley, USAShort Talk: Decipering the Splicing Code of Coordinated RN- BindingProteins PSI and hrp48 in Sculpting the Drosophila Transcriptome

Poster Session 2

WEDNESDAY, FEBRUARY 27lncRNAs in Disease: Tools for Discovery (X2)*Fabrizio d'Adda di Fagagna, IFOM, The FIRC Institute of MolecularOncology, ItalyHoward Y. Chang, Stanford University, USAGenome Regulation by Long Noncoding RNAsJoakim Lundeberg, KTH-Royal Institute of Technology, SwedenSpatial Transcriptome Analysis and DiseaseNicholas J. Proudfoot, University of Oxford, UKDifferent Mechanisms Define lncRNA and Protein Coding GeneTranscription Units in Mammalian CellsJin Chen, University of California, San Francisco, USASystematic Discovery of Novel Peptides from the NoncanonicalTranslation of Non-Coding RegionsPer Johnsson, Karolinska Institutet, SwedenShort Talk: Functional Prediction and Validation of lncRNAs usingAllele-Sensitive Single-Cell RNA-SequencingLydia M. Contreras, University of Texas at Austin, USAShort Talk: Novel High-Throughput Tools for in vivo FunctionalCharacterization of Regulatory RNAsBojan Losic, Icahn School of Medicine at Sinai, USAShort Talk: Circular RNA Mediate IBD Genetic Risk

RNA Transport and Localization (X1)*Kimberly L. Mowry, Brown University, USA*Erik J. Sontheimer, University of Massachusetts Medical School,USAAnne Ephrussi, European Molecular Biology Laboratory, GermanyMotor-Mediated RNA Transport and LocalizationRobert H. Singer, Albert Einstein College of Medicine, USANeuronal Targets for RNA Binding ProteinsDierk Niessing, Ulm University, GermanyMolecular Architecture and Dynamics of mRNA Transport ComplexesAnob Chakrabarti, Francis Crick Institute, UKShort Talk: Exploring the Characteristics and Functions of RNASecondary Structures Bound in vivo by StaufenHong Cheng, Shanghai Institute of Biological Science, ChineseAcademy of Sciences, ChinaShort Talk: NRDE2 Negatively Regulates Nuclear Exosome Functionsand Controls Embryonic Stem Cell Self-Renewal

Mehdi Pirouz, Boston Children's Hospital, USAShort Talk: The Perlman Syndrome Dis3l2 Exonuclease as Guardianof ER-associated TranslationDhara Patel, Universite de Montreal, CanadaShort Talk: Complementary 3’UTRs Derived from Overlapping Genescan Promote Cytoplasmic Co-Localization of Distinct mRNAsJernej Murn, University of California, Riverside, USAShort Talk: Transcriptional Control of Neuronal Differentiation by anRNA-Binding Protein

Novel Insights into Functional Mechanism of lncRNAs (X2)*Joshua T. Mendell, University of Texas Southwestern MedicalCenter, USAMichael G. Rosenfeld, University of California, San Diego, USAeRNAs Mediate Phase Separation of Ligand-Activated Enhancers toLicense Cooperative Chromosomal Enhancer AssemblyJohn L. Rinn, University of Colorado Boulder, USAThe Firre Locus Produces a Trans-Acting RNA Molecule thatFunctions in HematopoiesisKaveh Daneshvar, Harvard Medical School, USAShort Talk: lncRNA DIGIT and BRD3 Protein Form Phase-SeparatedCondensates and Regulate Endoderm Differentiation.Karan Joshua Abraham, University of Toronto, CanadaShort Talk: Intergenic Non-Coding RNA-DNA Hybrids MaintainNucleolar Biomolecular Condensates and Ribosome Biogenesis

Structure and Function of RBPs (X1)*Rui Zhao, University of Colorado, USADouglas L. Black, University of California, Los Angeles, USASplicing Activation by Rbfox Requires Self-Aggregation of itsTyrosine-Rich DomainFrédéric H.T. Allain, ETH Zurich, SwitzerlandInteraction of U1snRNP with Drugs and RNA-Binding Proteins inSplicing RegulationTraci M.T. Hall, NIEHS, National Institutes of Health, USACollaborative RNA Recognition Specificity by PUF ProteinsAndreas Schlundt, Goethe University Frankfurt, GermanyShort Talk: The Individual Contributions of Single IMP3 RNA-BindingDomains to the Recognition of Clustered Sequences in Target mRNAsJanosch Hennig, European Molecular Biology Laboratory, GermanyShort Talk: Structural Insights into MLE-Unr-roX2 Complex Assemblyduring Early Steps of Drosophila Dosage Compensation

Poster Session 3

THURSDAY, FEBRUARY 28lncRNAs: Diversity in Form and Function (X2)







*Jeannie T. Lee, Massachusetts General Hospital / Harvard MedicalSchool, USAKarissa Y. Sanbonmatsu, Los Alamos National Laboratory, USATwo-Dimensional and Three-Dimensional Structure-FunctionRelationships for Individual Long Noncoding RNAsJay W. Shin, RIKEN Yokohama, JapanFunctional Elucidation of Long Noncoding RNAsLing-Ling Chen, Shanghai Institutes for Biological Sciences, ChineseAcademy of Sciences, ChinalncRNAs of Novel OriginXiao Liu, Yale University, USAShort Talk: A ncRNA Derived from xbp-1 mRNA Cleavage PromotesAxon RegenerationYoo Jane Han, University of Chicago, USAShort Talk: Circular RNAs Expressed from the BRCA1 PseudogeneRegulates Antiviral Immune Signaling in Breast Cancer CellsPrasanth V. Kannanganattu, University of Illinois, USAShort Talk: Nucleolus-Enriched Repeat-Containing Noncoding RNARegulates rDNA Transcription.Filipp Frank, Emory University, USAShort Talk: SHAPE-MaP Identifies Two Structural Modules withDistinct Function in the lncRNA Growth Arrest Specific 5 (Gas5)Haobo Li, Massachusetts General Hospital, USAShort Talk: Inhibition of Novel Long Noncoding RNA lncExACT1Induces Physiological Cardiac HypertrophyFu-Kai Hsieh, Massachusetts General Hospital, USAShort Talk: The lncRNA HERVH Negatively Regulates ChromatinTargeting and Remodeling Mediated by CHD7

RNP Machines and Regulation (X1)*Eric Lecuyer, Institut de Recherches Cliniques de Montreal, CanadaJoint Institute, CanadaV. Narry Kim, Institute for Basic Science, South KoreaThe Barricade Complex as A Rate-Limiting Blockade against mRNADeadenylationRui Zhao, University of Colorado, USAStructure and Function of the Spliceosome Yanli Wang, Chinese Academy of Sciences, ChinaCRISPR-Cas Mediated Cleavage of Invading RNAsErik J. Sontheimer, University of Massachusetts Medical School, USAEnhancing Genome Editing with New Cas9s and Fully StabilizedGuidesHuating Wang, Chinese University of Hong Kong, ChinaShort Talk: MyoD-Induced Enhancer RNA Interacts with hnRNPLProtein via CAAA Motif to Activate Target Gene Transcription duringMyogenic Differentiation

Simone Hoefler, Leibniz University Hanover, GermanyShort Talk: Structural and Functional Dissection of Eukaryotic snoRNPComplexes Catalyzing rRNA 2'-O-Ribose MethylationsJiarui Song, Texas A&M University, USAShort Talk: A Novel Plant-Specific Structural Element within theArabidopsis Telomerase RNA

Workshop 2: Mechanistic Diversity of lncRNA (X2)*Jay W. Shin, RIKEN Yokohama, Japan*Paulo P. Amaral, University of Cambridge, UKGabrijela Dumbovic, University of Colorado Boulder, USAThe Tug1 lncRNA Locus Is Essential for Male Fertility and Harbors aTripartite DNA, lncRNA and Protein FunctionalityKaren Wing Yee Yuen, University of Hong Kong, Hong KongPoint Centromere Activity Requires an Optimal Level of CentromericNon-Coding RNAThomas Alan Dixon-McDougall, University of British Columbia,CanadaThe Identity of the Discontinuous Regions of the lncRNA XIST thatCooperatively Inactivate a ChromosomeJin-Wu Nam, Hanyang University, South KoreaEn Bloc and Segmental Deletions of Human XIST Reveal XChromosome Inactivation-Involving RNA ElementsEddie Grinman, The Scripps Research Institute – Florida, USAInvestigating the Role of a Synaptically Targeted Intronic lncRNA inMemory StorageRotem Ben Tov Perry, Weizmann Institute of Science, IsraelRegulation of Neuroregeneration by Long Noncoding RNAsQing Lyu, University of Rochester, USAB2M RNA Facilitates HSV-1 Gene Expression via Interacting withASH2L and VP16Karoline Kragh Ebbesen, Aarhus University, DenmarkUnraveling the Biogenesis and Function of the Circular RNA ciRS-7

Workshop 2: RNA Modifications and Regulated RNA Processing(X1)Erin K. Borchardt, Yale University, USAInvestigating RNA Pseudouridylation Patterns in Viral InfectionMarisa J. L. Aitken, MD Anderson Cancer Center, USAhnRNP K Overexpression Drives Myeloid Malignancy via Interactionwith RUNX1Alexander M. Price, Children's Hospital of Philadelphia, USAAdenovirus Co-Opts Cellular m6A Modification Machinery to FacilitateViral RNA Splicing and Protein Production*Ramesh S. Pillai, University of Geneva, SwitzerlandRNA Modifications and Regulation of Gene Expression







Sushant Bangru, University of Illinois, Urbana-Champaign, USATemporal Control of ESRP2 Licenses Fetal-to-Adult Switch inAlternative Splicing Required for Hepatocyte Maturation*Bobby J. Hogg, NHLBI, National Institutes of Health, USAhnRNP L-Dependent Protection of Normal mRNAs from NMDSubverts Quality Control in B Cell LymphomaEleonora D'Ambra, Sapienza University of Rome, ItalyStudy of FUS-Dependent circRNAs Function and Localization inMurine Motor NeuronsXiao Song, Northwestern University, USASRSF3 Promotes Glioblastoma Progression Via Splicing Regulationof Alternative Exons

RNA and RBP in Disease (Joint) *Susan L. Ackerman, University of California, San Diego, USA*Joakim Lundeberg, KTH-Royal Institute of Technology, SwedenFabrizio d'Adda di Fagagna, IFOM, The FIRC Institute of MolecularOncology, ItalySequence-Specific Inhibition of Noncoding RNA Generated atDysfunctional Telomeres Improves Progeric Phenotypes and ExtendsLifespan in two Animal SpeciesMofang Liu, Shanghai Institutes for Biological Sciences, ChineseAcademy of Sciences, ChinaA Novel Function of MIWI/piRNA in Activating Translation ofSpermiogenic mRNAs during SpermiogenesisFrank Rigo, Ionis Pharmaceuticals, USATargeting RNA with Antisense Oligonucleotides to Treat Disease

Meeting Wrap-Up: Outcomes and Future Directions (Joint) *Xiang-Dong Fu, University of California, San Diego, USA*Saba Valadkhan, Case Western Reserve University, USA*Piero Carninci, RIKEN Center for Integrative Medical Sciences,Japan

FRIDAY, MARCH 1Departure







Keystone Symposia in Whistler Long Noncoding RNAs

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