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Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 1
Developmental switches and gene Developmental switches and gene regulatory networks in the most regulatory networks in the most
completely described animal, the completely described animal, the nematode nematode C. elegansC. elegans
Joel RothmanJoel RothmanUC Santa BarbaraUC Santa Barbara
Generating developmental diversity:Generating developmental diversity:Symmetry breakingSymmetry breaking
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 2
BB CC
AA
==
Asymmetric cell divisionAsymmetric cell division
C. elegansC. elegans
geneticsgeneticscomplete anatomy and complete anatomy and
development development complete genomecomplete genome
(100,258,171 bp)(100,258,171 bp)overnight gene overnight gene
“ knockouts” (RNAi)“ knockouts” (RNAi)conserved genetic conserved genetic
toolkittoolkit
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 3
Sir John SulstonSir John Sulston2002 Nobel2002 Nobel
C. elegans developmentC. elegans development
Major cell types made by founder cells
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 4
The first symmetry break: A/P axisThe first symmetry break: A/P axis
Wallenfang, M.R. and Seydoux, G., 2000
AntAnt PostPost
Establishing A/P polarity Establishing A/P polarity
after after CuencaCuenca et al., Develop. 130, 235 (2003)et al., Develop. 130, 235 (2003)
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 5
Asymmetric first divisionAsymmetric first division
SKNSKN--11
ABAB P1P1
Asymmetric cell divisionAsymmetric cell division
=
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 6
EMS
mesodermmesoderm mesectodermmesectodermendodermendoderm
EEMSMS CCEMSEMS
formation of the formation of the C. elegans C. elegans endodermendoderm
formation of the formation of the C. elegans C. elegans endodermendoderm
EMS
gutgut
mesodermmesoderm mesectodermmesectoderm
MSMS CCEE
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 7
formation of the formation of the C. elegans C. elegans mesodermmesoderm
EMS
mesectodermmesectoderm
MSMS CCEE
pharynx, body muscle, somatic gonad, etc.
endodermendoderm
formation of the formation of the C. elegans C. elegans endodermendoderm
EMS
gutgut
mesodermmesoderm mesectodermmesectoderm
MSMS CCEE
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 8
SKN-1
MED-1,2
MSfate
Efate
MEDMED--1/2 1/2 GATAsGATAs specify mesendodermspecify mesendoderm
MS E
wild type
Cmaternal
zygotic
“ C”
med(-)
“ C”
C
((mesectodermmesectoderm))
EMSEMS
MSMSgenesgenes
SKNSKN--11
MEDsMEDs
ENDsENDs
MSMS EE
CCgenesgenes
EMSEMS
PALPAL--11
EMSEMS
MSMSgenesgenes
SKNSKN--11
MEDsMEDs
ENDsENDs CCgenesgenes
CC
PALPAL--11
GSKGSK--33
Mesendoderm developmentMesendoderm development
P1P1
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 9
Ea Cp
wild type
Ea
end-1/3(-)
gastrulationrepression of C
SKN-1
MED-1,2
END-1,3
Efate
ENDEND--1/3 1/3 GATAsGATAs specify endodermspecify endoderm
ENDEND--1/3 specify endoderm1/3 specify endoderm
SKN-1
MED-1,2
END-1,3
Efate
wild type ubiquitous
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 10
ENDEND--1/3 specify endoderm1/3 specify endoderm
SKN-1
MED-1,2
END-1,3
ELT-2,7
Efate
Shoichet, S.A., Malik, T.H., Rothman, J.H., and Shivdasani, R.A. PNAS 97, 4076 (2000)
END-1::EnR
WT
ELTELT--2/7 2/7 GATAsGATAs control gut differentiationcontrol gut differentiation
SKN-1
MED-1,2
END-1,3
ELT-2,7
differentiation
wtwt
eltelt--2/7(2/7(--))
gut structuralproteins, enzymes
maternal
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 11
zygote
SKN-1
MED-1,2
END-1,3
ELT-2,7
EMSEMS
EMSMS
specification
differentiation
E fate
properties of endoderm properties of endoderm regulatory cascaderegulatory cascade
zygote
SKN-1
MED-1,2
END-1,3
ELT-2,7
EMSEMS
EMSMS
E fate
AB
MS fate
cell cyclegastrulation
inducer
repression of C
1. Redundancy(GATAs)
Features
2. cell division
3. dedicated functions
properties of endoderm properties of endoderm regulatory cascaderegulatory cascade
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 12
Asymmetric cell divisionAsymmetric cell division
=
MS fate E fate
PP22 induces E fateinduces E fate
EMSEMS
P2P2
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 13
MEDsMEDs
specification of E and MSspecification of E and MS
EMSEMS
P2P2
MS fate E fate
SKN-1SKN-1 SKN-1SKN-1
ENDsENDsENDs
POP-1repPOP-1repMEDsMEDs
POP-1actPOP-1act
Wnt,MAPK
MEDsMEDs
specification of E and MSspecification of E and MS
EMSEMS
P2P2
MS fate E fate
SKN-1SKN-1 SKN-1SKN-1
ENDsENDsENDs
POP-1repPOP-1repMEDsMEDs
POP-1actPOP-1act
Wnt,MAPK
POPPOP--1 HIGH1 HIGH POPPOP--1 LOW1 LOW
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 14
High POP-1
Low POP-1
recursive POP-1 asymmetry
A P
Lin et al. (1998) Cell 92, 229–239
dynamics of POP-1dynamics of POP-1
HIGHHIGH
LOWLOW
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 15
what are thewhat are the medmed--1,21,2 targets?targets?
pharynx, body muscle, somatic gonad, etc.pharynx, body muscle, somatic gonad, etc. intestineintestine
medmed--1,21,2 medmed--1,21,2
-MED-1
AAGTATACCTTTTG
CTGTATACTTCCCGC
end-1
end-3
GATA factor
MED-1
H G A T A R
A G A T A CA T
consensus
MEDMED--1 binds a novel target site1 binds a novel target site
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 16
GFPGFP GFPGFP GFPGFPXX XX
EE 44
GTATA sites are required for GTATA sites are required for endend--1 1 expressionexpression
genomic search for MED targetsgenomic search for MED targets
A G A T A C][A T A G A T A C][A TN25-100
query with query with WormEnhancerWormEnhancer::
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 17
putative MED targetsA G A T A CA T A G A T A CA TN
25-100
gene MED sites
F58E10.2F58E10.5F35H8.7ceh-20/F31E3.2F58G4.4C32E12.5ZK849.2T07D1.2ZK177.10, ZK177.1T11A5.5C17C3.7, C17C3.10B0303.8, 9
product
end-1end-3wee-1.1homeoboxLAG-2-likeSox family (HMG)RCC1unknownT-box/unknownoxygen transportbHLH (2)unknown
T07D1.2 ::GFP
sox-1::GFP +
wee-1.1 ::GFP
E2MS4
E2
E2
three classes of candidate MED targetsthree classes of candidate MED targets
hlh-25 ::GFP
tbx-35 ::GFP
MS2
MS4
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 18
MED-1,2
end-1,3
wee-1.1
sox-1sox-1
EMS
POP-1
T07D1.2
bHLH
T-Boxwnt-dependent
repressionbHLH
T-Box
end-1,3
wee-1.1
T07D1.2
the evolving EMS gene regulatory networkthe evolving EMS gene regulatory network
MED-1,2
end-1,3
wee-1.1
sox-1sox-1
EMS
POP-1
T07D1.2
bHLH
T-Box
bHLH
T-Box
end-1,3
wee-1.1
T07D1.2
the evolving EMS gene regulatory networkthe evolving EMS gene regulatory network
POP-1
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 19
Sea urchin regulatory networkSea urchin regulatory network
Rothman Lab
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 20
CollaboratorsCollaborators
T. Fukushige and Jim McGhee (Calgary)R. Shivdasani (Dana Farber)M. Meneghini and B. Bowerman (Oregon)B. Shraiman, Ruadhan O'Flanagan et al. (KITP, UCSB)
Research GroupResearch Group
Developmental Switches and Gene Regulatory Networks in the Most Completely Described Animal, the Nematode C. Elegans
Dr. Joel Rothman, MCD Biology, UCSB (KITP Bio Seminars 10/12/04) 21
MEDs, POPMEDs, POP--1, END1, END--3, 3, ELTsELTs
Morris MaduroMorris MaduroGina BroitmanGina Broitman-- MaduroMaduro
FarzanehFarzaneh MasoudMasoud
Keith StrohmaierKeith Strohmaier