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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



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



Sir John SulstonSir John Sulston2002 Nobel2002 Nobel

C. elegans developmentC. elegans development

Major cell types made by founder cells



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)



Asymmetric first divisionAsymmetric first division

SKNSKN--11

ABAB P1P1


=



EMS

mesodermmesoderm mesectodermmesectodermendodermendoderm

EEMSMS CCEMSEMS

formation of the formation of the C. elegans C. elegans endodermendoderm


EMS

gutgut

mesodermmesoderm mesectodermmesectoderm

MSMS CCEE



formation of the formation of the C. elegans C. elegans mesodermmesoderm

EMS

mesectodermmesectoderm

MSMS CCEE

pharynx, body muscle, somatic gonad, etc.

endodermendoderm


EMS

gutgut

mesodermmesoderm mesectodermmesectoderm

MSMS CCEE



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



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



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



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




=

MS fate E fate

PP22 induces E fateinduces E fate

EMSEMS

P2P2



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



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



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



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::



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



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



Sea urchin regulatory networkSea urchin regulatory network

Rothman Lab



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



MEDs, POPMEDs, POP--1, END1, END--3, 3, ELTsELTs

Morris MaduroMorris MaduroGina BroitmanGina Broitman-- MaduroMaduro

FarzanehFarzaneh MasoudMasoud

Keith StrohmaierKeith Strohmaier

uc santa barbaraonline.itp.ucsb.edu/online/bio99/rothman/pdf/rothman.pdf · dr. joel rothman, mcd...

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