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How do embryos build themselves?. Nested Networks – and other problems In GRN analysis. Dave McClay. You arrive at differentiation genes and then what?. Gene activation. GRN. Induction. Cadherin. Cadherin. Adhesion. Protein- Protein Interaction. Signal transduction. Cell shape

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slide2

Nested Networks – and other problems

In GRN analysis

Dave McClay

slide4

Gene

activation

GRN

Induction

Cadherin

Cadherin

Adhesion

Protein-

Protein

Interaction

Signal

transduction

Cell shape

Change - motility

Adhesion

Adhesion

Kinase-

phosphatase

Cell shape

Change - motility

slide5

Too often, “networks” are actually glossaries.

Zaidel-bar lab Singapore,

Short, B., JCB 2009

slide6

Integrin “adhesome”

From Zaidel-bar et al Nature Cell biology, 2007

slide7

Integrin Glossary

From Zaidel-bar et al Nature Cell biology, 2007

slide8

Chromosome maintenance

And duplication machinery

Merico, et al., 2009 Nature

slide9

Protein interaction data comparing data from

Two species

Sharan and Ideker, Nature Biotech. 2006

slide11

Actin regulatory network

From Springer after Lee, SH,. 2010

slide12

Gilfillan and Rivera, 2009, Immunol Rev

Mast cell activation network

slide13

Cdc protein kinase and phosphatase network

Breitkreutz et al., Science 2011

slide16

Gene

activation

GRN

Induction

Cadherin

Cadherin

Adhesion

Protein-

Protein

Interaction

Signal

transduction

Cell shape

Change - motility

Adhesion

Adhesion

Kinase-

phosphatase

Cell shape

Change - motility

slide18

b

outside

Endo-mes

Fig. 2

Mat cb

LiCl

Endo-Mes

Mat Otx

c

GSK-3

frizzled

Micr

Mat Otx

nb-TCF

Maternal

& early

interactions

Wnt8

Ets

4th cleavage

SoxB1

Krl

Otx

Eve

Krox

b

a

Interactions

in definitive

territories

LiCl

Colored boxes indicate post gastrular domains of expression genes

cb

c

GSK-3

Endoderm

Mesoderm

Frz

to 4th – 6th

Cleavage

Endo-Mes

nb-TCF

Wnt8

Rep. of Wnt8

(18 hrs)

Otx

a

Krox

Late Wnt8

signal from

veg2

Hnf 6

MV2L

Mat. N.

N

Su(H)+

Repressor

PMC

E(S) ?

7th-9th cleavage

Eve

Bra

GataE

FoxA

Ub

Hmx

Delta

Pmar1

Delta

Lim

Zyg. N.

UI

Eve

Gcm

GataC

FoxB

Ets

Dri

Notch

Not

Elk

Hox11/13b

Veg1

endoderm

Endomes up to 20-24hours

TBr

Nrl

Cyclophilin, EpHx, Ficolin, Sm37, Sm27, MSP130L

Post gastrular terminal or

peripheral

downstream genes

Sm30

Sm50

Kakapo

Apo bec

OrCT

SuTx

Pks

CAPK

Dpt

Gelsolin

Endo16

Decorin

Mes

Endo

Msp130

FvMo

slide21

Progression of network

states

Morphogenesis

slide22

Progression of network

states

Morphogenesis

slide23

In the micromeres:

In the ectoderm

Redox asymmetry

ß-catenin

P38-P in oral

Pmar1

Mic Repressor

Nodal in oral

Alx1

Gsc

BMP

Snail

Oral

Aboral

FoxN2/3

Post

EMT

GRN

PMCs move to new site

VEGF

VegfR

FGFR

FGF

Skeletogenic

Network

Skeleton production

slide25

ß-catenin

Veg 2 ring (16 cells)

Large Micromeres (8)

Small Micromeres (4)

  • ß-catenin enters specific
  • nuclei in a precise
  • temporal sequence.

Cati Logan

slide26

Nuclear

-catenin

Signaling is dynamic

Transcription Factor

expression is dynamic

i.e. GRN states are

dynamic

Wnt 8

Blimp1

Logan et al 1999

Smith et al. 2007

slide28

Logan et al 1999

Smith et al 2007

slide33

Network states change so that cells in the

Same germ layer, or same territory of a germ

Layer assume different GRN states.

slide34

Problem: Network

State Dynamics

Hatched blastula

Mesenchyme

blastula

slide35

Brachy

As cells converge toward the

Blastopore they rapidly alter

Their GRN state

Jeff Gross

slide36

Gcm

HB

Bra

Gcm

MB

Bra

Gcm

MB

FoxA

Bra

FoxA

slide37

Delta

Delta + Gcm

FoxA

FoxA+Bra

Bra

slide39

Brachyury

Fox A

Endo

NSM

BP

Expression of Brachyury and FoxA upstream

of Hh and invagination is dynamic -

Network state running in Endoderm cells

rapidly changes as cells converge on Blastopore

Jeni Croce

slide40

Developmental Biology

Functional Genomics

Molecular Biology

Perturbation

experiments

Systems biology

slide42

Problems with Networks:

It is difficult to reflect dynamics – parameters are missing

It is difficult to pair a GRN to events happening in an organism