Abstracts - Society for Developmental Biology

9
Program/Abstract # 26
On the combinatorial function of multiple cis-regulatory modules
Nam, Jongmin, CALTECH, Pasadena, United States
Cis-regulatory modules (CRMs) for gene expression control are modular in the sense that they can activate basal promoters
from other genes in small reporter constructs. We have learned from decades of studies that, although only a small fraction
of CRMs have been identified in the metazoan genomes, CRMs outnumber genes in the genome and that multiple CRMs
control expression of a gene. Two alternative models for how multiple CRMs control gene expression prevail, each with
supporting experimental data .However, little is known about the relative prevalence of the two models. In the first model
different CRMs control gene expression differentially in time and space, and there is no overlapping activity between
CRMs; any changes in CRM activity will result in coherent gene expression changes. In the second model multiple CRMs
function in a combinatorial manner. In this model, a group of activator CRMs and/or repressor CRMs function together,
and overlapping activities between CRMs may happen; changes in CRM activity may not result in coherent gene
expression changes. Using high-resolution temporal activity profiles of 47 genes and their 126 CRMs in developing and
perturbed sea urchin embryos, I tested the two alternative models of CRM function. The results predominantly supported
the second model: Overlapping activities between CRMs located around/within the same gene were common and
incoherent responses between genes and their CRMs to the same perturbation were prevalent. Functional and evolutionary
significance of this finding will be discussed.
Program/Abstract # 27
Identifying regulators of early differentiation and primary germ layer induction
Oron, Efrat, Yale University, New Haven, United States; Wu, Jiaqian; Snyder, Michael (Stanford University, United
States); Ivanova, Natalia (Yale University, New Haven, United States)
Embryonic stem (ES) cell research lies at the interface between developmental biology and medicine. Fundamental
questions such as how do cells become restricted in their developmental potential and differentiate giving rise to all the
cells and tissues that make up an organism will ultimately help us learn how to efficiently manipulate ES cells grown in
culture for therapeutic use. Among the first processes of differentiation is specification of the primary germ layers:
Endoderm, Mesoderm and Ectoderm. Using an in vitro ES cell differentiation system combined with a functional genomics
approach we identified genes required for ES cell differentiation and build a simplistic model of their transcription
regulation hierarchy during germ layer induction. To identify genes that are important for early differentiation we
generated RNAseq mRNA time course profiles from mouse embryos sampled at five developmental timepoints, and ES
cells differentiated as embryoid bodies (EBs) for eleven days. Comparative analysis of expression from embryo vs. cell
lines was used to identify matching developmental time windows between mouse embryos and ES cell lines and to further
select a panel of 160 candidate transcription factors with expression patterns suggestive of an involvement in
differentiation. Candidate genes were individually inactivated in ES cells by lentiviral shRNAs. shRNA-expressing cells
were differentiated as EBs and evaluated for primary germ layers induction using a panel of markers. 44 genes were found
to affect differentiation to at least one of the three primary germ layers and a simplistic model of transcription regulation
hierarchy during germ layer differentiation is suggested based on germlayer-specific markers.
Program/Abstract # 28
Good at being bad: Counterintuitive genomic responses to developmental signals via low-affinity transcription
factor binding sites.
Barolo, Scott, U Michigan Med Sch, Ann Arbor, United States
Signaling pathways such as Hedgehog, RTK/MAPK, Notch, BMP, and Wnt relay patterning information to transcription
factors (TFs), which in turn control developmental cell fate by regulating gene expression. Because these pathways are
extremely pleiotropic— that is, they are active in many cell types during development and adult life—we are particularly
interested in how cis-regulatory DNA sequences interpret these "generic" signals in a tissue-specific manner. By altering
the affinity of signal response elements in vivo, we have discovered important, sometimes surprising roles for low-affinity,
non-consensus binding sites for signal-regulated TFs in the regulation of wingless, dpp (a BMP ligand), Pax2, and patched.
In certain enhancers of these genes, weak binding is specifically required for proper responses to Hedgehog or Notch
signaling; improving binding affinity can either cause ectopic responses to a signal or, unexpectedly, switch the response
from activation to direct repression. The regulation of the patched gene is particularly interesting: what first appeared to be
a simple constitutive response to Hedgehog in all tissues is in fact mediated by a large number of enhancers, all of which
respond to the same signal, but in different developing tissues and adult stem cell systems—including large numbers of
"shadow" enhancers in multiple tissue types. Our preliminary data suggest fascinating new mechanisms by which the
patched locus has solved the patterning problem of responding to a single generic signal across diverse tissues. I will