Congress Abstracts - Society for Developmental Biology

stage. Among these, only 1,000 genes were Foxh1-bound at both stages, suggesting that Foxh1 has both common and unique
regulatory roles at each stage. De novo motif analysis identified TF binding motifs with strong enrichment under the Foxh1 peaks,
including Foxh1, Smad2/3, HEB, and others representing potential novel co-factors. Our current results illustrate the dynamics of
Foxh1-mediated gene regulation during early embryogenesis, demonstrating the crucial need for a temporal understanding of the
Nodal signaling gene regulatory network controlling mesendoderm specification.
Program/Abstract # 264
A whole genome approach to explore the gene regulatory network controlling germ layer patterning in the Xenopus tropicalis
gastrula
Paraiso, Kitt; Blitz, Ira; Chiu, William; Cho, Ken W.Y. (University of California-Irvine, USA)
The vertebrate body plan is laid out during the blastula and gastrula stages. Differential expression of genes in specific regions of the
embryo acts as markers and specifiers of future cell fates. The complex circuitry that governs the regulation of gene transcription can
be usefully summarized with gene regulatory networks. In Xenopus, multiple published gene regulatory networks exist to explain
gastrulation but most of the work done thus far involve probing interactions between a small subset of expressed genes. With the
power of high-throughput sequencing, we have the opportunity to probe for network interactions on the genome-wide scale. Here, we
explore for possible network interactions through correlations between gene expression in different embryonic regions and DNAse I
hypersensitive regions gene promoter. First, we dissected the early gastrula embryo into five regions – the animal cap (ectoderm),
dorsal marginal zone (dorsal mesoendoderm), ventral marginal zone (ventral mesoendoderm), lateral marginal zones (lateral
mesoderm), and vegetal (endoderm). We performed RNA-seq on each region and compared their transcriptomes. Using DNAse-seq
on early gastrula, we identified possible regulatory regions actively interacting with transcription factors. Given these information,
cross-referenced to known transcription factor expression patterns and consensus binding sites, we can infer the regulation of gene
transcription with regionally specific expression. We will present the most current findings.
Program/Abstract # 265
Coordinating neurogenesis: Roles of REST and Hoxb1 binding modules integrating neural fate determination
De Kumar, Bony; Parrish, Mark; Paulson, Ariel; Gottschalk, Aaron; Scott, Carrie; Conaway, Ron; Krumlauf, Robb (Stowers Institute
for Medical Research, USA)
Hox genes encode a family of transcription factors that play key regulatory roles in determining the anterior–posterior properties of
many tissues in developing embryos. An excellent example of this regulatory role is Hoxb1, which displays restricted expression in a
segment (rhombomere 4) of the developing hindbrain. Loss of Hoxb1 results into a transformation of rhombomere (r) 4 to and r2
identity and leads to abnormal neuronal differentiation, defective axonal guidance, abnormal facial nerve development and partial
neonatal lethality. However, very little is known about how Hox genes control the cellular processes and programs through
downstream target genes to fulfill these roles in the CNS. We used programmed differentiation of mouse embryonic stem (ES) cells
into neuro-ectoderm fates and mouse tissues in combination with ChIP-Seq technology to perform genome-wide analyses of Hoxb1
binding regions and identity potential target genes. In addition to known types of Hox binding motifs our analyses revealed
enrichments for novel classes of sequences that integrate input from Hoxb1. These include sites for REST, SP1, Blimp-1, Pax-4,
Gata6, Krox and Lmo2 binding motifs. Furthermore, unbiased motif sampling using MEME identified novel binding motifs with no
previously defined binding properties. Regulatory assays in chicken embryos demonstrated that many of these sites functioned as
neuronal enhancers. The REST sites are of particular interest because REST represents a repressor complex that actively blocks genes
important in neuronal differentiation. REST activity is maintained in non-neuronal tissues to prevent neural fates and it must be
down-regulated or eliminated in the CNS to properly coordinate neurogenesis. A significant number of Hoxb1 binding peaks have
closely associated REST Motifs and ChIP-seq data indicate that the REST complex binds to these sites in undifferentiated ES cells.
The close association or tethering of the REST and Hoxb1 binding sites provide a potential mechanism for coordinating cell
differentiation programs in neurogenesis. Hoxb1 may remove the REST repressor complex and activate selected loci to regulate
neurogenesis. Our analyses are uncovering novel interactions between Hox proteins and other factors that underlie their role as master
regulators of patterning and morphogenesis.
Program/Abstract # 266
Genomic differences between spontaneously aborted fetuses and live-born patients with trisomy 21
Torres, Leda; de Robles, Ximena; Sanchez, Silvia; del Castillo, Victoria (Instituto Nacional de Pediatría, Mexico); Orozco, Lorena;
Carnevale, Alessandra (Instituto Nacional de Medicina Genómica, Mexico); Grether, Patricia (Instituto Nacional de Pediatría,
Mexico); Mayen, Dora Gilda (Hospital Angeles Lomas, Mexico); Frias, Sara (Instituto Nacional de Pediatría/Instituto de
Investigaciones Biomédicas, UNAM, Mexico)
Aneuploidies have been identified in at least 5% of pregnancies and are the leading genetic cause of spontaneous abortions and birth
defects, 1 of 150 abortions with aneuploidies has trisomy of chromosome 21 (T21). To date there is not known why a fetus with T21
continues to develop or is aborted. In order to found genomic differences between live births and abortions with T21 we studied 12
patients, 8 of them with congenital heart defects (CHD), 5 abortions with T21 and 10 healthy donors. gDNA was extracted from every
individual. Affymetrix Genome Wide Human SNP 6.0 microarrays were performed; we identified common regions with loss or gain
of genomic material employing the Chromosome Analysis Suite of Affymetrix; each region was analyzed using UCSC genome
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