Cis-regulatory properties of medaka synexpression groups

Abstract

SUMMARYDuring embryogenesis, tissue specification is triggered by the expression of a unique combination of developmental genes and their expression in time and space is crucial for successful development. Synexpression groups are batteries of spatiotemporally co-expressed genes that act in shared biological processes through their coordinated expression. Although several synexpression groups have been described in numerous vertebrate species, the regulatory mechanisms that orchestrate their common complex expression pattern remain to be elucidated. Here we performed a pilot screen on 560 genes of the vertebrate model system medaka (Oryzias latipes) to systematically identify synexpression groups and investigate their regulatory properties by searching for common regulatory cues. We find that synexpression groups share DNA motifs that are arranged in various combinations into cis-regulatory modules that drive co-expression. In contrast to previous assumptions that these genes are located randomly in the genome, we discovered that genes belonging to the same synexpression group frequently occur in synexpression clusters in the genome. This work presents a first repertoire of synexpression group common signatures, a resource that will contribute to deciphering developmental gene regulatory networks.

Spatiotemporal regulation of GLI target genes in the mammalian limb bud

“…1C–E). The coordinated expression of developmentally expressed genes, termed syn-expression groups, has been proposed to be involved in regulating common biological pathways (Gawantka et al, 1998; Ramialison et al, 2012; Visel et al, 2007). Category 1 genes, expressed in the posterior and posterior-distal limb, are enriched for GO processes involved in transcriptional regulation and cell proliferation (supplementary material Fig.…”

A Conserved Developmental Mechanism Builds Complex Visual Systems in Insects and Vertebrates

“…Secondly, the progeny of the peripheral stem cells form an intermediate layer (CMZi/TMZi) of rapidly dividing progenitor cells (‘amplifying progenitors’; Figure 4A,B). These cells accumulate proliferation-associated genes [39] that represent another large synexpression group between the CMZ and TMZ, as already noted by Ramialison et al [43]. Proliferation of cells within the CMZi/TMZi is limited to a few rounds [39] of divisions before cells exit the mitotic cycle.…”

Zebrafish midbrain slow-amplifying progenitors exhibit high levels of transcripts for nucleotide and ribosome biogenesis

“…Cytological and molecular signatures may help to define cell type homologies from an 'evo-devo' perspective (Arendt, 2005). Synexpression of genes in retinal CMZ cells and midbrain progenitors has been noted (Cerveny et al, 2012;Ramialison et al, 2012) and the phenotypes of mutants for at least 18 PML-specific genes are illustrated on the ZIRC website (supplementary material Table S3). These mutants share strikingly similar neuroectodermal and ocular defects.…”