ChIP-seq Identification of Weakly Conserved Heart Enhancers
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE22549 | GEO | 2010/08/22
SECONDARY ACCESSION(S): PRJNA128177
REPOSITORIES: GEO
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Project description:Accurate control of tissue-specific gene expression plays a pivotal role in heart development. However, few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of enhancers active in the heart. We used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic heart tissue to identify over three thousand candidate heart enhancers genome-wide. In contrast to other studied tissues at this time-point, most candidate heart enhancers are not deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for tissue-dependent differences in evolutionary constraint of enhancers acting through the transcriptional co-activator p300 at this time-point, and identify a large population of poorly conserved heart enhancers. Examination of p300 binding in embryonic stage 11.5 mouse heart and midbrain
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Project description:We report a method for high throughput mapping of transcriptional enhancers, genomic regulatory regions that activate lineage-specific transcription. Since tissue-specific enhancers are bound by the transcriptional co-activator p300, we developed murine knock-in alleles that permit Cre-dependent, lineage-specific p300 in vivo biotinylation and high affinity pulldown on immobilized streptavidin. Subsequent next generation sequencing of p300-bound genomic DNA identified lineage-specific enhancers. By driving this system with lineage-specific Cre transgenes, we mapped enhancers active in embryonic endothelial cells/blood or skeletal muscle. Analysis of these enhancer sequences identified new transcription factor heterodimer motifs that likely regulate transcription in these lineages. Furthermore, we identified candidate enhancers that regulate adult heart- or lung- specific endothelial cell specialization.
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Project description:Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. We tested this concept experimentally using the human X chromosome. We describe a scoring method to identify evolutionary maintenance of linkage between conserved non-coding elements and neighbouring genes. Chromatin marks associated with enhancer function are strongly correlated with the linkage score. We tested more than 1,000 putative enhancers by transgenesis assays in zebrafish to ascertain the identity of the target gene, with a focus on genes involved in X-linked intellectual disabilities (ID). The majority of active enhancers drive a transgenic expression in a pattern consistent with the known expression of a linked gene. These results show that evolutionary maintenance of linkage is a reliable predictor of an enhancer's function, and provide new information to discover the genetic basis of diseases caused by the mis-regulation of gene expression. ChIP-chip from mouse 14.5 days fetal brain using P300 or H3K4Me1 antibodies. Biological replicates: P300_Rep1, P300_Rep2 Biological replicates: H3K4Me1_Rep1,H3K4Me1_Rep2
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