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Cis-regulation of Grem1 expression during limb development [E10.5 H3K27Ac ChIP-Seq]

ABSTRACT: Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. The BMP antagonist Gremlin1 (Grem1) is an important node in the gene regulatory network that controls vertebrate limb development. In this study, we used a combination of open chromatin profiling (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) in mouse and chick to identify putative cis-regulatory modules (CRMs) that regulate Grem1 in limb buds. Using CRISPR/Cas genome editing we generated different Grem1 regulatory alleles lacking either individual CRMs, combinations or entire enhancer clusters. To study potential interactions of these CRMs with the Grem1 promoter, we generated 4C-seq profiles of specific regulatory alleles. Taken together our results revealed that the spatio-temporal changes in Grem1 expression are caused by cis-regulatory alterations due to the deletions of enhancer clusters rather than global changes in chromatin architecture.

ORGANISM(S): Mus musculus

PROVIDER: GSE164905 | GEO | 2021/07/30

REPOSITORIES: GEO

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cis-regulation of Grem1 expression during limb development [ATAC HH24]

Project description:Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. The BMP antagonist Gremlin1 (Grem1) is an important node in the gene regulatory network that controls vertebrate limb development. In this study, we used a combination of open chromatin profiling (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) in mouse and chick to identify putative cis-regulatory modules (CRMs) that regulate Grem1 in limb buds. Using CRISPR/Cas genome editing we generated different Grem1 regulatory alleles lacking either individual CRMs, combinations or entire enhancer clusters. To study potential interactions of these CRMs with the Grem1 promoter, we generated 4C-seq profiles of specific regulatory alleles. Taken together our results revealed that the spatio-temporal changes in Grem1 expression are caused by cis-regulatory alterations due to the deletions of enhancer clusters rather than global changes in chromatin architecture.

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Project description:Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. In this study, we identified cis regulatory modules (CRMs) within the Fmn1/Grem1 cis-regulatory landscape that participate in controlling spatiotemporal expression of Grem1. We generated different Grem1 alleles lacking either individual CRMs, combinations or entire enhancer clusters (EC1 and EC2) using CRISPR/Cas genome editing. To study potential interactions of these CRMs with the Grem1 promoter, we generated 4C-seq profiles of different alleles. Our analysis of 4C-seq shows that the overall structure of the Grem1 TAD is maintained in CRM2-/- and EC1-/- forelimb buds. Similar to EC1, the chromatin architecture of the Grem1 TAD is not disrupted outside the EC2 and EC1EC2 deletions. In all the genotypes, the contacts of the promoter with the remainder of the Grem1 TAD are rather increased. Thus, our results revealed that the spatio-temporal changes in Grem1 expression are caused by cis-regulatory alterations due to the deletions of EC1 and EC2 and not global changes in chromatin architecture.

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cis-regulation of Grem1 during limb development [ChIP-seq]

Project description:Chromatin immunoprecipitation in combination with sequencing (ChIP-seq) was used to identify the interactions of CRMs with key regulators of Grem1 expression, namely SMAD4 (mediating response to BMP signal transduction) and GLI3 (SHH signal transduction). This analysis revealed the presence of a single significantly enriched SMAD4 ChIP-seq peak in CRM2 during initiation of forelimb bud development, when BMP4 is required to initiate/upregulate the Grem1 transcription. During progression of limb development, GLI3 chromatin complexes interact with all enhancers except CRM5. which agrees with the predominant role of SHH-mediated Grem1 regulation during outgrowth and/or GLI3R-mediated repression during termination. Thus, the Grem1 TAD encodes an array of CRM enhancers that integrate inputs from BMP and SHH signaling into the dynamic regulation of Grem1 during limb bud outgrowth.

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cis-regulation of Grem1 during limb development

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Differential expression of mouse Grem1+ Vs. Grem1- bone-marrow cells

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