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SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression

ABSTRACT: The homeotic (Hox) genes are highly conserved in metazoans, where they are required for various processes in development and misregulation of their expression is associated with human cancer. In the developing embryo, Hox genes are sequentially activated in time and space according to their genomic position within Hox gene clusters. Accumulating evidence implicates both enhancer elements and non-coding RNAs in controlling this spatiotemporal expression of Hox genes, but disentangling their relative contributions is challenging. Here, we identify two cis-regulatory elements (E1 and E2) functioning as shadow enhancers to regulate the early expression of the HoxA genes. Simultaneous deletion of these shadow enhancers in embryonic stem cells leads to impaired activation of HoxA genes upon differentiation, while knockdown of a long non-coding RNA overlapping E1 has no detectable effect on their expression. Although MLL/COMPASS family of histone methyltransferases are known to activate transcription of Hox genes in other contexts, we find that individual inactivation of the MLL1-4/COMPASS family members has little effect on early Hox gene activation. Instead, we demonstrate that SET1A/COMPASS is required for full transcriptional activation of multiple Hox genes, but functions independently of the E1 and E2 cis-regulatory elements. Our results reveal multiple regulatory layers for Hox genes to fine-tune transcriptional programs essential for development.

ORGANISM(S): Mus musculus

PROVIDER: GSE98140 | GEO | 2017/05/09

SECONDARY ACCESSION(S): PRJNA384079

REPOSITORIES: GEO

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SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression.

Project description:The homeotic (Hox) genes are highly conserved in metazoans, where they are required for various processes in development, and misregulation of their expression is associated with human cancer. In the developing embryo, Hox genes are activated sequentially in time and space according to their genomic position within Hox gene clusters. Accumulating evidence implicates both enhancer elements and noncoding RNAs in controlling this spatiotemporal expression of Hox genes, but disentangling their relative contributions is challenging. Here, we identify two cis-regulatory elements (E1 and E2) functioning as shadow enhancers to regulate the early expression of the HoxA genes. Simultaneous deletion of these shadow enhancers in embryonic stem cells leads to impaired activation of HoxA genes upon differentiation, while knockdown of a long noncoding RNA overlapping E1 has no detectable effect on their expression. Although MLL/COMPASS (complex of proteins associated with Set1) family of histone methyltransferases is known to activate transcription of Hox genes in other contexts, we found that individual inactivation of the MLL1-4/COMPASS family members has little effect on early Hox gene activation. Instead, we demonstrate that SET1A/COMPASS is required for full transcriptional activation of multiple Hox genes but functions independently of the E1 and E2 cis-regulatory elements. Our results reveal multiple regulatory layers for Hox genes to fine-tune transcriptional programs essential for development.

| S-EPMC5435891 | biostudies-literature

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Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation [Hi-C]

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