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Defining a critical Nanog enhancer using chromatin-focused approaches identifies RNAPII recruitment as required for expression [CUT&Tag]

ABSTRACT: Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid reporters rather than native chromatin. We employed a combination of approaches to investigate the Nanog locus in mouse embryonic stem cells (ESCs) and an associated cis regulatory element (CRE) which may operate as either a super-enhancer (SE) or alternative promoter. We establish this element is a SE within chromatin using distance- and orientation-independence as criteria, and that it regulates Nanog by recruiting and/or initiating RNA Polymerase II. Our work highlights that enhancers can regulate gene expression through a diverse set of mechanisms.

ORGANISM(S): Mus musculus

PROVIDER: GSE143991 | GEO | 2020/12/07

REPOSITORIES: GEO

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Defining a critical Nanog enhancer using chromatin-focused approaches identifies RNAPII recruitment as required for expression [ATAC-Seq]

Project description:Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid reporter assays, rather than within native chromatin. We employed a combination of approaches to investigate the Nanog locus in mouse embryonic stem cells (ESCs) and an associated cis regulatory element (CRE) which may operate as a super-enhancer (SE) or alternative promoter. We establish the element is a SE within chromatin using distance- and orientation-independence as criteria. We next demonstrate this SE regulates Nanog by recruiting and/or initiating RNA Polymerase II. Our work highlights that enhancers likely operate through a diverse set of mechanisms.

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Defining a critical Nanog enhancer using chromatin-focused approaches identifies RNAPII recruitment as required for expression [-5delRNASeq]

Project description:Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid reporters rather than native chromatin. We employed a combination of approaches to investigate the Nanog locus in mouse embryonic stem cells (ESCs) and an associated cis regulatory element (CRE) which may operate as either a super-enhancer (SE) or alternative promoter. We establish this element is a SE within chromatin using distance- and orientation-independence as criteria, and that it regulates Nanog by recruiting and/or initiating RNA Polymerase II. Our work highlights that enhancers can regulate gene expression through a diverse set of mechanisms.

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Project description:Enhancers are critical regulators of gene expression which are historically defined using plasmid-based approaches. Recent work has emphasized that enhancers operate by alleviating promoter-proximal pause release, implying that a single enhancer operates on a gene at any given moment. By contrast, our previous work postulated that two super-enhancers (SEs) may simultaneously operate on a single gene. To address this discrepancy we employed genomic editing, single cell analyses, and genome-wide approaches to assess how two SEs regulate Nanog expression in embryonic stem cells. We first demonstrate both distance and orientation independence in native chromatin, eliminating the issues raised with plasmid-based approaches. We also demonstrate that two SEs simultaneously operate on Nanog by regulating different phases of transcription, with one SE operating by recruiting and/or initiating RNA Polymerase II, and the second promoting transcriptional elongation after promoter-proximal pause release. These findings imply SEs can use different mechanisms to regulate expression.

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Project description:Rattus norvegicus Nanog, Nanog homeobox [Source:RGD Symbol;Acc:1303178], is expressed in 2 baseline experiment(s);

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NANOG

Project description:Homo sapiens NANOG, Nanog homeobox [Source:HGNC Symbol;Acc:HGNC:20857], is expressed in 19 baseline experiment(s);

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NANOG

Project description:Homo sapiens NANOG, Nanog homeobox [Source:HGNC Symbol;Acc:HGNC:20857], is differentially expressed in 35 experiment(s);

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Nanog

Project description:Mus musculus Nanog, Nanog homeobox [Source:MGI Symbol;Acc:MGI:1919200], is differentially expressed in 16 experiment(s);

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Nanog

Project description:Mus musculus Nanog, Nanog homeobox [Source:MGI Symbol;Acc:MGI:1919200], is expressed in 12 baseline experiment(s);

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Project description:Sus scrofa NANOG, Nanog homeobox [Source:NCBI gene (formerly Entrezgene);Acc:100170132], is expressed in 1 baseline experiment(s);

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