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Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells
Enhancer elements control mammalian transcription largely in a cell-type-specific manner. The genome-wide identification of enhancer elements and their activity status in a cellular context is therefore fundamental to understanding cell identity and function. We determined enhancer activity in mouse...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
SAGE Publications
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7876754/ https://www.ncbi.nlm.nih.gov/pubmed/33623376 http://dx.doi.org/10.1177/1177932220974623 |
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author | Mantsoki, Anna Parussel, Karla Joshi, Anagha |
author_facet | Mantsoki, Anna Parussel, Karla Joshi, Anagha |
author_sort | Mantsoki, Anna |
collection | PubMed |
description | Enhancer elements control mammalian transcription largely in a cell-type-specific manner. The genome-wide identification of enhancer elements and their activity status in a cellular context is therefore fundamental to understanding cell identity and function. We determined enhancer activity in mouse embryonic stem (ES) cells using chromatin modifications and characterised their global properties. Specifically, we first grouped enhancers into 5 groups using multiple H3K4me1, H3K27ac, and H3K27me3 modification data sets. Active enhancers (simultaneous presence of H3K4me1 and H3K27ac) were enriched for binding of pluripotency factors and were found near pluripotency-related genes. Although both H3K4me1-only and active enhancers were enriched for super-enhancers and a TATA box like motif, active enhancers were preferentially bound by RNA polII (s2) and were enriched for bidirectional transcription, while H3K4me1-only enhancers were enriched for RNA polII (8WG16) suggesting they were likely poised. Bivalent enhancers (simultaneous presence of H3K4me1 and H3K27me3) were preferentially in the vicinity of bivalent genes. They were enriched for binding of components of polycomb complex as well as Tcf3 and Oct4. Moreover, a ‘CTTTCTC’ de-novo motif was enriched at bivalent enhancers, previously identified at bivalent promoters in ES cells. Taken together, 3 histone modifications successfully demarcated active, bivalent, and poised enhancers with distinct sequence and binding features. |
format | Online Article Text |
id | pubmed-7876754 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | SAGE Publications |
record_format | MEDLINE/PubMed |
spelling | pubmed-78767542021-02-22 Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells Mantsoki, Anna Parussel, Karla Joshi, Anagha Bioinform Biol Insights Original Research Enhancer elements control mammalian transcription largely in a cell-type-specific manner. The genome-wide identification of enhancer elements and their activity status in a cellular context is therefore fundamental to understanding cell identity and function. We determined enhancer activity in mouse embryonic stem (ES) cells using chromatin modifications and characterised their global properties. Specifically, we first grouped enhancers into 5 groups using multiple H3K4me1, H3K27ac, and H3K27me3 modification data sets. Active enhancers (simultaneous presence of H3K4me1 and H3K27ac) were enriched for binding of pluripotency factors and were found near pluripotency-related genes. Although both H3K4me1-only and active enhancers were enriched for super-enhancers and a TATA box like motif, active enhancers were preferentially bound by RNA polII (s2) and were enriched for bidirectional transcription, while H3K4me1-only enhancers were enriched for RNA polII (8WG16) suggesting they were likely poised. Bivalent enhancers (simultaneous presence of H3K4me1 and H3K27me3) were preferentially in the vicinity of bivalent genes. They were enriched for binding of components of polycomb complex as well as Tcf3 and Oct4. Moreover, a ‘CTTTCTC’ de-novo motif was enriched at bivalent enhancers, previously identified at bivalent promoters in ES cells. Taken together, 3 histone modifications successfully demarcated active, bivalent, and poised enhancers with distinct sequence and binding features. SAGE Publications 2021-02-09 /pmc/articles/PMC7876754/ /pubmed/33623376 http://dx.doi.org/10.1177/1177932220974623 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/ This article is distributed under the terms of the Creative Commons Attribution 4.0 License (https://creativecommons.org/licenses/by/4.0/) which permits any use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). |
spellingShingle | Original Research Mantsoki, Anna Parussel, Karla Joshi, Anagha Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells |
title | Identification and Characterisation of Putative Enhancer Elements in
Mouse Embryonic Stem Cells |
title_full | Identification and Characterisation of Putative Enhancer Elements in
Mouse Embryonic Stem Cells |
title_fullStr | Identification and Characterisation of Putative Enhancer Elements in
Mouse Embryonic Stem Cells |
title_full_unstemmed | Identification and Characterisation of Putative Enhancer Elements in
Mouse Embryonic Stem Cells |
title_short | Identification and Characterisation of Putative Enhancer Elements in
Mouse Embryonic Stem Cells |
title_sort | identification and characterisation of putative enhancer elements in
mouse embryonic stem cells |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7876754/ https://www.ncbi.nlm.nih.gov/pubmed/33623376 http://dx.doi.org/10.1177/1177932220974623 |
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