Cargando…
H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells
BACKGROUND: Bivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differen...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6029396/ https://www.ncbi.nlm.nih.gov/pubmed/29969988 http://dx.doi.org/10.1186/s12864-018-4886-4 |
_version_ | 1783336953603686400 |
---|---|
author | Xu, Jian Kidder, Benjamin L. |
author_facet | Xu, Jian Kidder, Benjamin L. |
author_sort | Xu, Jian |
collection | PubMed |
description | BACKGROUND: Bivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differentiation. However, it is unknown whether another repressive histone modification, histone 4 lysine 20 trimethylation (H4K20me3), co-localizes with activating histone marks in ES cells. RESULTS: Here, we describe the previously uncharacterized coupling of the repressive H4K20me3 heterochromatin mark with the activating histone modifications H3K4me3 and histone 3 lysine 36 trimethylation (H3K36me3), and transcriptional machinery (RNA polymerase II; RNAPII), in ES cells. These newly described bivalent domains consisting of H3K4me3/H4K20me3 are predominantly located in intergenic regions and near transcriptional start sites of active genes, while H3K36me3/H4K20me3 are located in intergenic regions and within gene body regions of active genes. Global sequential ChIP, also termed reChIP-Seq, confirmed the simultaneous presence of H3K4me3 and H4K20me3 at the same genomic regions in ES cells. Genes containing H3K4me3/H4K20me3 exhibit decreased RNAPII pausing and are poised for deactivation of RNAPII binding during differentiation relative to H3K4me3 marked genes. An evaluation of transcription factor (TF) binding motif enrichment revealed that DNA sequence may play a role in shaping the landscape of these novel bivalent domains. Moreover, H3K4me3/H4K20me3 and H3K36me3/H4K20me3 bound regions are enriched with repetitive LINE and LTR elements. CONCLUSIONS: Overall, these findings highlight a previously undescribed subnetwork of ES cell transcriptional circuitry that utilizes dual marking of the repressive H4K20me3 mark with activating histone modifications. |
format | Online Article Text |
id | pubmed-6029396 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-60293962018-07-09 H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells Xu, Jian Kidder, Benjamin L. BMC Genomics Research Article BACKGROUND: Bivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differentiation. However, it is unknown whether another repressive histone modification, histone 4 lysine 20 trimethylation (H4K20me3), co-localizes with activating histone marks in ES cells. RESULTS: Here, we describe the previously uncharacterized coupling of the repressive H4K20me3 heterochromatin mark with the activating histone modifications H3K4me3 and histone 3 lysine 36 trimethylation (H3K36me3), and transcriptional machinery (RNA polymerase II; RNAPII), in ES cells. These newly described bivalent domains consisting of H3K4me3/H4K20me3 are predominantly located in intergenic regions and near transcriptional start sites of active genes, while H3K36me3/H4K20me3 are located in intergenic regions and within gene body regions of active genes. Global sequential ChIP, also termed reChIP-Seq, confirmed the simultaneous presence of H3K4me3 and H4K20me3 at the same genomic regions in ES cells. Genes containing H3K4me3/H4K20me3 exhibit decreased RNAPII pausing and are poised for deactivation of RNAPII binding during differentiation relative to H3K4me3 marked genes. An evaluation of transcription factor (TF) binding motif enrichment revealed that DNA sequence may play a role in shaping the landscape of these novel bivalent domains. Moreover, H3K4me3/H4K20me3 and H3K36me3/H4K20me3 bound regions are enriched with repetitive LINE and LTR elements. CONCLUSIONS: Overall, these findings highlight a previously undescribed subnetwork of ES cell transcriptional circuitry that utilizes dual marking of the repressive H4K20me3 mark with activating histone modifications. BioMed Central 2018-07-03 /pmc/articles/PMC6029396/ /pubmed/29969988 http://dx.doi.org/10.1186/s12864-018-4886-4 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Xu, Jian Kidder, Benjamin L. H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells |
title | H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells |
title_full | H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells |
title_fullStr | H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells |
title_full_unstemmed | H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells |
title_short | H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells |
title_sort | h4k20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6029396/ https://www.ncbi.nlm.nih.gov/pubmed/29969988 http://dx.doi.org/10.1186/s12864-018-4886-4 |
work_keys_str_mv | AT xujian h4k20me3colocalizeswithactivatinghistonemodificationsattranscriptionallydynamicregionsinembryonicstemcells AT kidderbenjaminl h4k20me3colocalizeswithactivatinghistonemodificationsattranscriptionallydynamicregionsinembryonicstemcells |