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Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation

BACKGROUND: Mammalian dosage compensation is achieved by the inactivation of one X chromosome in XX individuals. In eutheria this process is initiated early in development by the long non-coding RNA XIST. Studies of the initiation of silencing by XIST have focussed on mouse models, so the domains of...

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Autores principales: Dixon-McDougall, Thomas, Brown, Carolyn J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8815261/
https://www.ncbi.nlm.nih.gov/pubmed/35120578
http://dx.doi.org/10.1186/s13072-022-00438-7
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author Dixon-McDougall, Thomas
Brown, Carolyn J.
author_facet Dixon-McDougall, Thomas
Brown, Carolyn J.
author_sort Dixon-McDougall, Thomas
collection PubMed
description BACKGROUND: Mammalian dosage compensation is achieved by the inactivation of one X chromosome in XX individuals. In eutheria this process is initiated early in development by the long non-coding RNA XIST. Studies of the initiation of silencing by XIST have focussed on mouse models, so the domains of XIST required to induce silencing in humans, and their relationship with domains required to establish heterochromatin remain to be determined. METHODS: We have previously established an inducible XIST cDNA in somatic cells and shown it can induce silencing and recruit heterochromatic features. We now assess a series of deletions across the transgene for the ability to induce silencing and integrate these results with time-course and chromatin-remodelling inhibitor treatments to follow the steps of XIST-induced silencing and heterochromatinization. DISCUSSION: We find that in addition to the previously reported necessity of the 5’ A repeat region for XIST-induced silencing, the 1 kb around the small F repeat region and a non-repetitive region at the 3’ end of the RNA are also required to silence genes. Silencing of genes up to 17 Mb from the XIST integration occurs within 2 days, while formation of a Cot-1 depleted domain is slower, and more dependent on the region encompassing Repeat F. The role of this region encompassing Repeat F in both the silencing of actively transcribed genes, the spread of H3K27me3 and the formation of a transcriptionally inert domain suggests a role in a pathway crucial for the spread of XIST across the chromatin to target distal regions of inactivation. Histone deacetylation requires only the A repeat region, with HDAC3 inhibition showing limited effect on silencing, but an impact on H3K27me3 recruitment, and as a result the recruitment of MacroH2A. Global HDAC inhibition impacted silencing in both a distance and dose-dependent fashion. The E repeat region was required for CIZ1 and H4K20me1 recruitment as well as H3K27me3; however, these appeared to act relatively independently. The H3K27me3 mark established by PRC2 integrated silencing and many of the heterochromatic features, while the PRC1 mark ubH2A appeared to be downstream of silencing in these human somatic cells. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13072-022-00438-7.
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spelling pubmed-88152612022-02-07 Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation Dixon-McDougall, Thomas Brown, Carolyn J. Epigenetics Chromatin Research BACKGROUND: Mammalian dosage compensation is achieved by the inactivation of one X chromosome in XX individuals. In eutheria this process is initiated early in development by the long non-coding RNA XIST. Studies of the initiation of silencing by XIST have focussed on mouse models, so the domains of XIST required to induce silencing in humans, and their relationship with domains required to establish heterochromatin remain to be determined. METHODS: We have previously established an inducible XIST cDNA in somatic cells and shown it can induce silencing and recruit heterochromatic features. We now assess a series of deletions across the transgene for the ability to induce silencing and integrate these results with time-course and chromatin-remodelling inhibitor treatments to follow the steps of XIST-induced silencing and heterochromatinization. DISCUSSION: We find that in addition to the previously reported necessity of the 5’ A repeat region for XIST-induced silencing, the 1 kb around the small F repeat region and a non-repetitive region at the 3’ end of the RNA are also required to silence genes. Silencing of genes up to 17 Mb from the XIST integration occurs within 2 days, while formation of a Cot-1 depleted domain is slower, and more dependent on the region encompassing Repeat F. The role of this region encompassing Repeat F in both the silencing of actively transcribed genes, the spread of H3K27me3 and the formation of a transcriptionally inert domain suggests a role in a pathway crucial for the spread of XIST across the chromatin to target distal regions of inactivation. Histone deacetylation requires only the A repeat region, with HDAC3 inhibition showing limited effect on silencing, but an impact on H3K27me3 recruitment, and as a result the recruitment of MacroH2A. Global HDAC inhibition impacted silencing in both a distance and dose-dependent fashion. The E repeat region was required for CIZ1 and H4K20me1 recruitment as well as H3K27me3; however, these appeared to act relatively independently. The H3K27me3 mark established by PRC2 integrated silencing and many of the heterochromatic features, while the PRC1 mark ubH2A appeared to be downstream of silencing in these human somatic cells. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13072-022-00438-7. BioMed Central 2022-02-04 /pmc/articles/PMC8815261/ /pubmed/35120578 http://dx.doi.org/10.1186/s13072-022-00438-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Dixon-McDougall, Thomas
Brown, Carolyn J.
Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation
title Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation
title_full Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation
title_fullStr Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation
title_full_unstemmed Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation
title_short Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation
title_sort multiple distinct domains of human xist are required to coordinate gene silencing and subsequent heterochromatin formation
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8815261/
https://www.ncbi.nlm.nih.gov/pubmed/35120578
http://dx.doi.org/10.1186/s13072-022-00438-7
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