Cargando…
En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements
The XIST RNA is a non-coding RNA that induces X chromosome inactivation (XCI). Unlike the mouse Xist RNA, how the human XIST RNA controls XCI in female cells is less well characterized, and its functional motifs remain unclear. To systematically decipher the XCI-involving elements of XIST RNA, 11 sm...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486550/ https://www.ncbi.nlm.nih.gov/pubmed/30783652 http://dx.doi.org/10.1093/nar/gkz109 |
_version_ | 1783414358932455424 |
---|---|
author | Lee, Hyeon J Gopalappa, Ramu Sunwoo, Hongjae Choi, Seo-Won Ramakrishna, Suresh Lee, Jeannie T Kim, Hyongbum H Nam, Jin-Wu |
author_facet | Lee, Hyeon J Gopalappa, Ramu Sunwoo, Hongjae Choi, Seo-Won Ramakrishna, Suresh Lee, Jeannie T Kim, Hyongbum H Nam, Jin-Wu |
author_sort | Lee, Hyeon J |
collection | PubMed |
description | The XIST RNA is a non-coding RNA that induces X chromosome inactivation (XCI). Unlike the mouse Xist RNA, how the human XIST RNA controls XCI in female cells is less well characterized, and its functional motifs remain unclear. To systematically decipher the XCI-involving elements of XIST RNA, 11 smaller XIST segments, including repeats A, D and E; human-specific repeat elements; the promoter; and non-repetitive exons, as well as the entire XIST gene, were homozygously deleted in K562 cells using the Cas9 nuclease and paired guide RNAs at high efficiencies, followed by high-throughput RNA sequencing and RNA fluorescence in situ hybridization experiments. Clones containing en bloc and promoter deletions that consistently displayed no XIST RNAs and a global up-regulation of X-linked genes confirmed that the deletion of XIST reactivates the inactive X chromosome. Systematic analyses of segmental deletions delineated that exon 5 harboring the non-repeat element is important for X-inactivation maintenance, whereas exons 2, 3 and 4 as well as the other repeats in exon 1 are less important, a different situation from that of mouse Xist. This Cas9-assisted dissection of XIST allowed us to understand the unique functional domains within the human XIST RNA. |
format | Online Article Text |
id | pubmed-6486550 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-64865502019-05-01 En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements Lee, Hyeon J Gopalappa, Ramu Sunwoo, Hongjae Choi, Seo-Won Ramakrishna, Suresh Lee, Jeannie T Kim, Hyongbum H Nam, Jin-Wu Nucleic Acids Res Gene regulation, Chromatin and Epigenetics The XIST RNA is a non-coding RNA that induces X chromosome inactivation (XCI). Unlike the mouse Xist RNA, how the human XIST RNA controls XCI in female cells is less well characterized, and its functional motifs remain unclear. To systematically decipher the XCI-involving elements of XIST RNA, 11 smaller XIST segments, including repeats A, D and E; human-specific repeat elements; the promoter; and non-repetitive exons, as well as the entire XIST gene, were homozygously deleted in K562 cells using the Cas9 nuclease and paired guide RNAs at high efficiencies, followed by high-throughput RNA sequencing and RNA fluorescence in situ hybridization experiments. Clones containing en bloc and promoter deletions that consistently displayed no XIST RNAs and a global up-regulation of X-linked genes confirmed that the deletion of XIST reactivates the inactive X chromosome. Systematic analyses of segmental deletions delineated that exon 5 harboring the non-repeat element is important for X-inactivation maintenance, whereas exons 2, 3 and 4 as well as the other repeats in exon 1 are less important, a different situation from that of mouse Xist. This Cas9-assisted dissection of XIST allowed us to understand the unique functional domains within the human XIST RNA. Oxford University Press 2019-05-07 2019-02-20 /pmc/articles/PMC6486550/ /pubmed/30783652 http://dx.doi.org/10.1093/nar/gkz109 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Gene regulation, Chromatin and Epigenetics Lee, Hyeon J Gopalappa, Ramu Sunwoo, Hongjae Choi, Seo-Won Ramakrishna, Suresh Lee, Jeannie T Kim, Hyongbum H Nam, Jin-Wu En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements |
title |
En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements |
title_full |
En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements |
title_fullStr |
En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements |
title_full_unstemmed |
En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements |
title_short |
En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements |
title_sort | en bloc and segmental deletions of human xist reveal x chromosome inactivation-involving rna elements |
topic | Gene regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486550/ https://www.ncbi.nlm.nih.gov/pubmed/30783652 http://dx.doi.org/10.1093/nar/gkz109 |
work_keys_str_mv | AT leehyeonj enblocandsegmentaldeletionsofhumanxistrevealxchromosomeinactivationinvolvingrnaelements AT gopalapparamu enblocandsegmentaldeletionsofhumanxistrevealxchromosomeinactivationinvolvingrnaelements AT sunwoohongjae enblocandsegmentaldeletionsofhumanxistrevealxchromosomeinactivationinvolvingrnaelements AT choiseowon enblocandsegmentaldeletionsofhumanxistrevealxchromosomeinactivationinvolvingrnaelements AT ramakrishnasuresh enblocandsegmentaldeletionsofhumanxistrevealxchromosomeinactivationinvolvingrnaelements AT leejeanniet enblocandsegmentaldeletionsofhumanxistrevealxchromosomeinactivationinvolvingrnaelements AT kimhyongbumh enblocandsegmentaldeletionsofhumanxistrevealxchromosomeinactivationinvolvingrnaelements AT namjinwu enblocandsegmentaldeletionsofhumanxistrevealxchromosomeinactivationinvolvingrnaelements |