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High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies

The mammalian cell nucleus contains numerous discrete suborganelles named nuclear bodies. While recruitment of specific genomic regions into these large ribonucleoprotein (RNP) complexes critically contributes to higher-order functional chromatin organization, such regions remain ill-defined. We hav...

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Autores principales: Baudement, Marie-Odile, Cournac, Axel, Court, Franck, Seveno, Marie, Parrinello, Hugues, Reynes, Christelle, Sabatier, Robert, Bouschet, Tristan, Yi, Zhou, Sallis, Sephora, Tancelin, Mathilde, Rebouissou, Cosette, Cathala, Guy, Lesne, Annick, Mozziconacci, Julien, Journot, Laurent, Forné, Thierry
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211644/
https://www.ncbi.nlm.nih.gov/pubmed/30287550
http://dx.doi.org/10.1101/gr.237073.118
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author Baudement, Marie-Odile
Cournac, Axel
Court, Franck
Seveno, Marie
Parrinello, Hugues
Reynes, Christelle
Sabatier, Robert
Bouschet, Tristan
Yi, Zhou
Sallis, Sephora
Tancelin, Mathilde
Rebouissou, Cosette
Cathala, Guy
Lesne, Annick
Mozziconacci, Julien
Journot, Laurent
Forné, Thierry
author_facet Baudement, Marie-Odile
Cournac, Axel
Court, Franck
Seveno, Marie
Parrinello, Hugues
Reynes, Christelle
Sabatier, Robert
Bouschet, Tristan
Yi, Zhou
Sallis, Sephora
Tancelin, Mathilde
Rebouissou, Cosette
Cathala, Guy
Lesne, Annick
Mozziconacci, Julien
Journot, Laurent
Forné, Thierry
author_sort Baudement, Marie-Odile
collection PubMed
description The mammalian cell nucleus contains numerous discrete suborganelles named nuclear bodies. While recruitment of specific genomic regions into these large ribonucleoprotein (RNP) complexes critically contributes to higher-order functional chromatin organization, such regions remain ill-defined. We have developed the high-salt–recovered sequences-sequencing (HRS-seq) method, a straightforward genome-wide approach whereby we isolated and sequenced genomic regions associated with large high-salt insoluble RNP complexes. By using mouse embryonic stem cells (ESCs), we showed that these regions essentially correspond to the most highly expressed genes, and to cis-regulatory sequences like super-enhancers, that belong to the active A chromosomal compartment. They include both cell-type–specific genes, such as pluripotency genes in ESCs, and housekeeping genes associated with nuclear bodies, such as histone and snRNA genes that are central components of Histone Locus Bodies and Cajal bodies. We conclude that HRSs are associated with the active chromosomal compartment and with large RNP complexes including nuclear bodies. Association of such chromosomal regions with nuclear bodies is in agreement with the recently proposed phase separation model for transcription control and might thus play a central role in organizing the active chromosomal compartment in mammals.
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spelling pubmed-62116442019-05-01 High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies Baudement, Marie-Odile Cournac, Axel Court, Franck Seveno, Marie Parrinello, Hugues Reynes, Christelle Sabatier, Robert Bouschet, Tristan Yi, Zhou Sallis, Sephora Tancelin, Mathilde Rebouissou, Cosette Cathala, Guy Lesne, Annick Mozziconacci, Julien Journot, Laurent Forné, Thierry Genome Res Method The mammalian cell nucleus contains numerous discrete suborganelles named nuclear bodies. While recruitment of specific genomic regions into these large ribonucleoprotein (RNP) complexes critically contributes to higher-order functional chromatin organization, such regions remain ill-defined. We have developed the high-salt–recovered sequences-sequencing (HRS-seq) method, a straightforward genome-wide approach whereby we isolated and sequenced genomic regions associated with large high-salt insoluble RNP complexes. By using mouse embryonic stem cells (ESCs), we showed that these regions essentially correspond to the most highly expressed genes, and to cis-regulatory sequences like super-enhancers, that belong to the active A chromosomal compartment. They include both cell-type–specific genes, such as pluripotency genes in ESCs, and housekeeping genes associated with nuclear bodies, such as histone and snRNA genes that are central components of Histone Locus Bodies and Cajal bodies. We conclude that HRSs are associated with the active chromosomal compartment and with large RNP complexes including nuclear bodies. Association of such chromosomal regions with nuclear bodies is in agreement with the recently proposed phase separation model for transcription control and might thus play a central role in organizing the active chromosomal compartment in mammals. Cold Spring Harbor Laboratory Press 2018-11 /pmc/articles/PMC6211644/ /pubmed/30287550 http://dx.doi.org/10.1101/gr.237073.118 Text en © 2018 Baudement et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Method
Baudement, Marie-Odile
Cournac, Axel
Court, Franck
Seveno, Marie
Parrinello, Hugues
Reynes, Christelle
Sabatier, Robert
Bouschet, Tristan
Yi, Zhou
Sallis, Sephora
Tancelin, Mathilde
Rebouissou, Cosette
Cathala, Guy
Lesne, Annick
Mozziconacci, Julien
Journot, Laurent
Forné, Thierry
High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
title High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
title_full High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
title_fullStr High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
title_full_unstemmed High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
title_short High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
title_sort high-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211644/
https://www.ncbi.nlm.nih.gov/pubmed/30287550
http://dx.doi.org/10.1101/gr.237073.118
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