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Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells

In mammalian cells genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthe...

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Autores principales: Lensch, Sarah, Herschl, Michael H, Ludwig, Connor H, Sinha, Joydeb, Hinks, Michaela M, Mukund, Adi, Fujimori, Taihei, Bintu, Lacramioara
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9183234/
https://www.ncbi.nlm.nih.gov/pubmed/35678392
http://dx.doi.org/10.7554/eLife.75115
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author Lensch, Sarah
Herschl, Michael H
Ludwig, Connor H
Sinha, Joydeb
Hinks, Michaela M
Mukund, Adi
Fujimori, Taihei
Bintu, Lacramioara
author_facet Lensch, Sarah
Herschl, Michael H
Ludwig, Connor H
Sinha, Joydeb
Hinks, Michaela M
Mukund, Adi
Fujimori, Taihei
Bintu, Lacramioara
author_sort Lensch, Sarah
collection PubMed
description In mammalian cells genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthetic gene regulation circuits. Here, we systematically dissect this process in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters, and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that silencing by KRAB, associated with histone methylation, spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by PRC2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. Gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment.
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spelling pubmed-91832342022-06-10 Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells Lensch, Sarah Herschl, Michael H Ludwig, Connor H Sinha, Joydeb Hinks, Michaela M Mukund, Adi Fujimori, Taihei Bintu, Lacramioara eLife Chromosomes and Gene Expression In mammalian cells genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthetic gene regulation circuits. Here, we systematically dissect this process in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters, and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that silencing by KRAB, associated with histone methylation, spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by PRC2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. Gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment. eLife Sciences Publications, Ltd 2022-06-09 /pmc/articles/PMC9183234/ /pubmed/35678392 http://dx.doi.org/10.7554/eLife.75115 Text en © 2022, Lensch et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Chromosomes and Gene Expression
Lensch, Sarah
Herschl, Michael H
Ludwig, Connor H
Sinha, Joydeb
Hinks, Michaela M
Mukund, Adi
Fujimori, Taihei
Bintu, Lacramioara
Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells
title Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells
title_full Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells
title_fullStr Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells
title_full_unstemmed Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells
title_short Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells
title_sort dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells
topic Chromosomes and Gene Expression
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9183234/
https://www.ncbi.nlm.nih.gov/pubmed/35678392
http://dx.doi.org/10.7554/eLife.75115
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