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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2022
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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. |
format | Online Article Text |
id | pubmed-9183234 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
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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