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Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico

Gene regulation plays essential roles in all multicellular organisms, allowing for different specialized tissue types to be generated from a complex genome. Heterochromatin-driven gene repression, associated with a physical compaction of the genome, is a pathway involving core components that are co...

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Autores principales: Yan, Xiaokang, Williams, Michael R, Barboza Castillo, Ameriks D, Kireev, Dmitri, Hathaway, Nathaniel A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10069619/
https://www.ncbi.nlm.nih.gov/pubmed/37020498
http://dx.doi.org/10.1093/pnasnexus/pgad062
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author Yan, Xiaokang
Williams, Michael R
Barboza Castillo, Ameriks D
Kireev, Dmitri
Hathaway, Nathaniel A
author_facet Yan, Xiaokang
Williams, Michael R
Barboza Castillo, Ameriks D
Kireev, Dmitri
Hathaway, Nathaniel A
author_sort Yan, Xiaokang
collection PubMed
description Gene regulation plays essential roles in all multicellular organisms, allowing for different specialized tissue types to be generated from a complex genome. Heterochromatin-driven gene repression, associated with a physical compaction of the genome, is a pathway involving core components that are conserved from yeast to human. Posttranslational modification of chromatin is a critical component of gene regulation. Specifically, tri-methylation of the nucleosome component histone 3 at lysine 9 (H3K9me3) is a key feature of this pathway along with the hallmark heterochromatin protein 1 (HP1). Histone methyltransferases are recruited by HP1 to deposit H3K9me3 marks which nucleate and recruit more HP1 in a process that spreads from the targeting site to signal for gene repression. One of the enzymes recruited is SETDB1, a methyltransferase which putatively catalyzes posttranslational methylation marks on H3K9. To better understand the contribution of SETDB1 in heterochromatin formation, we downregulated SETDB1 through knockdown by a dCas9-KRAB system and examined heterochromatin formation in a chromatin in vivo assay (CiA-Oct4). We studied the contribution of SETDB1 to heterochromatin formation kinetics in a developmentally crucial locus, Oct4. Our data demonstrate that SETDB1 reduction led to a delay in both gene silencing and in H3K9me3 accumulation. Importantly, SETDB1 knockdown to a ∼50% level did not stop heterochromatin formation completely. Particle-based Monte Carlo simulations in 3D space with explicit representation of key molecular processes enabled the elucidation of how SETDB1 downregulation affects the individual molecular processes underlying heterochromatin formation.
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spelling pubmed-100696192023-04-04 Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico Yan, Xiaokang Williams, Michael R Barboza Castillo, Ameriks D Kireev, Dmitri Hathaway, Nathaniel A PNAS Nexus Biological, Health, and Medical Sciences Gene regulation plays essential roles in all multicellular organisms, allowing for different specialized tissue types to be generated from a complex genome. Heterochromatin-driven gene repression, associated with a physical compaction of the genome, is a pathway involving core components that are conserved from yeast to human. Posttranslational modification of chromatin is a critical component of gene regulation. Specifically, tri-methylation of the nucleosome component histone 3 at lysine 9 (H3K9me3) is a key feature of this pathway along with the hallmark heterochromatin protein 1 (HP1). Histone methyltransferases are recruited by HP1 to deposit H3K9me3 marks which nucleate and recruit more HP1 in a process that spreads from the targeting site to signal for gene repression. One of the enzymes recruited is SETDB1, a methyltransferase which putatively catalyzes posttranslational methylation marks on H3K9. To better understand the contribution of SETDB1 in heterochromatin formation, we downregulated SETDB1 through knockdown by a dCas9-KRAB system and examined heterochromatin formation in a chromatin in vivo assay (CiA-Oct4). We studied the contribution of SETDB1 to heterochromatin formation kinetics in a developmentally crucial locus, Oct4. Our data demonstrate that SETDB1 reduction led to a delay in both gene silencing and in H3K9me3 accumulation. Importantly, SETDB1 knockdown to a ∼50% level did not stop heterochromatin formation completely. Particle-based Monte Carlo simulations in 3D space with explicit representation of key molecular processes enabled the elucidation of how SETDB1 downregulation affects the individual molecular processes underlying heterochromatin formation. Oxford University Press 2023-03-07 /pmc/articles/PMC10069619/ /pubmed/37020498 http://dx.doi.org/10.1093/pnasnexus/pgad062 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of National Academy of Sciences. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Biological, Health, and Medical Sciences
Yan, Xiaokang
Williams, Michael R
Barboza Castillo, Ameriks D
Kireev, Dmitri
Hathaway, Nathaniel A
Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico
title Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico
title_full Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico
title_fullStr Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico
title_full_unstemmed Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico
title_short Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico
title_sort relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico
topic Biological, Health, and Medical Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10069619/
https://www.ncbi.nlm.nih.gov/pubmed/37020498
http://dx.doi.org/10.1093/pnasnexus/pgad062
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