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H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks
Background: Transposons are selfish genetic elements that self-reproduce in host DNA. They were active during evolutionary history and now occupy almost half of mammalian genomes. Close insertions of transposons reshaped structure and regulation of many genes considerably. Co-evolution of transposon...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770625/ https://www.ncbi.nlm.nih.gov/pubmed/31491936 http://dx.doi.org/10.3390/cells8091034 |
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author | Igolkina, Anna A. Zinkevich, Arsenii Karandasheva, Kristina O. Popov, Aleksey A. Selifanova, Maria V. Nikolaeva, Daria Tkachev, Victor Penzar, Dmitry Nikitin, Daniil M. Buzdin, Anton |
author_facet | Igolkina, Anna A. Zinkevich, Arsenii Karandasheva, Kristina O. Popov, Aleksey A. Selifanova, Maria V. Nikolaeva, Daria Tkachev, Victor Penzar, Dmitry Nikitin, Daniil M. Buzdin, Anton |
author_sort | Igolkina, Anna A. |
collection | PubMed |
description | Background: Transposons are selfish genetic elements that self-reproduce in host DNA. They were active during evolutionary history and now occupy almost half of mammalian genomes. Close insertions of transposons reshaped structure and regulation of many genes considerably. Co-evolution of transposons and host DNA frequently results in the formation of new regulatory regions. Previously we published a concept that the proportion of functional features held by transposons positively correlates with the rate of regulatory evolution of the respective genes. Methods: We ranked human genes and molecular pathways according to their regulatory evolution rates based on high throughput genome-wide data on five histone modifications (H3K4me3, H3K9ac, H3K27ac, H3K27me3, H3K9me3) linked with transposons for five human cell lines. Results: Based on the total of approximately 1.5 million histone tags, we ranked regulatory evolution rates for 25075 human genes and 3121 molecular pathways and identified groups of molecular processes that showed signs of either fast or slow regulatory evolution. However, histone tags showed different regulatory patterns and formed two distinct clusters: promoter/active chromatin tags (H3K4me3, H3K9ac, H3K27ac) vs. heterochromatin tags (H3K27me3, H3K9me3). Conclusion: In humans, transposon-linked histone marks evolved in a coordinated way depending on their functional roles. |
format | Online Article Text |
id | pubmed-6770625 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-67706252019-10-30 H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks Igolkina, Anna A. Zinkevich, Arsenii Karandasheva, Kristina O. Popov, Aleksey A. Selifanova, Maria V. Nikolaeva, Daria Tkachev, Victor Penzar, Dmitry Nikitin, Daniil M. Buzdin, Anton Cells Article Background: Transposons are selfish genetic elements that self-reproduce in host DNA. They were active during evolutionary history and now occupy almost half of mammalian genomes. Close insertions of transposons reshaped structure and regulation of many genes considerably. Co-evolution of transposons and host DNA frequently results in the formation of new regulatory regions. Previously we published a concept that the proportion of functional features held by transposons positively correlates with the rate of regulatory evolution of the respective genes. Methods: We ranked human genes and molecular pathways according to their regulatory evolution rates based on high throughput genome-wide data on five histone modifications (H3K4me3, H3K9ac, H3K27ac, H3K27me3, H3K9me3) linked with transposons for five human cell lines. Results: Based on the total of approximately 1.5 million histone tags, we ranked regulatory evolution rates for 25075 human genes and 3121 molecular pathways and identified groups of molecular processes that showed signs of either fast or slow regulatory evolution. However, histone tags showed different regulatory patterns and formed two distinct clusters: promoter/active chromatin tags (H3K4me3, H3K9ac, H3K27ac) vs. heterochromatin tags (H3K27me3, H3K9me3). Conclusion: In humans, transposon-linked histone marks evolved in a coordinated way depending on their functional roles. MDPI 2019-09-05 /pmc/articles/PMC6770625/ /pubmed/31491936 http://dx.doi.org/10.3390/cells8091034 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Igolkina, Anna A. Zinkevich, Arsenii Karandasheva, Kristina O. Popov, Aleksey A. Selifanova, Maria V. Nikolaeva, Daria Tkachev, Victor Penzar, Dmitry Nikitin, Daniil M. Buzdin, Anton H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks |
title | H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks |
title_full | H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks |
title_fullStr | H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks |
title_full_unstemmed | H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks |
title_short | H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks |
title_sort | h3k4me3, h3k9ac, h3k27ac, h3k27me3 and h3k9me3 histone tags suggest distinct regulatory evolution of open and condensed chromatin landmarks |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770625/ https://www.ncbi.nlm.nih.gov/pubmed/31491936 http://dx.doi.org/10.3390/cells8091034 |
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