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Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence

BACKGROUND: Histone methylation can dramatically affect chromatin structure and gene expression and was considered irreversible until recent discoveries of two families of histone demethylases, the KDM1 (previously LSD1) and JmjC domain-containing proteins. These two types of proteins have different...

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Autores principales: Zhou, Xiaofan, Ma, Hong
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579438/
https://www.ncbi.nlm.nih.gov/pubmed/18950507
http://dx.doi.org/10.1186/1471-2148-8-294
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author Zhou, Xiaofan
Ma, Hong
author_facet Zhou, Xiaofan
Ma, Hong
author_sort Zhou, Xiaofan
collection PubMed
description BACKGROUND: Histone methylation can dramatically affect chromatin structure and gene expression and was considered irreversible until recent discoveries of two families of histone demethylases, the KDM1 (previously LSD1) and JmjC domain-containing proteins. These two types of proteins have different functional domains and distinct substrate specificities. Although more and more KDM1 and JmjC proteins have been shown to have histone demethylase activity, our knowledge about their evolution history is limited. RESULTS: We performed systematic phylogenetic analysis of these histone demethylase families and uncovered different evolutionary patterns. The KDM1 genes have been maintained with a stable low copy number in most organisms except for a few duplication events in flowering plants. In contrast, multiple genes for JmjC proteins with distinct domain architectures were present before the split of major eukaryotic groups, and experienced subsequent birth-and-death evolution. In addition, distinct evolutionary patterns can also be observed between animal and plant histone demethylases in both families. Furthermore, our results showed that some JmjC subfamilies contain only animal genes with specific demethylase activities, but do not have plant members. CONCLUSION: Our study improves the understanding about the evolutionary history of KDM1 and JmjC genes and provides valuable insights into their functions. Based on the phylogenetic relationship, we discussed possible histone demethylase activities for several plant JmjC proteins. Finally, we proposed that the observed differences in evolutionary pattern imply functional divergence between animal and plant histone demethylases.
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spelling pubmed-25794382008-11-06 Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence Zhou, Xiaofan Ma, Hong BMC Evol Biol Research Article BACKGROUND: Histone methylation can dramatically affect chromatin structure and gene expression and was considered irreversible until recent discoveries of two families of histone demethylases, the KDM1 (previously LSD1) and JmjC domain-containing proteins. These two types of proteins have different functional domains and distinct substrate specificities. Although more and more KDM1 and JmjC proteins have been shown to have histone demethylase activity, our knowledge about their evolution history is limited. RESULTS: We performed systematic phylogenetic analysis of these histone demethylase families and uncovered different evolutionary patterns. The KDM1 genes have been maintained with a stable low copy number in most organisms except for a few duplication events in flowering plants. In contrast, multiple genes for JmjC proteins with distinct domain architectures were present before the split of major eukaryotic groups, and experienced subsequent birth-and-death evolution. In addition, distinct evolutionary patterns can also be observed between animal and plant histone demethylases in both families. Furthermore, our results showed that some JmjC subfamilies contain only animal genes with specific demethylase activities, but do not have plant members. CONCLUSION: Our study improves the understanding about the evolutionary history of KDM1 and JmjC genes and provides valuable insights into their functions. Based on the phylogenetic relationship, we discussed possible histone demethylase activities for several plant JmjC proteins. Finally, we proposed that the observed differences in evolutionary pattern imply functional divergence between animal and plant histone demethylases. BioMed Central 2008-10-24 /pmc/articles/PMC2579438/ /pubmed/18950507 http://dx.doi.org/10.1186/1471-2148-8-294 Text en Copyright ©2008 Zhou and Ma; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Zhou, Xiaofan
Ma, Hong
Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence
title Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence
title_full Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence
title_fullStr Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence
title_full_unstemmed Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence
title_short Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence
title_sort evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579438/
https://www.ncbi.nlm.nih.gov/pubmed/18950507
http://dx.doi.org/10.1186/1471-2148-8-294
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