CTCF binding landscape in jawless fish with reference to Hox cluster evolution

Abstract The nuclear protein CCCTC-binding factor (CTCF) contributes as an insulator to chromatin organization in animal genomes. Currently, our knowledge of its binding property is confined mainly to mammals. In this study, we identified CTCF homologs in extant jawless fishes and performed ChIP-seq...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Mitsutaka Kadota, Yuichiro Hara, Kaori Tanaka, Wataru Takagi, Chiharu Tanegashima, Osamu Nishimura, Shigehiro Kuraku
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/000f1e4311804be694fb69c2ada280e4
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:000f1e4311804be694fb69c2ada280e4
record_format	dspace
spelling	oai:doaj.org-article:000f1e4311804be694fb69c2ada280e42021-12-02T16:05:59ZCTCF binding landscape in jawless fish with reference to Hox cluster evolution10.1038/s41598-017-04506-x2045-2322https://doaj.org/article/000f1e4311804be694fb69c2ada280e42017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-04506-xhttps://doaj.org/toc/2045-2322Abstract The nuclear protein CCCTC-binding factor (CTCF) contributes as an insulator to chromatin organization in animal genomes. Currently, our knowledge of its binding property is confined mainly to mammals. In this study, we identified CTCF homologs in extant jawless fishes and performed ChIP-seq for the CTCF protein in the Arctic lamprey. Our phylogenetic analysis suggests that the lamprey lineage experienced gene duplication that gave rise to its unique paralog, designated CTCF2, which is independent from the previously recognized duplication between CTCF and CTCFL. The ChIP-seq analysis detected comparable numbers of CTCF binding sites between lamprey, chicken, and human, and revealed that the lamprey CTCF protein binds to the two-part motif, consisting of core and upstream motifs previously reported for mammals. These findings suggest that this mode of CTCF binding was established in the last common ancestor of extant vertebrates (more than 500 million years ago). We analyzed CTCF binding inside Hox clusters, which revealed a reinforcement of CTCF binding in the region spanning Hox1-4 genes that is unique to lamprey. Our study provides not only biological insights into the antiquity of CTCF-based epigenomic regulation known in mammals but also a technical basis for comparative epigenomic studies encompassing the whole taxon Vertebrata.Mitsutaka KadotaYuichiro HaraKaori TanakaWataru TakagiChiharu TanegashimaOsamu NishimuraShigehiro KurakuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mitsutaka Kadota Yuichiro Hara Kaori Tanaka Wataru Takagi Chiharu Tanegashima Osamu Nishimura Shigehiro Kuraku CTCF binding landscape in jawless fish with reference to Hox cluster evolution
description	Abstract The nuclear protein CCCTC-binding factor (CTCF) contributes as an insulator to chromatin organization in animal genomes. Currently, our knowledge of its binding property is confined mainly to mammals. In this study, we identified CTCF homologs in extant jawless fishes and performed ChIP-seq for the CTCF protein in the Arctic lamprey. Our phylogenetic analysis suggests that the lamprey lineage experienced gene duplication that gave rise to its unique paralog, designated CTCF2, which is independent from the previously recognized duplication between CTCF and CTCFL. The ChIP-seq analysis detected comparable numbers of CTCF binding sites between lamprey, chicken, and human, and revealed that the lamprey CTCF protein binds to the two-part motif, consisting of core and upstream motifs previously reported for mammals. These findings suggest that this mode of CTCF binding was established in the last common ancestor of extant vertebrates (more than 500 million years ago). We analyzed CTCF binding inside Hox clusters, which revealed a reinforcement of CTCF binding in the region spanning Hox1-4 genes that is unique to lamprey. Our study provides not only biological insights into the antiquity of CTCF-based epigenomic regulation known in mammals but also a technical basis for comparative epigenomic studies encompassing the whole taxon Vertebrata.
format	article
author	Mitsutaka Kadota Yuichiro Hara Kaori Tanaka Wataru Takagi Chiharu Tanegashima Osamu Nishimura Shigehiro Kuraku
author_facet	Mitsutaka Kadota Yuichiro Hara Kaori Tanaka Wataru Takagi Chiharu Tanegashima Osamu Nishimura Shigehiro Kuraku
author_sort	Mitsutaka Kadota
title	CTCF binding landscape in jawless fish with reference to Hox cluster evolution
title_short	CTCF binding landscape in jawless fish with reference to Hox cluster evolution
title_full	CTCF binding landscape in jawless fish with reference to Hox cluster evolution
title_fullStr	CTCF binding landscape in jawless fish with reference to Hox cluster evolution
title_full_unstemmed	CTCF binding landscape in jawless fish with reference to Hox cluster evolution
title_sort	ctcf binding landscape in jawless fish with reference to hox cluster evolution
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/000f1e4311804be694fb69c2ada280e4
work_keys_str_mv	AT mitsutakakadota ctcfbindinglandscapeinjawlessfishwithreferencetohoxclusterevolution AT yuichirohara ctcfbindinglandscapeinjawlessfishwithreferencetohoxclusterevolution AT kaoritanaka ctcfbindinglandscapeinjawlessfishwithreferencetohoxclusterevolution AT watarutakagi ctcfbindinglandscapeinjawlessfishwithreferencetohoxclusterevolution AT chiharutanegashima ctcfbindinglandscapeinjawlessfishwithreferencetohoxclusterevolution AT osamunishimura ctcfbindinglandscapeinjawlessfishwithreferencetohoxclusterevolution AT shigehirokuraku ctcfbindinglandscapeinjawlessfishwithreferencetohoxclusterevolution
_version_	1718385126387220480

CTCF binding landscape in jawless fish with reference to Hox cluster evolution

Ejemplares similares