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

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...

Full description

Saved in:
Bibliographic Details
Published in:Scientific reports 2017-07, Vol.7 (1), p.4957-11, Article 4957
Main Authors: Kadota, Mitsutaka, Hara, Yuichiro, Tanaka, Kaori, Takagi, Wataru, Tanegashima, Chiharu, Nishimura, Osamu, Kuraku, Shigehiro
Format: Article
Language:English
Subjects:
13/1
38/39
38/91
631/136
631/181
631/208/177
82/58
Binding sites
Chromatin
CTCF protein
Gene duplication
Genomes
Humanities and Social Sciences
Mammals
multidisciplinary
Phylogeny
Proteins
Science
Science (multidisciplinary)
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-017-04506-x