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Characterization of the ICCE Repeat in Mammals Reveals an Evolutionary Relationship with the DXZ4 Macrosatellite through Conserved CTCF Binding Motifs.

Title: Characterization of the ICCE Repeat in Mammals Reveals an Evolutionary Relationship with the DXZ4 Macrosatellite through Conserved CTCF Binding Motifs.
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Name(s): Westervelt, Natalia, author
Chadwick, Brian P, author
Type of Resource: text
Genre: Journal Article
Text
Date Issued: 2018-09-01
Physical Form: computer
online resource
Extent: 1 online resource
Language(s): English
Abstract/Description: Appreciation is growing for how chromosomes are organized in three-dimensional space at interphase. Microscopic and high throughput sequence-based studies have established that the mammalian inactive X chromosome (Xi) adopts an alternate conformation relative to the active X chromosome. The Xi is organized into several multi-megabase chromatin loops called superloops. At the base of these loops are superloop anchors, and in humans three of these anchors are composed of large tandem repeat DNA that include DXZ4, Functional Intergenic Repeating RNA Element, and Inactive-X CTCF-binding Contact Element (ICCE). Each repeat contains a high density of binding sites for the architectural organization protein CCCTC-binding factor (CTCF) which exclusively associates with the Xi allele in normal cells. Removal of DXZ4 from the Xi compromises proper folding of the chromosome. In this study, we report the characterization of the ICCE tandem repeat, for which very little is known. ICCE is embedded within an intron of the Nobody (NBDY) gene locus at Xp11.21. We find that primary DNA sequence conservation of ICCE is only retained in higher primates, but that ICCE orthologs exist beyond the primate lineage. Like DXZ4, what is conserved is organization of the underlying DNA into a large tandem repeat, physical location within the NBDY locus and conservation of short DNA sequences corresponding to specific CTCF and Yin Yang 1 binding motifs that correlate with female-specific DNA hypomethylation. Unlike DXZ4, ICCE is not common to all eutherian mammals. Analysis of certain ICCE CTCF motifs reveal striking similarity with the DXZ4 motif and support an evolutionary relationship between DXZ4 and ICCE.
Identifier: FSU_pmch_30102341 (IID), 10.1093/gbe/evy176 (DOI), PMC6125249 (PMCID), 30102341 (RID), 30102341 (EID), 5068191 (PII)
Grant Number: R01 GM117003
Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125249.
Persistent Link to This Record: http://purl.flvc.org/fsu/fd/FSU_pmch_30102341
Host Institution: FSU
Is Part Of: Genome biology and evolution.
1759-6653
Issue: iss. 9, vol. 10

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Westervelt, N., & Chadwick, B. P. (2018). Characterization of the ICCE Repeat in Mammals Reveals an Evolutionary Relationship with the DXZ4 Macrosatellite through Conserved CTCF Binding Motifs. Genome Biology And Evolution. Retrieved from http://purl.flvc.org/fsu/fd/FSU_pmch_30102341