UMMS Affiliation

Department of Psychiatry, Brudnick Neuropsychiatric Research Institute

Date

9-1-2015

Document Type

Article

Disciplines

Genomics

Abstract

Centromeric alpha satellite (AS) is composed of highly identical higher-order DNA repetitive sequences, which make the standard assembly process impossible. Because of this the AS repeats were severely underrepresented in previous versions of the human genome assembly showing large centromeric gaps. The latest hg38 assembly (GCA_000001405.15) employed a novel method of approximate representation of these sequences using AS reference models to fill the gaps. Therefore, a lot more of assembled AS became available for genomic analysis. We used the PERCON program previously described by us to annotate various suprachromosomal families (SFs) of AS in the hg38 assembly and presented the results of our primary analysis as an easy-to-read track for the UCSC Genome Browser. The monomeric classes, characteristic of the five known SFs, were color-coded, which allowed quick visual assessment of AS composition in whole multi-megabase centromeres down to each individual AS monomer. Such comprehensive annotation of AS in the human genome assembly was performed for the first time. It showed the expected prevalence of the known major types of AS organization characteristic of the five established SFs. Also, some less common types of AS arrays were identified, such as pure R2 domains in SF5, apparent J/R and D/R mixes in SF1 and SF2, and several different SF4 higher-order repeats among reference models and in regular contigs. No new SFs or large unclassed AS domains were discovered. The dataset reveals the architecture of human centromeres and allows classification of AS sequence reads by alignment to the annotated hg38 assembly.

The data were deposited here: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38andhgt.customText=https://dl.dropbox usercontent.com/u/22994534/AS-tracks/human-GRC-hg38-M1SFs.bed.bz2.

Rights and Permissions

Citation: Genom Data. 2015 Sep 1;5:139-146. Link to article on publisher's site

DOI of Published Version

10.1016/j.gdata.2015.05.035

Comments

Copyright © 2015 The Authors This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Related Resources

Link to Article in PubMed

Keywords

Alpha satellite, Centromeres, Higher-order repeats, Suprachromosomal families, hg38 human genome assembly

Journal Title

Genomics data

PubMed ID

26167452

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

Included in

Genomics Commons

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