Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly

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=hg38&hgt.customText=https://dl.dropboxusercontent.com/u/22994534/AS-tracks/human-GRC-hg38-M1SFs.bed.bz2.

Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers

“…Classification of AS sequences into SFs was done using the PERCON program described in Kazakov et al (2003) and Shepelev et al (2015) and as shown in the hg38 assembly UCSC Genome Browser custom track (Shepelev et al 2015). PERCON classifies AS monomers into 12 major types (Alexandrov et al 2001) that define 5 AS SFs, of which SF1, 2 and 3 represent the live functional centromeres, and SFs 4+ and 5 represent the dead centromeric layers.…”

“…We also noted previously (Supplementary text S1 in Shepelev et al 2009) The program examines the alignment of a given monomer to ALPHA-ALL consensus (see details in Shepelev et al (2015)). If it does not include positions 16-26, the monomer remains unclassed ("u" in PERCON map), if it has a deletion in that region, the monomer is classed as "171 bp" and if it does not, the monomer is classed as "172 bp" (see the PERCON maps in Suppl.…”

“…These sequences were broken into 100 bp pieces to mimic the deep sequencing reads, subjected to PERCON analysis and the rs statistics for SF4+ monomers were gathered. Since PERCON starts the monomers at a fixed point (Kazakov et al 2003, Shepelev et al 2015, some 100 bp reads were divided into two monomers and some rather short monomeric fragments were generated. To avoid these short fragments which could spoil the analysis, we filtered PERCON-produced monomeric pieces for the length of 90-101 bp and then performed rs analysis.…”

“…and SF4+ groups are all composed of their own classes of monomers (Alexandrov et al 2001) recognizable by the PERCON program (Kazakov et al 2003, Shepelev et al 2015. Annotation of these groups in Human Genome assembly has recently been published (Shepelev et al 2015).…”

“…Annotation of these groups in Human Genome assembly has recently been published (Shepelev et al 2015).…”