Genomics

Dataset Information

237

Composition and organization of active centromere sequences in complex genomes


ABSTRACT: We report the sequences bound to CENP-A in the dog genome (Canis familiaris) for high-throughput characterization of centromeric sequences. We compare these ChIPSeq reads (72 bp, single read) against a reference centromeric satellite DNA domain database for the dog genome, resulting in the annotation of sequence variation and estimated abundance of seven satellite families together with adjacent, non-satellite sequences. To study global patterns of sequence diversity and characterizing the subset of sequences correlated with centromere function, these sequences were evaluated relative to a comprehensive centromere sequence domain k-mer library. From this analysis, we identify functional sequence features from two satellite families (CarSat1 and CarSat2) that are defined by distinct arrays subtypes. Sequences bound to CENP-A in MDCK (dog) cell line

ORGANISM(S): Canis lupus familiaris  

SUBMITTER: Karen Elizabeth Hayden   Karen E Hayden  Huntington F Willard 

PROVIDER: E-GEOD-38079 | ArrayExpress | 2012-07-23

SECONDARY ACCESSION(S): SRP013276GSE38079PRJNA167192

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Composition and organization of active centromere sequences in complex genomes.

Hayden Karen E KE   Willard Huntington F HF  

BMC Genomics 20120720


Centromeres are sites of chromosomal spindle attachment during mitosis and meiosis. While the sequence basis for centromere identity remains a subject of considerable debate, one approach is to examine the genomic organization at these active sites that are correlated with epigenetic marks of centromere function.We have developed an approach to characterize both satellite and non-satellite centromeric sequences that are missing from current assemblies in complex genomes, using the dog genome as  ...[more]

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