Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq).

ABSTRACT: Establishing the architecture of gene regulatory networks (GRNs) relies on chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) methods that provide genome-wide transcription factor binding sites (TFBSs). ChIP-Seq furnishes millions of short reads that, after alignment, describe the genome-wide binding sites of a particular TF. However, in all organisms investigated an average of 40% of reads fail to align to the corresponding genome, with some datasets having as much as 80% of reads failing to align. We describe here the provenance of previously unaligned reads in ChIP-Seq experiments from animals and plants. We show that a substantial portion corresponds to sequences of bacterial and metazoan origin, irrespective of the ChIP-Seq chromatin source. Unforeseen

SUBMITTER: Ouma WZ 

PROVIDER: S-EPMC4345404 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature