title: Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.
abstract: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.
authors.affiliation: Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America.
authors.forename: Dongjun
authors.initials: D
authors.lastname: Chung
authors.forename: Pei Fen
authors.initials: PF
authors.lastname: Kuan
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.forename: Rajendran
authors.initials: R
authors.lastname: Sanalkumar
authors.forename: Kun
authors.initials: K
authors.lastname: Liang
authors.forename: Emery H
authors.initials: EH
authors.lastname: Bresnick
authors.forename: Colin
authors.initials: C
authors.lastname: Dewey
authors.forename: Sündüz
authors.initials: S
authors.lastname: Keleş
mesh_terms: D000818:Animals; D001482:Base Composition; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002874:Chromosome Mapping / Q000379:methods; D050982:GATA1 Transcription Factor / Q000235:genetics; D016678:Genome; D023281:Genomics / Q000379:methods*; D006367:HeLa Cells; D057166:High-Throughput Screening Assays / Q000379:methods; D006801:Humans; D051379:Mice; D012091:Repetitive Sequences, Nucleic Acid; D015203:Reproducibility of Results; D050794:STAT1 Transcription Factor / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism*
chemical_list: D050982:GATA1 Transcription Factor; C494689:Gata1 protein, mouse; D050794:STAT1 Transcription Factor; C494079:STAT1 protein, human; D014157:Transcription Factors