title: Systematic evaluation of factors influencing ChIP-seq fidelity.
abstract: We evaluated how variations in sequencing depth and other parameters influence interpretation of chromatin immunoprecipitation-sequencing (ChIP-seq) experiments. Using Drosophila melanogaster S2 cells, we generated ChIP-seq data sets for a site-specific transcription factor (Suppressor of Hairy-wing) and a histone modification (H3K36me3). We detected a chromatin-state bias: open chromatin regions yielded higher coverage, which led to false positives if not corrected. This bias had a greater effect on detection specificity than any base-composition bias. Paired-end sequencing revealed that single-end data underestimated ChIP-library complexity at high coverage. Removal of reads originating at the same base reduced false-positives but had little effect on detection sensitivity. Even at mappable-genome coverage depth of ∼1 read per base pair, ∼1% of the narrow peaks detected on a tiling array were missed by ChIP-seq. Evaluation of widely used ChIP-seq analysis tools suggests that adjustments or algorithm improvements are required to handle data sets with deep coverage.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
authors.forename: Yiwen
authors.initials: Y
authors.lastname: Chen
authors.forename: Nicolas
authors.initials: N
authors.lastname: Negre
authors.forename: Qunhua
authors.initials: Q
authors.lastname: Li
authors.forename: Joanna O
authors.initials: JO
authors.lastname: Mieczkowska
authors.forename: Matthew
authors.initials: M
authors.lastname: Slattery
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Tae-Kyung
authors.initials: TK
authors.lastname: Kim
authors.forename: Housheng Hansen
authors.initials: HH
authors.lastname: He
authors.forename: Jennifer
authors.initials: J
authors.lastname: Zieba
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bickel
authors.forename: Richard M
authors.initials: RM
authors.lastname: Myers
authors.forename: Barbara J
authors.initials: BJ
authors.lastname: Wold
authors.forename: Kevin P
authors.initials: KP
authors.lastname: White
authors.forename: Jason D
authors.initials: JD
authors.lastname: Lieb
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D000818:Animals; D002843:Chromatin / Q000737:chemistry*; D047369:Chromatin Immunoprecipitation / Q000379:methods* / Q000592:standards; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster; D005189:False Positive Reactions; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012097:Repressor Proteins / Q000235:genetics; D012680:Sensitivity and Specificity
chemical_list: D002843:Chromatin; D029721:Drosophila Proteins; D012097:Repressor Proteins; C083738:su(Hw) protein, Drosophila; D011495:Histone-Lysine N-Methyltransferase