title: Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.
abstract: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. Recent advances in sequencing technologies and analyses enable us to compare hundreds of samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. Because many experimental considerations are relevant to the choice of a method in a ChIP-seq analysis, the overall design and quality management of the experiment are of critical importance. This review offers guiding principles of computation and sample preparation for ChIP-seq analyses, highlighting the validity and limitations of the state-of-the-art procedures at each step. We also discuss the latest challenges of single-cell analysis that will encourage a new era in this field.
authors.affiliation: Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.
authors.forename: Ryuichiro
authors.initials: R
authors.lastname: Nakato
authors.affiliation: Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.|Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Japan.
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Shirahige
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D004247:DNA; D016678:Genome; D006801:Humans; D011485:Protein Binding; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: chromatin immunoprecipitation; differential analysis; experimental design; large-scale analysis; quality management; single-cell analysis