title: Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology.
abstract: Gene transcription can be regulated through alteration of chromatin structure, such as changes in nucleosome positioning and histone-modification patterns. Recent development of techniques based on the next-generation sequencing technology has allowed high-resolution analysis of genome-wide distribution of these chromatin features. In this chapter, we describe in detail the protocols of ChIP-Seq and MNase-Seq, which have been developed to detect the genome-wide profiles of transcription factor binding, histone modifications, and nucleosome occupancy. We also describe RNA-Seq protocols used to map global gene expression profiles.
authors.affiliation: Systems Biology Center, NHLBI, NIH, Bethesda, Maryland, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Wei
authors.forename: Gangqing
authors.initials: G
authors.lastname: Hu
authors.forename: Kairong
authors.initials: K
authors.lastname: Cui
authors.forename: Keji
authors.initials: K
authors.lastname: Zhao
mesh_terms: D001483:Base Sequence; D042002:Chromatin Assembly and Disassembly; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D008836:Micrococcal Nuclease / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
chemical_list: D006657:Histones; D009707:Nucleosomes; D014157:Transcription Factors; D008836:Micrococcal Nuclease