title: Revolution of nephrology research by deep sequencing: ChIP-seq and RNA-seq.
abstract: The recent and rapid advent of next-generation sequencing (NGS) has made this technology broadly available not only to researchers in various molecular and cellular biology fields but also to those in kidney disease. In this paper, we describe the usage of ChIP-seq (chromatin immunoprecipitation with sequencing) and RNA-seq for sample preparation and interpretation of raw data in the investigation of biological phenomenon in renal diseases. ChIP-seq identifies genome-wide transcriptional DNA-binding sites as well as histone modifications, which are known to regulate gene expression, in the intragenic as well as in the intergenic regions. With regard to RNA-seq, this process analyzes not only the expression level of mRNA but also splicing variants, non-coding RNA, and microRNA on a genome-wide scale. The combination of ChIP-seq and RNA-seq allows the clarification of novel transcriptional mechanisms, which have important roles in various kinds of diseases, including chronic kidney disease. The rapid development of these techniques requires an update on the latest information and methods of NGS. In this review, we highlight the merits and characteristics of ChIP-seq and RNA-seq and discuss the use of the genome-wide analysis in kidney disease.
authors.affiliation: 1] Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan [2] Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
authors.forename: Imari
authors.initials: I
authors.lastname: Mimura
authors.affiliation: Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
authors.forename: Yasuharu
authors.initials: Y
authors.lastname: Kanki
authors.affiliation: Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
authors.forename: Tatsuhiko
authors.initials: T
authors.lastname: Kodama
authors.affiliation: Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan.
authors.forename: Masaomi
authors.initials: M
authors.lastname: Nangaku
mesh_terms: D035843:Biomedical Research / Q000639:trends*; D047369:Chromatin Immunoprecipitation; D006801:Humans; D007674:Kidney Diseases / Q000235:genetics / Q000378:metabolism; D009398:Nephrology / Q000639:trends*; D017421:Sequence Analysis / Q000639:trends*; D017423:Sequence Analysis, RNA / Q000639:trends*