Genome-wide profiling of transcription factor binding and epigenetic marks in adipocytes by ChIP-seq.
The recent advances in high-throughput sequencing combined with various other technologies have allowed detailed and genome-wide insight into the transcriptional networks that control adipogenesis. Chromatin immunoprecipitation (ChIP) combined with high-throughput sequencing (ChIP-seq) is one of the most widely used of these technologies. Using these methods, association of transcription factors, cofactors, and epigenetic marks can be mapped to DNA in a genome-wide manner. Here, we provide a detailed protocol for performing ChIP-seq analyses in preadipocytes and adipocytes. We have focused mainly on critical points, limitations of the assay, and quality controls required in order to obtain reproducible ChIP-seq data.
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
Ronni
R
Nielsen
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark. Electronic address: s.mandrup@bmb.sdu.dk.
Susanne
S
Mandrup
D017667:Adipocytes / Q000378:metabolism*; D050156:Adipogenesis / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D044127:Epigenesis, Genetic; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
D014157:Transcription Factors
Adipocyte; Adipogenesis; ChIP-seq; High-throughput sequencing; Library preparation; Transcription factors