title: ChIP-seq and RNA-seq methods to study circadian control of transcription in mammals.
abstract: Genome-wide analyses have revolutionized our ability to study the transcriptional regulation of circadian rhythms. The advent of next-generation sequencing methods has facilitated the use of two such technologies, ChIP-seq and RNA-seq. In this chapter, we describe detailed methods and protocols for these two techniques, with emphasis on their usage in circadian rhythm experiments in the mouse liver, a major target organ of the circadian clock system. Critical factors for these methods are highlighted and issues arising with time series samples for ChIP-seq and RNA-seq are discussed. Finally, detailed protocols for library preparation suitable for Illumina sequencing platforms are presented.
authors: Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA. Electronic address: joseph.takahashi@utsouthwestern.edu.
authors: Joseph S
authors: JS
authors: Takahashi
authors: Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
authors: Vivek
authors: V
authors: Kumar
authors: Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
authors: Prachi
authors: P
authors: Nakashe
authors: Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
authors: Nobuya
authors: N
authors: Koike
authors: Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
authors: Hung-Chung
authors: HC
authors: Huang
authors: Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
authors: Carla B
authors: CB
authors: Green
authors: Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
authors: Tae-Kyung
authors: TK
authors: Kim
mesh_terms: D000107:Acetylation; D000818:Animals; D056926:CLOCK Proteins / Q000302:isolation & purification / Q000378:metabolism; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D057906:Circadian Clocks; D005786:Gene Expression Regulation; D006657:Histones / Q000378:metabolism; D006801:Humans; D008745:Methylation; D011499:Protein Processing, Post-Translational; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D006657:Histones; D056926:CLOCK Proteins
keywords: Acetylation; ChIP-seq; Chromatin; Circadian; Histone; Methylation; RNA polymerase II; RNA-seq; Sequencing; Transcription