Genome-wide identification of transcription factor-binding sites in plants using chromatin immunoprecipitation followed by microarray (ChIP-chip) or sequencing (ChIP-seq).

Methods in Molecular Biology
Jia-Ying ZhuZhi-Yong Wang

Abstract

Nearly all signal transduction pathways lead to regulation of gene expression by controlling specific transcription factors (TFs). Chromatin immunoprecipitation (ChIP) is a powerful method for studying TF-DNA interactions in vivo. To identify all binding sites of a TF in the genome, the DNA obtained in ChIP experiments needs to be analyzed by hybridization to genome-tiling microarrays (ChIP-chip) or by next-generation sequencing (ChIP-seq). Here, we provide detailed protocols of ChIP for two model plant species Arabidopsis and rice, procedures of DNA sample preparation for ChIP-chip or ChIP-seq, and a general guide for computational data analysis. We have used these protocols to successfully identify direct target genes of the BZR1 TF of the brassinosteroid signaling pathway in both Arabidopsis and rice.

Citations

Mar 29, 2014·Plant Cell Reports·Cui ZhangKang Chong
Mar 5, 2013·Annual Review of Plant Biology·J Bailey-Serres
Apr 28, 2016·Scientific Reports·Chun-Ping YuWen-Hsiung Li
May 31, 2017·Plant Biotechnology Journal·Rakesh BhatiaMaurice Bosch
Apr 21, 2018·Plant, Cell & Environment·Chun-Lin ChenHong-Qing Ling
Jul 12, 2019·The New Phytologist·Yunmin XuGang Wu
May 29, 2020·Nature Communications·Lun ZhaoXingwang Li
Dec 5, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Wilfried RozhonBrigitte Poppenberger
Jun 29, 2013·Genome Biology·Gabriel KroukDennis Shasha
Jul 5, 2017·Proceedings of the National Academy of Sciences of the United States of America·Yan O ZuboG Eric Schaller
Jul 15, 2016·Molecular Plant Pathology·An-Chi Liu, Chiu-Ping Cheng
Nov 22, 2017·Proceedings of the National Academy of Sciences of the United States of America·Lu LuSusan R Wessler

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