ChIP-Seq peak calling and data analysis in woody plants

  • Wang Lina Northeast Forestry University


Chromatin immunoprecipitation (ChIP) followed by highthroughput sequencing (ChIP-Seq) provides an important tool to study genome-wide protein-DNA interactions to help understand gene regulation in the context of native chromatin. A complete ChIP-Seq workflow including peak calling, peak classification, transcription factor binding site overrepresentation and definition of new TFBS motifs. In this paper, ChIP-Seq peak calling and data analysis is described in detail.

Author Biography

Wang Lina, Northeast Forestry University

State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing
Road, Harbin ,150040, China


[1] Bolger A M , Lohse M , Usadel B . Trimmomatic: a flexible trimmer for Illumin
a sequence data[J]. Bioinformatics, 2014, 30 (15):2114-2120.
[2] Gupta S , Stamatoyannopoulos J A , Bailey T L , et al. Quantifying similarity between motif
s[J]. Genome Biology, 2007, 8(2):R24-R24.
[3] J. Ye , Coulouris G , Zaretskaya I , et al. Primer-BLAST: A tool to design target-specific pr
imers for polymerase chain reaction[J]. BMC Bioinformatics, 2012, 13(1):134.
[4] Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Meth
ods. 2012, 9:357-359.
[5] Martin R C , Vining K , Dombrowski J E . Genome-wide (ChIP-seq) identificatio
n of target genes regulated by BdbZIP10 during paraquat-induced oxidative stress[J].
Bmc Plant Biology, 2018, 18(1):58.
[6] Martin M . Cutadapt removes adapter sequences from high-throughput sequencing read[J]. Em
bnet Journal, 2011, 17(1). 2114–2120.
[7] Planet E , Attolini S O , Reina O , et al. htSeqTools: high-throughput sequencing
quality control, processing and visualization in R[J]. Bioinformatics, 2012, 28(4):589-
[8] T.L. Bailey, DREME: motif discovery in transcription factor ChIP-Seq data,Bioinfo
rmatics 27 (2011) 1653e1659.
[9] Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Gra
nt, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, "MEME SUITE:
tools for motif discovery and searching", Nucleic Acids Research, 37:W202-W208, 20
[10] T.L. Bailey, C. Elkan, Fitting a mixture model by expectation maximization to di
scover motifs in biopolymers, Proc. Int. Conf. Intell. Syst. Mol. Biol. 2 (1994) 28-36.
[11] Wang S, Sun H, Ma J, et al. Target analysis by integration of transcriptome and
ChIP-Seq data with BETA[J]. Nature Protocols, 2013, 8(12):2502-25.
[12] Zhang Y , Liu T , Meyer C A, et al. Model-based analysis of chip-seq (MACS)
[J]. Genome biology, 2008, 9(9):R137.
How to Cite
Lina, W. (2018). ChIP-Seq peak calling and data analysis in woody plants. Journal of Advance Research in Applied Science (ISSN: 2208-2352), 5(12), 11-20. Retrieved from