Computational Methodology for ChIP-seq Analysis

Overview

Journal Quant Biol

Publisher Wiley

Date 2015 Mar 6

PMID 25741452

Citations 16

Authors

Hyunjin Shin

Tao Liu

Xikun Duan

Yong Zhang

X Shirley Liu

Affiliations

Soon will be listed here.

Abstract

Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is a powerful technology to identify the genome-wide locations of DNA binding proteins such as transcription factors or modified histones. As more and more experimental laboratories are adopting ChIP-seq to unravel the transcriptional and epigenetic regulatory mechanisms, computational analyses of ChIP-seq also become increasingly comprehensive and sophisticated. In this article, we review current computational methodology for ChIP-seq analysis, recommend useful algorithms and workflows, and introduce quality control measures at different analytical steps. We also discuss how ChIP-seq could be integrated with other types of genomic assays, such as gene expression profiling and genome-wide association studies, to provide a more comprehensive view of gene regulatory mechanisms in important physiological and pathological processes.

Citing Articles

Statistical Analysis in ChIP-seq-Related Applications.

Teng M Methods Mol Biol. 2023; 2629:169-181.

PMID: 36929078 DOI: 10.1007/978-1-0716-2986-4_9.

2,3,7,8-Tetrachlorodibenzo-p-dioxin induces multigenerational alterations in the expression of microRNA in the thymus through epigenetic modifications.

Singh N, Yang X, Bam M, Nagarkatti M, Nagarkatti P PNAS Nexus. 2023; 2(1):pgac290.

PMID: 36712935 PMC: 9833045. DOI: 10.1093/pnasnexus/pgac290.

Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions.

Jungwirth E, Panzitt K, Marschall H, Thallinger G, Wagner M Hepatol Commun. 2021; 5(10):1721-1736.

PMID: 34558825 PMC: 8485886. DOI: 10.1002/hep4.1749.

RECOGNICER: A coarse-graining approach for identifying broad domains from ChIP-seq data.

Zang C, Wang Y, Peng W Quant Biol. 2021; 8(4):359-368.

PMID: 34327037 PMC: 8318318. DOI: 10.1007/s40484-020-0225-2.

CpG content-dependent associations between transcription factors and histone modifications.

Fischer J, Behjati Ardakani F, Kattler K, Walter J, Schulz M PLoS One. 2021; 16(4):e0249985.

PMID: 33857234 PMC: 8049299. DOI: 10.1371/journal.pone.0249985.

References

Wang Q, Li W, Zhang Y, Yuan X, Xu K, Yu J . Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell. 2009; 138(2):245-56. PMC: 2726827. DOI: 10.1016/j.cell.2009.04.056. View

Gerstein M, Lu Z, Van Nostrand E, Cheng C, Arshinoff B, Liu T . Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010; 330(6012):1775-87. PMC: 3142569. DOI: 10.1126/science.1196914. View

Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F . Tablet--next generation sequence assembly visualization. Bioinformatics. 2009; 26(3):401-2. PMC: 2815658. DOI: 10.1093/bioinformatics/btp666. View

Heintzman N, Stuart R, Hon G, Fu Y, Ching C, Hawkins R . Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007; 39(3):311-8. DOI: 10.1038/ng1966. View

Fujita P, Rhead B, Zweig A, Hinrichs A, Karolchik D, Cline M . The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2010; 39(Database issue):D876-82. PMC: 3242726. DOI: 10.1093/nar/gkq963. View

Kharchenko P, Tolstorukov M, Park P . Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008; 26(12):1351-9. PMC: 2597701. DOI: 10.1038/nbt.1508. View

Carroll J, Meyer C, Song J, Li W, Geistlinger T, Eeckhoute J . Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006; 38(11):1289-97. DOI: 10.1038/ng1901. View

Liao J, Boscolo R, Yang Y, Tran L, Sabatti C, Roychowdhury V . Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci U S A. 2003; 100(26):15522-7. PMC: 307600. DOI: 10.1073/pnas.2136632100. View

Crawford G, Holt I, Mullikin J, Tai D, Blakesley R, Bouffard G . Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. Proc Natl Acad Sci U S A. 2004; 101(4):992-7. PMC: 327130. DOI: 10.1073/pnas.0307540100. View

10.

Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M . Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102(43):15545-50. PMC: 1239896. DOI: 10.1073/pnas.0506580102. View

11.

Garber M, Grabherr M, Guttman M, Trapnell C . Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods. 2011; 8(6):469-77. DOI: 10.1038/nmeth.1613. View

12.

Bell O, Tiwari V, Thoma N, Schubeler D . Determinants and dynamics of genome accessibility. Nat Rev Genet. 2011; 12(8):554-64. DOI: 10.1038/nrg3017. View

13.

Dostie J, Richmond T, Arnaout R, Selzer R, Lee W, Honan T . Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006; 16(10):1299-309. PMC: 1581439. DOI: 10.1101/gr.5571506. View

14.

Verzi M, Shin H, Ho L, Liu X, Shivdasani R . Essential and redundant functions of caudal family proteins in activating adult intestinal genes. Mol Cell Biol. 2011; 31(10):2026-39. PMC: 3133364. DOI: 10.1128/MCB.01250-10. View

15.

Rhee H, Pugh B . Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell. 2011; 147(6):1408-19. PMC: 3243364. DOI: 10.1016/j.cell.2011.11.013. View

16.

Shin H, Liu T, Manrai A, Liu X . CEAS: cis-regulatory element annotation system. Bioinformatics. 2009; 25(19):2605-6. DOI: 10.1093/bioinformatics/btp479. View

17.

Li R, Yu C, Li Y, Lam T, Yiu S, Kristiansen K . SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009; 25(15):1966-7. DOI: 10.1093/bioinformatics/btp336. View

18.

. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011; 9(4):e1001046. PMC: 3079585. DOI: 10.1371/journal.pbio.1001046. View

19.

Liu T, Rechtsteiner A, Egelhofer T, Vielle A, Latorre I, Cheung M . Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res. 2010; 21(2):227-36. PMC: 3032926. DOI: 10.1101/gr.115519.110. View

20.

Johnson D, Mortazavi A, Myers R, Wold B . Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007; 316(5830):1497-502. DOI: 10.1126/science.1141319. View