Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

Many biologically significant processes, such as cell differentiation and cell cycle progression, gene transcription and DNA replication, chromosome stability and epigenetic silencing etc. depend on the crucial interactions between cellular proteins and DNA. Chromatin immunoprecipitation (ChIP) is an important experimental technique for studying interactions between specific proteins and DNA in the cell and determining their localization on a specific genomic locus. In recent years, the combination of ChIP with second generation DNA-sequencing technology (ChIP-seq) allows precise genomic functional assay. This review addresses the important applications of ChIP-seq with an emphasis on its role in genome-wide mapping of transcription factor binding sites, the revelation of underlying molecular mechanisms of differential gene regulation that are governed by specific transcription factors, and the identification of epigenetic marks. Furthermore, we also describe the ChIP-seq data analysis workflow and a perspective for the exciting potential advancement of ChIP-seq technology in the future.

[1]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[2]  Mark Gerstein,et al.  Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. , 2011, Genome research.

[3]  E. Mardis.  Next-generation DNA sequencing methods. , 2008, Annual review of genomics and human genetics.

[4]  P. Farnham,et al.  Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. , 2002, Methods.

[5]  P. Farnham,et al.  Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. , 2002, Methods.

[6]  G. Stark,et al.  Role of lysine methylation of NF-κB in differential gene regulation , 2013, Proceedings of the National Academy of Sciences.

[7]  V. Beneš,et al.  SUMOylation regulates the chromatin occupancy and anti-proliferative gene programs of glucocorticoid receptor , 2013, Nucleic acids research.

[8]  A. Brasier,et al.  Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation. , 2005, BioTechniques.

[9]  M. Facciotti,et al.  Evaluation of Algorithm Performance in ChIP-Seq Peak Detection , 2010, PloS one.

[10]  Howard Y. Chang,et al.  High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation. , 2012, Lab on a chip.

[11]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[12]  Philip Machanick,et al.  MEME-ChIP: motif analysis of large DNA datasets , 2011, Bioinform..

[13]  J. Lis,et al.  Detecting protein-DNA interactions in vivo: distribution of RNA polymerase on specific bacterial genes. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[14]  R. Quatrano.  Genomics , 1998, Plant Cell.

[15]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[16]  R. Singal,et al.  Methylation of α-type embryonic globin gene απrepresses transcription in primary erythroid cells , 2002 .

[17]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[18]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[19]  P. Park,et al.  Design and analysis of ChIP-seq experiments for DNA-binding proteins , 2008, Nature Biotechnology.

[20]  Yan Yan,et al.  Analysis of specific lysine histone H3 and H4 acetylation and methylation status in clones of cells with a gene silenced by nickel exposure. , 2003, Toxicology and applied pharmacology.

[21]  C. Peterson,et al.  Chromatin immunoprecipitation (ChIP). , 2009, Cold Spring Harbor protocols.

[22]  Tao Liu,et al.  Computational methodology for ChIP-seq analysis , 2013, Quantitative Biology.

[23]  Dominik Beck,et al.  BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells , 2013, Nucleic Acids Res..

[24]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[25]  Barbara J. Wold,et al.  Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies , 2014, Scientific Reports.

[26]  E. Mardis.  ChIP-seq: welcome to the new frontier , 2007, Nature Methods.

[27]  Edwin Cheung,et al.  A transcriptional repressor co‐regulatory network governing androgen response in prostate cancers , 2012, The EMBO journal.

[28]  Tim Hui-Ming Huang,et al.  Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. , 2002, Genes & development.

[29]  Alexander Varshavsky,et al.  Mapping proteinDNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene , 1988, Cell.

[30]  J. Lis,et al.  RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. , 1986, Molecular and cellular biology.

[31]  Kern Rei Chng,et al.  Sequencing the transcriptional network of androgen receptor in prostate cancer. , 2013, Cancer letters.

[32]  J. Lis,et al.  In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster , 1985, Molecular and cellular biology.

[33]  Jing Liu,et al.  CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse , 2013, Nucleic Acids Res..

[34]  R. Paro,et al.  Analysis of chromatin structure by in vivo formaldehyde cross-linking. , 1997, Methods.

[35]  J. Lieb,et al.  ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. , 2004, Genomics.

[36]  Ruiqiang Li,et al.  SOAP: short oligonucleotide alignment program , 2008, Bioinform..

[37]  Michael Q. Zhang,et al.  Use of Chromatin Immunoprecipitation To Clone Novel E2F Target Promoters , 2001, Molecular and Cellular Biology.

[38]  R. Singal,et al.  Methylation of alpha-type embryonic globin gene alpha pi represses transcription in primary erythroid cells. , 2002, Blood.

[39]  Renato Paro,et al.  A chromatin-modifying function of JNK during stem cell differentiation , 2011, Nature Genetics.

[40]  A. Brasier,et al.  Two-step cross-linking for analysis of protein-chromatin interactions. , 2012, Methods in molecular biology.

[41]  Jie Zhang,et al.  Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data , 2013, PLoS Comput. Biol..

[42]  H. Rehrauer,et al.  Genome-wide analysis of H4K5 acetylation associated with fear memory in mice , 2013, BMC Genomics.

[43]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[44]  Lin Li,et al.  Chromatin immunoprecipitation: a tool for studying histone acetylation and transcription factor binding. , 2003, Methods.

[45]  J. van Helden,et al.  RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets , 2011, Nucleic acids research.

[46]  M. A. Vega-Palas,et al.  Analysis of the epigenetic status of telomeres by using ChIP-seq data , 2012, Nucleic acids research.