ChIP-Seq/HT-ChIP/ChIP-exo/Mint-ChIP

Chromatin Immunoprecipitation Sequencing / High-Throughput ChIP / Exonuclease trimmed ChIP / Multiplexed ChIP

ChIP-Seq is a well-established method to map specific protein-binding sites (Solomon et al., 1988). It has given rise to a vast number of derivatives, such as AHT-ChIP-Seq (Aldridge et al., 2013), BisChIP-Seq (Statham et al., 2012), CAST-ChIP (Schauer et al., 2013), ChIP-BMS (Li et al., 2011), ChIP-BS-seq (Brinkman et al., 2012), ChIPmentation (Schmidl et al., 2015), Drop-ChIP (Rotem et al., 2015), Mint-ChIP (van Galen et al., 2016), PAT_ChIP (Fanelli et al., 2011), reChIP-seq (Truax et al., 2012), scChIP-seq (Rotem et al., 2015), and X-ChIP (Skene et al., 2014). Sequential ChIP-seq (reChIP) can also show the association of different proteins on the chromatin (Elsasser et al., 2015). In this method, DNA-protein complexes are crosslinked in vivo. Next, samples are fragmented and treated with an exonuclease to trim unbound oligonucleotides. Protein-specific antibodies are used to immunoprecipitate the DNA-protein complex. The DNA is extracted, purified, and sequenced, giving high-resolution sequences of the protein-binding sites.

Advantages:

  • Base-pair resolution of protein-binding sites
  • Can map specific regulatory factors or proteins
  • Exonuclease use eliminates contamination by unbound DNA (Zentner et al., 2012)

Disadvantages:

  • Nonspecific antibodies can dilute the pool of DNA-protein complexes of interest
  • Target protein must be known and be able to raise an antibody


Reagents:

Illumina Library prep and Array Kit Selector



Reviews:

Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109



References:

Rinaldi L., Datta D., Serrat J., et al. Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis. Cell Stem Cell. 2016;19:491-501

Woolnough J. L., Atwood B. L., Liu Z., Zhao R. and Giles K. E. The Regulation of rRNA Gene Transcription during Directed Differentiation of Human Embryonic Stem Cells. PLoS One. 2016;11:e0157276

Schmidt S. F., Madsen J. G., Frafjord K. O., et al. Integrative Genomics Outlines a Biphasic Glucose Response and a ChREBP-RORgamma Axis Regulating Proliferation in beta Cells. Cell Rep. 2016;16:2359-2372

Nelson D. M., Jaber-Hijazi F., Cole J. J., et al. Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability. Genome Biol. 2016;17:158

Wu T. P., Wang T., Seetin M. G., et al. DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature. 2016;532:329-333

Zwart W., Flach K. D., Rudraraju B., et al. SRC3 Phosphorylation at Serine 543 Is a Positive Independent Prognostic Factor in ER-Positive Breast Cancer. Clin Cancer Res. 2016;22:479-491

Yasuma K., Yasunaga J., Takemoto K., et al. HTLV-1 bZIP Factor Impairs Anti-viral Immunity by Inducing Co-inhibitory Molecule, T Cell Immunoglobulin and ITIM Domain (TIGIT). PLoS Pathog. 2016;12:e1005372

De S., Mitra A., Cheng Y., Pfeifer K. and Kassis J. A. Formation of a Polycomb-Domain in the Absence of Strong Polycomb Response Elements. PLoS Genet. 2016;12:e1006200

Bevington S. L., Cauchy P., Piper J., et al. Inducible chromatin priming is associated with the establishment of immunological memory in T cells. EMBO J. 2016;35:515-535

Hay D., Hughes J. R., Babbs C., et al. Genetic dissection of the alpha-globin super-enhancer in vivo. Nat Genet. 2016;48:895-903

Weiner A., Hsieh T. H., Appleboim A., et al. High-resolution chromatin dynamics during a yeast stress response. Mol Cell. 2015;58:371-386