[en] As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and precise analysis helps us to identify the effects of protocol optimizations. We applied iterative sonication - sending the fragmented DNA after ChIP through additional round(s) of shearing - to a number of samples, testing the effects on different histone marks, aiming to uncover potential benefits of inactive histone marks specifically. We developed an analysis pipeline that utilizes our unique, enrichment-type specific approach to peak calling. With the help of this pipeline, we managed to accurately describe the advantages and disadvantages of the iterative refragmentation technique, and we successfully identified possible fields for its applications, where it enhances the results greatly. In addition to the resonication protocol description, we provide guidelines for peak calling optimization and a freely implementable pipeline for data analysis.
Disciplines :
Life sciences: Multidisciplinary, general & others Biochemistry, biophysics & molecular biology
Marino-Ramirez L, Kann MG, Shoemaker BA, Landsman D. Histone structure and nucleosome stability. Expert Rev Proteomics. 2005;2(5):719-29.
Oike T, Ogiwara H, Amornwichet N, Nakano T, Kohno T. Chromatin-regulating proteins as targets for cancer therapy. J Radiat Res. 2014;55(4):613-28.
Baylin SB, Jones PA. A decade of exploring the cancer epigenome-biological and translational implications. Nat Rev Cancer. 2011;11(10):726-34.
Dawson MA, Kouzarides T. Cancer epigenetics: from mechanism to therapy. Cell. 2012;150(1):12-27.
Hendrich B, Bickmore W. Human diseases with underlying defects in chromatin structure and modification. Hum Mol Genet. 2001;10(20):2233-42.
Ho JW, Bishop E, Karchenko PV, Negre N, White KP, Park PJ. ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics. 2011;12:134.
Fanelli M, Amatori S, Barozzi I, Minucci S. Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue. Nat Protoc. 2011;6(12):1905-19.
Gilfillan GD, Hughes T, Sheng Y, et al. Limitations and possibilities of low cell number ChIP-seq. BMC Genomics. 2012;13:645.
Shankaranarayanan P, Mendoza-Parra MA, Walia M, et al. Single-tube linear DNA amplification (LinDA) for robust ChIP-seq. Nat Methods. 2011;8(7):565-7.
Kasoji SK, Pattenden SG, Malc EP, et al. Cavitation enhancing nanodroplets mediate efficient DNA fragmentation in a bench top ultrasonic water bath. PLoS One. 2015;10(7):e0133014.
Mokry M, Hatzis P, de Bruijn E, et al. Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles. PLoS One. 2010;5(11):e15092.
Schwartz YB, Pirrotta V. Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet. 2007;8(1):9-22.
Wang J, Lawry ST, Cohen AL, Jia S. Chromosome boundary elements and regulation of heterochromatin spreading. Cell Mol Life Sci. 2014;71(24):4841-52.
Teytelman L, Ozaydin B, Zill O, et al. Impact of chromatin structures on DNA processing for genomic analyses. PLoS One. 2009;4(8):e6700.
Auerbach RK, Euskirchen G, Rozowsky J, et al. Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A. 2009;106(35):14926-31.
Meyer CA, Liu XS. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet. 2014;15(11):709-21.
Gentsch GE, Smith JC. Investigating physical chromatin associations across the Xenopus genome by chromatin immunoprecipitation. Cold Spring Harb Protoc. 2014;2014(5). doi: 10.1101/pdb.prot080614.
Barrilleaux BL, Cotterman R, Knoepfler PS. Chromatin immunoprecipitation assays for Myc and N-Myc. Methods Mol Biol. 2013;1012:117-33.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10-12.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-60.
Landt SG, Marinov GK, Kundaje A, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012;22(9):1813-31.
Bailey T, Krajewski P, Ladunga I, et al. Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol. 2013;9(11):e1003326.
Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics. 2009;25(15):1952-8.
Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol. 2011;12(7):R67.
Starmer J, Magnuson T. Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains. BMC Bioinformatics. 2016;17:144.
Wang J, Lunyak VV, Jordan IK. BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets. Bioinformatics. 2013;29(4):492-3.
Song Q, Smith AD. Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics. 2011;27(6):870-1.
Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178-92.
Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime CIS-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576-89.
R Development Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: 2013.
Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078-9.
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841-2.
Itahana Y, Zhang J, Goke J, et al. Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells. Sci Rep. 2016;6:28112.
Li G, Zhou L. Genome-wide identification of chromatin transitional regions reveals diverse mechanisms defining the boundary of facultative heterochromatin. PLoS One. 2013;8(6):e67156.
Hardy K, Wu F, Tu W, et al. Identification of chromatin accessibility domains in human breast cancer stem cells. Nucleus. 2016;7(1):50-67.
Feng J, Liu T, Qin B, Zhang Y, Liu XS. Identifying ChIP-seq enrichment using MACS. Nat Protoc. 2012;7(9):1728-40.
Martin C, Zhang Y. The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol. 2005;6(11):838-49.