MAnorm: một mô hình mạnh mẽ cho việc so sánh định lượng các bộ dữ liệu ChIP-Seq

Genome Biology - Tập 13 - Trang 1-17 - 2012
Zhen Shao1,2, Yijing Zhang3, Guo-Cheng Yuan1, Stuart H Orkin1,2,4, David J Waxman3
1Departments of Pediatric Oncology and Computational Biology, Dana-Farber Cancer Institute, Boston, USA
2Division of Pediatric Hematology-Oncology, The Karp Family Research Laboratories, Children's Hospital, Boston, USA
3Division of Cell and Molecular Biology, Department of Biology, Boston University, Boston, USA
4Harvard Stem Cell Institute and the Howard Hughes Medical Institute, 1 Blackfan Circle, Karp Research Building, Children's Hospital, Boston, USA

Tóm tắt

ChIP-Seq được sử dụng phổ biến để xác định các mẫu gắn kết trên toàn bộ genome của các yếu tố phiên mã và các protein liên kết với chromatin khác. Mặc dù việc so sánh các bộ dữ liệu ChIP-Seq là rất quan trọng để hiểu các kiểu tế bào và trạng thái tế bào cụ thể, và do đó nghiên cứu quy định gene đặc hiệu cho tế bào, nhưng rất ít phương pháp định lượng đã được phát triển. Tại đây, chúng tôi trình bày một phương pháp đơn giản và hiệu quả, MAnorm, để so sánh định lượng các bộ dữ liệu ChIP-Seq mô tả các vị trí gắn kết của các yếu tố phiên mã và các sửa đổi di truyền. Những khác biệt về gắn kết được suy ra bởi MAnorm cho thấy mối tương quan mạnh mẽ với cả những thay đổi trong biểu hiện của các gene mục tiêu và sự gắn kết của các thành phần điều tiết đặc hiệu cho tế bào.

Từ khóa

#ChIP-Seq #phương pháp định lượng #yếu tố phiên mã #sửa đổi di truyền #quy định gene đặc hiệu cho tế bào

Tài liệu tham khảo

Park PJ: ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009, 10: 669-680. Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol. 2008, 26: 1293-1300. 10.1038/nbt.1505. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB: PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009, 27: 66-75. 10.1038/nbt.1518. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS: Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008, 9: R137-10.1186/gb-2008-9-9-r137. Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, Choi K, Farnham PJ, Bresnick EH: Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell. 2009, 36: 667-681. 10.1016/j.molcel.2009.11.001. Liu W, Tanasa B, Tyurina OV, Zhou TY, Gassmann R, Liu WT, Ohgi KA, Benner C, Garcia-Bassets I, Aggarwal AK, Desai A, Dorrestein PC, Glass CK, Rosenfeld MG: PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature. 2010, 466: 508-512. 10.1038/nature09272. Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB: Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell. 2009, 36: 682-695. 10.1016/j.molcel.2009.11.002. Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT: Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science. 2010, 328: 1036-1040. 10.1126/science.1186176. Smagulova F, Gregoretti IV, Brick K, Khil P, Camerini-Otero RD, Petukhova GV: Genome-wide analysis reveals novel molecular features of mouse recombination hotspots. Nature. 2011, 472: 375-378. 10.1038/nature09869. Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PA, Rappsilber J, Helin K: TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature. 2011, 473: 343-348. 10.1038/nature10066. Xu H, Wei CL, Lin F, Sung WK: An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics. 2008, 24: 2344-2349. 10.1093/bioinformatics/btn402. Taslim C, Wu J, Yan P, Singer G, Parvin J, Huang T, Lin S, Huang K: Comparative study on ChIP-seq data: normalization and binding pattern characterization. Bioinformatics. 2009, 25: 2334-2340. 10.1093/bioinformatics/btp384. Smyth GK: Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Edited by: Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S. 2005, New York: Springer, 397-420. Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003, 19: 185-193. 10.1093/bioinformatics/19.2.185. Burdge GC, Lillycrop KA: Nutrition, epigenetics, and developmental plasticity: implications for understanding human disease. Annu Rev Nutr. 2010, 30: 315-339. 10.1146/annurev.nutr.012809.104751. Audic S, Claverie JM: The significance of digital gene expression profiles. Genome Res. 1997, 7: 986-995. Lennartsson A, Ekwall K: Histone modification patterns and epigenetic codes. Biochim Biophys Acta. 2009, 1790: 863-868. 10.1016/j.bbagen.2008.12.006. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R: Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA. 2010, 107: 21931-21936. 10.1073/pnas.1016071107. Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J: A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011, 470: 279-283. 10.1038/nature09692. Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA: Core transcriptional regulatory circuitry in human embryonic stem cells. Cell. 2005, 122: 947-956. 10.1016/j.cell.2005.08.020. Chambers I, Smith A: Self-renewal of teratocarcinoma and embryonic stem cells. Oncogene. 2004, 23: 7150-7160. 10.1038/sj.onc.1207930. Kim J, Woo AJ, Chu J, Snow JW, Fujiwara Y, Kim CG, Cantor AB, Orkin SH: A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell. 2010, 143: 313-324. 10.1016/j.cell.2010.09.010. Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA: c-Myc regulates transcriptional pause release. Cell. 2010, 141: 432-445. 10.1016/j.cell.2010.03.030. Ling G, Sugathan A, Mazor T, Fraenkel E, Waxman DJ: Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. Mol Cell Biol. 2010, 30: 5531-5544. 10.1128/MCB.00601-10. Zhang Y, Laz EV, Waxman DJ: Dynamic, sex-differential STAT5 and BCL6 binding to sex-biased, growth hormone-regulated genes in adult mouse liver. Mol Cell Biol. 2012, 32: 880-896. 10.1128/MCB.06312-11. Jiang H, Shukla A, Wang X, Chen WY, Bernstein BE, Roeder RG: Role for Dpy-30 in ES cell-fate specification by regulation of H3K4 methylation within bivalent domains. Cell. 2011, 144: 513-525. 10.1016/j.cell.2011.01.020. Bernstein BE, Meissner A, Lander ES: The mammalian epigenome. Cell. 2007, 128: 669-681. 10.1016/j.cell.2007.01.033. Ernst J, Kellis M: Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010, 28: 817-825. 10.1038/nbt.1662. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE: Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011, 473: 43-49. 10.1038/nature09906. Larson JL, Yuan GC: Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. BMC Bioinformatics. 2010, 11: 557-10.1186/1471-2105-11-557. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ: Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011, 471: 480-485. 10.1038/nature09725. Negre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Morrison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, et al: A cis-regulatory map of the Drosophila genome. Nature. 2011, 471: 527-531. 10.1038/nature09990. McKean JW: Robust analysis of linear models. Stat Sci. 2004, 19: 562-570. 10.1214/088342304000000549. ENCODE ChIP-Seq data describing histone modifications. [http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/] ENCODE ChIP-Seq data describing transcription factor binding. [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/] Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH: Unlocking the secrets of the genome. Nature. 2009, 459: 927-930. 10.1038/459927a. Brodsky AS, Meyer CA, Swinburne IA, Hall G, Keenan BJ, Liu XS, Fox EA, Silver PA: Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol. 2005, 6: R64-10.1186/gb-2005-6-8-r64. Pellegrini M, Cheng JC, Voutila J, Judelson D, Taylor J, Nelson SF, Sakamoto KM: Expression profile of CREB knockdown in myeloid leukemia cells. BMC Cancer. 2008, 8: 264-10.1186/1471-2407-8-264. Li C: Automating dChip: toward reproducible sharing of microarray data analysis. BMC Bioinformatics. 2008, 9: 231-10.1186/1471-2105-9-231. Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA. 2001, 98: 5116-5121. 10.1073/pnas.091062498. Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B: JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2004, 32: D91-94. 10.1093/nar/gkh012. Liu Y, Shao Z, Yuan GC: Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics. 2010, 96: 17-26. 10.1016/j.ygeno.2010.03.012. Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET: Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet. 2007, 3: e87-10.1371/journal.pgen.0030087.