蛋白質轉譯後修飾是蛋白質生物合成的較後步驟。被修飾後的轉錄因子如何調控基因體、其與疾病相關性，是表觀遺傳學(epigenetics)領域的重要研究課題。利用次世代定序技術可以得到同一時間點被修飾過的多種轉錄因子如何與染色體作用，但卻無法得知被修飾的轉錄因子為何。本研究提供一分析次世代定序序列資料的平台，可預測潛在被修飾的轉錄因子為何，並且利用不同時間點序列資料比對分析，推測被修飾轉錄因子的動態變化。

SUMO (small ubiquitin-related modifier) was discovered to be a reversible post-translational protein modifier. SUMOylation is a highly dynamic process and its outcomes are extremely diverse. Chromatin immunoprecipitation (ChIP) in combination with high-throughput sequencing (ChIP-seq) is being applied as a gold standard when studying the genome-wide binding sites of transcription factor (TFs). This has greatly improved our understanding of protein-DNA interactions on a genomic-wide scale. However, current ChIP-seq peak calling tools are not sufficiently sensitive and are unable to simultaneously identify post-translational modified TFs based on ChIP-seq analysis; this is largely due to the wide-spread presence of multiple modified TFs. Using SUMO modification as an example; we propose a methodology that analyses SUMO ChIP-seq patterns and predicts related TFs. Our analysis uses three peak calling tools. The fusion of these different tools increases the precision of the peak calling results. TFBS annotation method is able to predict potential SUMOylated TFs. Here, we offer a new approach that enhances ChIP-seq data analysis and allows the identification of multiple SUMOylated TF binding sites simultaneously.

Publication List
 Chia-Yang Cheng, Pei-Ching Chang, Campbell Mel, Yi-Cheng Yang, Hung-Wei Hsu, Chia-Han Chu, Chiu-Lan Huang, Shi-Mei Lai, Clifford G Tepper and Hsing-Jien Kung: The chromatin modification by SUMO-2/3 but not SUMO-1 mediates the epigenetic silencing of key immune-related genes during Kaposi's sarcoma associated herpesvirus reactivation. BMC Genomics
 Chia-Yang Cheng, Chia-Han Chu, Fang-Rong Hsu, Chung Yi Tang, Wen-Ching Wang, Hsing-Jien Kung, Pei-Ching Chang: An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example. BMC Genomics
Reference
1. Geiss-Friedlander R, Melchior F: Concepts in sumoylation: a decade on. Nature reviews Molecular cell biology 2007, 8(12):947-956.
2. Tirard M, Almeida OF, Hutzler P, Melchior F, Michaelidis TM: Sumoylation and proteasomal activity determine the transactivation properties of the mineralocorticoid receptor. Molecular and cellular endocrinology 2007, 268(1-2):20-29.
3. Oshima M, Mimura J, Sekine H, Okawa H, Fujii-Kuriyama Y: SUMO modification regulates the transcriptional repressor function of aryl hydrocarbon receptor repressor. The Journal of biological chemistry 2009, 284(17):11017-11026.
4. Hay RT: SUMO: a history of modification. Molecular cell 2005, 18(1):1-12.
5. Saitoh H, Hinchey J: Functional heterogeneity of small ubiquitin-related protein modifiers SUMO-1 versus SUMO-2/3. The Journal of biological chemistry 2000, 275(9):6252-6258.
6. Rosas-Acosta G, Russell WK, Deyrieux A, Russell DH, Wilson VG: A universal strategy for proteomic studies of SUMO and other ubiquitin-like modifiers. Molecular & cellular proteomics : MCP 2005, 4(1):56-72.
7. Garee JP, Meyer R, Oesterreich S: Co-repressor activity of scaffold attachment factor B1 requires sumoylation. Biochemical and biophysical research communications 2011, 408(4):516-522.
8. Bettermann K, Benesch M, Weis S, Haybaeck J: SUMOylation in carcinogenesis. Cancer letters 2011.
9. Hoffman BG, Jones SJ: Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. The Journal of endocrinology 2009, 201(1):1-13.
10. Li H, Durbin R: Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26(5):589-595.
11. 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. Nature biotechnology 2009, 27(1):66-75.
12. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W et al: Model-based analysis of ChIP-Seq (MACS). Genome biology 2008, 9(9):R137.
13. Kharchenko PV, Tolstorukov MY, Park PJ: Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nature biotechnology 2008, 26(12):1351-1359.
14. Whitington T, Frith MC, Johnson J, Bailey TL: Inferring transcription factor complexes from ChIP-seq data. Nucleic acids research 2011, 39(15):e98.
15. Liu GE, Weirauch MT, Van Tassell CP, Li RW, Sonstegard TS, Matukumalli LK, Connor EE, Hanson RW, Yang J: Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. Genomics, proteomics & bioinformatics / Beijing Genomics Institute 2008, 6(3-4):129-143.
16. Wasserman WW, Sandelin A: Applied bioinformatics for the identification of regulatory elements. Nature reviews Genetics 2004, 5(4):276-287.
17. Pepke S, Wold B, Mortazavi A: Computation for ChIP-seq and RNA-seq studies. Nature methods 2009, 6(11 Suppl):S22-32.
18. Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL: A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC genomics 2009, 10.
19. Wilbanks EG, Facciotti MT: Evaluation of algorithm performance in ChIP-seq peak detection. PloS one 2010, 5(7):e11471.
20. Machanick P, Bailey TL: MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 2011, 27(12):1696-1697.
21. Li L: GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. Journal of computational biology : a journal of computational molecular cell biology 2009, 16(2):317-329.
22. Bardet AF, He Q, Zeitlinger J, Stark A: A computational pipeline for comparative ChIP-seq analyses. Nature protocols 2012, 7(1):45-61.
23. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S et al: Ensembl 2012. Nucleic acids research 2012, 40(Database issue):D84-90.
24. Davies L, Gather, U: The identification of multiple outliers. Journal of the American Statistical Association 1993(88).
25. Perarson RK: Outliers in process modeling and identification. IEEE Transactions On Control Systems Technology 2002, 10.
26. Davies L, Gather U: The Identification of Multiple Outliers. Journal of the American Statistical Association 1993, 88(423):782-792.
27. Yang SH, Jaffray E, Hay RT, Sharrocks AD: Dynamic interplay of the SUMO and ERK pathways in regulating Elk-1 transcriptional activity. Molecular cell 2003, 12(1):63-74.
28. Ryan CM, Kindle KB, Collins HM, Heery DM: SUMOylation regulates the nuclear mobility of CREB binding protein and its association with nuclear bodies in live cells. Biochemical and biophysical research communications 2010, 391(1):1136-1141.
29. Ji Z, Degerny C, Vintonenko N, Deheuninck J, Foveau B, Leroy C, Coll J, Tulasne D, Baert JL, Fafeur V: Regulation of the Ets-1 transcription factor by sumoylation and ubiquitinylation. Oncogene 2007, 26(3):395-406.
30. Spengler ML, Brattain MG: Sumoylation inhibits cleavage of Sp1 N-terminal negative regulatory domain and inhibits Sp1-dependent transcription. The Journal of biological chemistry 2006, 281(9):5567-5574.
31. Begitt A, Droescher M, Knobeloch KP, Vinkemeier U: SUMO conjugation of STAT1 protects cells from hyperresponsiveness to IFNgamma. Blood 2011, 118(4):1002-1007.
32. Hamard PJ, Boyer-Guittaut M, Camuzeaux B, Dujardin D, Hauss C, Oelgeschlager T, Vigneron M, Kedinger C, Chatton B: Sumoylation delays the ATF7 transcription factor subcellular localization and inhibits its transcriptional activity. Nucleic acids research 2007, 35(4):1134-1144.
33. Lu D, Han C, Wu T: Microsomal prostaglandin E synthase-1 promotes hepatocarcinogenesis through activation of a novel EGR1/beta-catenin signaling axis. Oncogene 2012, 31(7):842-857.
34. Iwasaki K, Hailemariam K, Tsuji Y: PIAS3 interacts with ATF1 and regulates the human ferritin H gene through an antioxidant-responsive element. The Journal of biological chemistry 2007, 282(31):22335-22343.
35. Lomeli H, Vazquez M: Emerging roles of the SUMO pathway in development. Cellular and molecular life sciences : CMLS 2011, 68(24):4045-4064.
36. Nacerddine K, Lehembre F, Bhaumik M, Artus J, Cohen-Tannoudji M, Babinet C, Pandolfi PP, Dejean A: The SUMO pathway is essential for nuclear integrity and chromosome segregation in mice. Developmental cell 2005, 9(6):769-779.
37. Prudden J, Perry JJ, Nie M, Vashisht AA, Arvai AS, Hitomi C, Guenther G, Wohlschlegel JA, Tainer JA, Boddy MN: DNA repair and global sumoylation are regulated by distinct Ubc9 noncovalent complexes. Molecular and cellular biology 2011, 31(11):2299-2310.
38. Rosonina E, Duncan SM, Manley JL: SUMO functions in constitutive transcription and during activation of inducible genes in yeast. Genes & development 2010, 24(12):1242-1252.
39. Makhnevych T, Sydorskyy Y, Xin X, Srikumar T, Vizeacoumar FJ, Jeram SM, Li Z, Bahr S, Andrews BJ, Boone C et al: Global map of SUMO function revealed by protein-protein interaction and genetic networks. Molecular cell 2009, 33(1):124-135.
40. Tatham MH, Jaffray E, Vaughan OA, Desterro JM, Botting CH, Naismith JH, Hay RT: Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9. The Journal of biological chemistry 2001, 276(38):35368-35374.
41. Matic I, van Hagen M, Schimmel J, Macek B, Ogg SC, Tatham MH, Hay RT, Lamond AI, Mann M, Vertegaal AC: In vivo identification of human small ubiquitin-like modifier polymerization sites by high accuracy mass spectrometry and an in vitro to in vivo strategy. Molecular & cellular proteomics : MCP 2008, 7(1):132-144.
42. Ayaydin F, Dasso M: Distinct in vivo dynamics of vertebrate SUMO paralogues. Molecular biology of the cell 2004, 15(12):5208-5218.
43. Kolli N, Mikolajczyk J, Drag M, Mukhopadhyay D, Moffatt N, Dasso M, Salvesen G, Wilkinson KD: Distribution and paralogue specificity of mammalian deSUMOylating enzymes. The Biochemical journal 2010, 430(2):335-344.
44. Lin DY, Huang YS, Jeng JC, Kuo HY, Chang CC, Chao TT, Ho CC, Chen YC, Lin TP, Fang HI et al: Role of SUMO-interacting motif in Daxx SUMO modification, subnuclear localization, and repression of sumoylated transcription factors. Molecular cell 2006, 24(3):341-354.
45. Adamson AL, Kenney S: Epstein-barr virus immediate-early protein BZLF1 is SUMO-1 modified and disrupts promyelocytic leukemia bodies. Journal of virology 2001, 75(5):2388-2399.
46. Chang LK, Lee YH, Cheng TS, Hong YR, Lu PJ, Wang JJ, Wang WH, Kuo CW, Li SS, Liu ST: Post-translational modification of Rta of Epstein-Barr virus by SUMO-1. The Journal of biological chemistry 2004, 279(37):38803-38812.
47. Chang LK, Liu ST, Kuo CW, Wang WH, Chuang JY, Bianchi E, Hong YR: Enhancement of transactivation activity of Rta of Epstein-Barr virus by RanBPM. Journal of molecular biology 2008, 379(2):231-242.
48. Hagemeier SR, Dickerson SJ, Meng Q, Yu X, Mertz JE, Kenney SC: Sumoylation of the Epstein-Barr virus BZLF1 protein inhibits its transcriptional activity and is regulated by the virus-encoded protein kinase. Journal of virology 2010, 84(9):4383-4394.
49. Izumiya Y, Ellison TJ, Yeh ET, Jung JU, Luciw PA, Kung HJ: Kaposi's sarcoma-associated herpesvirus K-bZIP represses gene transcription via SUMO modification. Journal of virology 2005, 79(15):9912-9925.
50. Wimmer P, Schreiner S, Dobner T: Human pathogens and the host cell SUMOylation system. Journal of virology 2012, 86(2):642-654.
51. Chang PC, Izumiya Y, Wu CY, Fitzgerald LD, Campbell M, Ellison TJ, Lam KS, Luciw PA, Kung HJ: Kaposi's sarcoma-associated herpesvirus (KSHV) encodes a SUMO E3 ligase that is SIM-dependent and SUMO-2/3-specific. The Journal of biological chemistry 2010, 285(8):5266-5273.
52. Lyst MJ, Stancheva I: A role for SUMO modification in transcriptional repression and activation. Biochemical Society transactions 2007, 35(Pt 6):1389-1392.
53. Liu HW, Zhang J, Heine GF, Arora M, Gulcin Ozer H, Onti-Srinivasan R, Huang K, Parvin JD: Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes. Nucleic acids research 2012, 40(20):10172-10186.