基于ChIP-Seq数据分析前列腺癌中雄激素受体相关基因
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摘要
雄激素受体（AR）是属于核受体超家族中一种非常重要的类固醇受体。在细胞内AR的主要功能是作为转录因子与DNA结合调控基因表达。虽然雄激素受体在前列腺癌治疗中扮演重要角色，但是它的作用机制还不是很清楚。本文利用前列腺癌相关的ChIP-Seq数据，对雄激素受体在基因组上的结合位点做了生物信息学的注释和分析，以期找到在前列腺癌中AR相关的生物调控通路。对来自于三种前列腺癌细胞系的6组数据的分析发现，AR在基因组上的结合区大部分落在内含子上，平均比例约为83.46%;而其它的16.54%则分别落在启动子，增强子，外显子，3’UTR区，5’UTR区，转录起始位点下游区和基因间区。查找AR结合的启动子序列发现了4条新的AR结合序列的motif。对AR调控的基因功能富集分析得到了21个GeneOntology条目，1条KEGG通路和26条GeneGo通路。分别对基因和富集通路之间的重复性分析验证了不同数据集的分子特征在系统水平上的相似性高于基因水平上的相似性。对26条GeneGo通路的文献报道验证发现其中5条被之前的研究报道过，其它的21条为新通路，并通过前列腺癌相关的基因表达数据和microRNA数据验证了它们与前列腺癌的相关性。
As a member of Nuclear Receptor Superfamily, Androgen Receptor (AR) is animportant steroid receptor. The most important role of AR is acting as a DNA-bindingtranscript factor which regulates gene expression. AR is an important therapy target ofprostate cancer, but the mechanism of action is still unclear. In this study, we annotatedthose AR binding gens in the genome by ChIP-Seq data, and tried to discover some novelbiological pathways in prostate cancer. Analysis on6ChIP-Seq datasets from threeprostate cancer cell lines indicated that83.46%of AR binding sites were located in theintron region; the other16.54%located in the promoter, enhancer, exon,3’UTR,5’UTR,downstream and intergenic region, respectively. In the promoter region we found4novelAR binding motifs. The enrichment analysis of AR-binding genes identified21GeneOntology terms，1KEGG pathway and26GeneGo pathways. The pair-wise overlapanalysis for AR binding genes and AR related pathways verified the hypothesis that thesignificant signatures of different data sets are more similar at pathway level than at genelevel. Literature validation of26GeneGo pathways demonstrated that5pathways had beenreported previously, the rest21are novel pathways. We also verified association of thesenovel pathways and prostate cancer by prostate cancer related gene expression data andmicroRNA data.
As a member of Nuclear Receptor Superfamily, Androgen Receptor (AR) is animportant steroid receptor. The most important role of AR is acting as a DNA-bindingtranscript factor which regulates gene expression. AR is an important therapy target ofprostate cancer, but the mechanism of action is still unclear. In this study, we annotatedthose AR binding gens in the genome by ChIP-Seq data, and tried to discover some novelbiological pathways in prostate cancer. Analysis on6ChIP-Seq datasets from threeprostate cancer cell lines indicated that83.46%of AR binding sites were located in theintron region; the other16.54%located in the promoter, enhancer, exon,3’UTR,5’UTR,downstream and intergenic region, respectively. In the promoter region we found4novelAR binding motifs. The enrichment analysis of AR-binding genes identified21GeneOntology terms，1KEGG pathway and26GeneGo pathways. The pair-wise overlapanalysis for AR binding genes and AR related pathways verified the hypothesis that thesignificant signatures of different data sets are more similar at pathway level than at genelevel. Literature validation of26GeneGo pathways demonstrated that5pathways had beenreported previously, the rest21are novel pathways. We also verified association of thesenovel pathways and prostate cancer by prostate cancer related gene expression data andmicroRNA data.
引文
1. Mooradian, A.D., J.E. Morley, and S.G. Korenman, Biological actions of androgens.Endocr Rev,1987.8(1): p.1-28.
2. Heinlein, C.A. and C. Chang, The roles of androgen receptors and androgen-bindingproteins in nongenomic androgen actions. Mol Endocrinol,2002.16(10): p.2181-7.
3. Trapman, J., et al., Cloning, structure and expression of a cDNA encoding the humanandrogen receptor. Biochem Biophys Res Commun,1988.153(1): p.241-8.
4. Heemers, H.V. and D.J. Tindall, Androgen receptor (AR) coregulators: a diversity offunctions converging on and regulating the AR transcriptional complex. Endocr Rev,2007.28(7): p.778-808.
5. Pandini, G., et al., Androgens up-regulate the insulin-like growth factor-I receptor inprostate cancer cells. Cancer Res,2005.65(5): p.1849-57.
6. Lin, H.K., et al., Akt suppresses androgen-induced apoptosis by phosphorylating andinhibiting androgen receptor. Proc Natl Acad Sci U S A,2001.98(13): p.7200-5.
7. Park, J.J., et al., Breast cancer susceptibility gene1(BRCAI) is a coactivator of theandrogen receptor. Cancer Res,2000.60(21): p.5946-9.
8. Niki, T., et al., DJBP: a novel DJ-1-binding protein, negatively regulates the androgenreceptor by recruiting histone deacetylase complex, and DJ-1antagonizes thisinhibition by abrogation of this complex. Mol Cancer Res,2003.1(4): p.247-61.
9. Gaughan, L., et al., Tip60and histone deacetylase1regulate androgen receptoractivity through changes to the acetylation status of the receptor. J Biol Chem,2002.277(29): p.25904-13.
10. Kotaja, N., et al., ARIP3(androgen receptor-interacting protein3) and other PIAS(protein inhibitor of activated STAT) proteins differ in their ability to modulate steroidreceptor-dependent transcriptional activation. Mol Endocrinol,2000.14(12): p.1986-2000.
11. Heinlein, C.A. and C. Chang, Androgen receptor in prostate cancer. Endocr Rev,2004.25(2): p.276-308.
12. Chng, K.R. and E. Cheung, Sequencing the transcriptional network of androgenreceptor in prostate cancer. Cancer Lett,2012.
13. Massie, C.E. and I.G. Mills, Global identification of androgen response elements.Methods Mol Biol,2011.776: p.255-73.
14. Lin, B., et al., Integrated expression profiling and ChIP-seq analyses of the growthinhibition response program of the androgen receptor. PLoS One,2009.4(8): p. e6589.
15. Rickman, D.S., et al., ERG cooperates with androgen receptor in regulating trefoilfactor3in prostate cancer disease progression. Neoplasia,2010.12(12): p.1031-40.
16. Tan, P.Y., et al., Integration of regulatory networks by NKX3-1promotes androgen-dependent prostate cancer survival. Mol Cell Biol,2012.32(2): p.399-414.
17. Guseva, N.V., et al., Inhibition of p53expression modifies the specificity of chromatinbinding by the androgen receptor. Oncotarget,2012.3(2): p.183-94.
18. Urbanucci, A., et al., Overexpression of androgen receptor enhances the binding of thereceptor to the chromatin in prostate cancer. Oncogene,2012.31(17): p.2153-63.
19. Tewari, A.K., et al., Chromatin accessibility reveals insights into androgen receptoractivation and transcriptional specificity. Genome Biol,2012.13(10): p. R88.
20. Chen, H., et al., Regulation of hormone-induced histone hyperacetylation and geneactivation via acetylation of an acetylase. Cell,1999.98(5): p.675-86.
21. Shang, Y., et al., Cofactor dynamics and sufficiency in estrogen receptor-regulatedtranscription. Cell,2000.103(6): p.843-52.
22. Park, P.J., ChIP-seq: advantages and challenges of a maturing technology. Nat RevGenet,2009.10(10): p.669-80.
23. Li, M.-L., W. Wang, and Z.-H. Lu, Genomic analysis of DNA-protein interaction bychromatin immunoprecipitation. Hereditas (Beijing),2010.32(3): p.219-228.
24. Schmidt, D., et al., ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods,2009.48(3): p.240-8.
25. Fejes, A.P., et al., FindPeaks3.1: a tool for identifying areas of enrichment frommassively parallel short-read sequencing technology. Bioinformatics,2008.24(15): p.1729-1730.
26. Rozowsky, J., et al., PeakSeq enables systematic scoring of ChIP-seq experimentsrelative to controls. Nat Biotechnol,2009.27(1): p.66-75.
27. Jothi, R., et al., Genome-wide identification of in vivo protein-DNA binding sites fromChIP-Seq data. Nucleic Acids Research,2008.36(16): p.5221-5231.
28. Albert, GeneTrack--a genomic data processing and visualization framework.Bioinformatics,2008
29. Boyle, A.P., et al., F-Seq: a feature density estimator for high-throughput sequencetags. Bioinformatics,2008.24(21): p.2537-2538.
30. Valouev, A., et al., Genome-wide analysis of transcription factor binding sites basedon ChIP-Seq data. Nature Methods,2008.5(9): p.829-834.
31. Zhang, Y., et al., Model-based Analysis of ChIP-Seq. Genome Biology,2008.9(9): p.R137.
32. Xu, H. and W.K. Sung, Identifying differential histone modification sites from ChIP-seq data. Methods Mol Biol,2012.802: p.293-303.
33. Ji, H., et al., An integrated software system for analyzing ChIP-chip and ChIP-seqdata. Nature Biotechnology,2008.26(11): p.1293-1300.
34. Qin, Z.S., et al., HPeak: an HMM-based algorithm for defining read-enriched regionsin ChIP-Seq data. BMC Bioinformatics,2010.11: p.369.
35. Zang, C., et al., A clustering approach for identification of enriched domains fromhistone modification ChIP-Seq data. Bioinformatics,2009.25(15): p.1952-1958.
36. Johnson, D.S., et al., Genome-Wide Mapping of in Vivo Protein-DNA Interactions.Science,2007.316(5830): p.1497-1502.
37. Laajala, T.D., et al., A practical comparison of methods for detecting transcriptionfactor binding sites in ChIP-seq experiments. BMC Genomics,2009.10: p.618.
38. Cai, C., et al., Androgen receptor gene expression in prostate cancer is directlysuppressed by the androgen receptor through recruitment of lysine-specificdemethylase1. Cancer Cell,2011.20(4): p.457-71.
39. Massie, C.E., et al., The androgen receptor fuels prostate cancer by regulating centralmetabolism and biosynthesis. EMBO J,2011.30(13): p.2719-33.
40. Choudhary, V., et al., Novel role of androgens in mitochondrial fission and apoptosis.Mol Cancer Res,2011.9(8): p.1067-77.
41. Sahu, B., et al., Dual role of FoxA1in androgen receptor binding to chromatin,androgen signalling and prostate cancer. EMBO J,2011.30(19): p.3962-76.
42. Quinlan, A.R. and I.M. Hall, BEDTools: a flexible suite of utilities for comparinggenomic features. Bioinformatics,2010.26(6): p.841-842.
43. Hinrichs, A.S., et al., The UCSC Genome Browser Database: update2006. NucleicAcids Res,2006.34(Database issue): p. D590-8.
44. Salmon-Divon, M., et al., PeakAnalyzer: Genome-wide annotation of chromatinbinding and modification loci. BMC Bioinformatics,2010.11(1): p.415.
45. Thomas-Chollier, M., et al., RSAT peak-motifs: motif analysis in full-size ChIP-seqdatasets. Nucleic Acids Res,2012.40(4): p. e31.
46. Bailey, T.L., et al., MEME SUITE: tools for motif discovery and searching. NucleicAcids Res,2009.37(Web Server issue): p. W202-8.
47. Portales-Casamar, E., et al., JASPAR2010: the greatly expanded open-access databaseof transcription factor binding profiles. Nucleic Acids Res,2010.38(Database issue):p. D105-10.
48. Wang, Y., et al., Identifying novel prostate cancer associated pathways based onintegrative microarray data analysis. Comput Biol Chem,2011.35(3): p.151-8.
49. Tang, Y., et al., A practical comparison and application of heterogeneity consideredoutlier detection algorithms for prostate cancer driven microRNA expression data. Tobe submitted.
50. Wilson, A.C., et al., Leuprolide acetate: a drug of diverse clinical applications. ExpertOpin Investig Drugs,2007.16(11): p.1851-63.
51.丁红梅,邵根宝,徐银学,内含子与基因表达调控. Animal husbandry&VeterinaryMedicine,2006.38(3): p.8.
2. Heinlein, C.A. and C. Chang, The roles of androgen receptors and androgen-bindingproteins in nongenomic androgen actions. Mol Endocrinol,2002.16(10): p.2181-7.
3. Trapman, J., et al., Cloning, structure and expression of a cDNA encoding the humanandrogen receptor. Biochem Biophys Res Commun,1988.153(1): p.241-8.
4. Heemers, H.V. and D.J. Tindall, Androgen receptor (AR) coregulators: a diversity offunctions converging on and regulating the AR transcriptional complex. Endocr Rev,2007.28(7): p.778-808.
5. Pandini, G., et al., Androgens up-regulate the insulin-like growth factor-I receptor inprostate cancer cells. Cancer Res,2005.65(5): p.1849-57.
6. Lin, H.K., et al., Akt suppresses androgen-induced apoptosis by phosphorylating andinhibiting androgen receptor. Proc Natl Acad Sci U S A,2001.98(13): p.7200-5.
7. Park, J.J., et al., Breast cancer susceptibility gene1(BRCAI) is a coactivator of theandrogen receptor. Cancer Res,2000.60(21): p.5946-9.
8. Niki, T., et al., DJBP: a novel DJ-1-binding protein, negatively regulates the androgenreceptor by recruiting histone deacetylase complex, and DJ-1antagonizes thisinhibition by abrogation of this complex. Mol Cancer Res,2003.1(4): p.247-61.
9. Gaughan, L., et al., Tip60and histone deacetylase1regulate androgen receptoractivity through changes to the acetylation status of the receptor. J Biol Chem,2002.277(29): p.25904-13.
10. Kotaja, N., et al., ARIP3(androgen receptor-interacting protein3) and other PIAS(protein inhibitor of activated STAT) proteins differ in their ability to modulate steroidreceptor-dependent transcriptional activation. Mol Endocrinol,2000.14(12): p.1986-2000.
11. Heinlein, C.A. and C. Chang, Androgen receptor in prostate cancer. Endocr Rev,2004.25(2): p.276-308.
12. Chng, K.R. and E. Cheung, Sequencing the transcriptional network of androgenreceptor in prostate cancer. Cancer Lett,2012.
13. Massie, C.E. and I.G. Mills, Global identification of androgen response elements.Methods Mol Biol,2011.776: p.255-73.
14. Lin, B., et al., Integrated expression profiling and ChIP-seq analyses of the growthinhibition response program of the androgen receptor. PLoS One,2009.4(8): p. e6589.
15. Rickman, D.S., et al., ERG cooperates with androgen receptor in regulating trefoilfactor3in prostate cancer disease progression. Neoplasia,2010.12(12): p.1031-40.
16. Tan, P.Y., et al., Integration of regulatory networks by NKX3-1promotes androgen-dependent prostate cancer survival. Mol Cell Biol,2012.32(2): p.399-414.
17. Guseva, N.V., et al., Inhibition of p53expression modifies the specificity of chromatinbinding by the androgen receptor. Oncotarget,2012.3(2): p.183-94.
18. Urbanucci, A., et al., Overexpression of androgen receptor enhances the binding of thereceptor to the chromatin in prostate cancer. Oncogene,2012.31(17): p.2153-63.
19. Tewari, A.K., et al., Chromatin accessibility reveals insights into androgen receptoractivation and transcriptional specificity. Genome Biol,2012.13(10): p. R88.
20. Chen, H., et al., Regulation of hormone-induced histone hyperacetylation and geneactivation via acetylation of an acetylase. Cell,1999.98(5): p.675-86.
21. Shang, Y., et al., Cofactor dynamics and sufficiency in estrogen receptor-regulatedtranscription. Cell,2000.103(6): p.843-52.
22. Park, P.J., ChIP-seq: advantages and challenges of a maturing technology. Nat RevGenet,2009.10(10): p.669-80.
23. Li, M.-L., W. Wang, and Z.-H. Lu, Genomic analysis of DNA-protein interaction bychromatin immunoprecipitation. Hereditas (Beijing),2010.32(3): p.219-228.
24. Schmidt, D., et al., ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods,2009.48(3): p.240-8.
25. Fejes, A.P., et al., FindPeaks3.1: a tool for identifying areas of enrichment frommassively parallel short-read sequencing technology. Bioinformatics,2008.24(15): p.1729-1730.
26. Rozowsky, J., et al., PeakSeq enables systematic scoring of ChIP-seq experimentsrelative to controls. Nat Biotechnol,2009.27(1): p.66-75.
27. Jothi, R., et al., Genome-wide identification of in vivo protein-DNA binding sites fromChIP-Seq data. Nucleic Acids Research,2008.36(16): p.5221-5231.
28. Albert, GeneTrack--a genomic data processing and visualization framework.Bioinformatics,2008
29. Boyle, A.P., et al., F-Seq: a feature density estimator for high-throughput sequencetags. Bioinformatics,2008.24(21): p.2537-2538.
30. Valouev, A., et al., Genome-wide analysis of transcription factor binding sites basedon ChIP-Seq data. Nature Methods,2008.5(9): p.829-834.
31. Zhang, Y., et al., Model-based Analysis of ChIP-Seq. Genome Biology,2008.9(9): p.R137.
32. Xu, H. and W.K. Sung, Identifying differential histone modification sites from ChIP-seq data. Methods Mol Biol,2012.802: p.293-303.
33. Ji, H., et al., An integrated software system for analyzing ChIP-chip and ChIP-seqdata. Nature Biotechnology,2008.26(11): p.1293-1300.
34. Qin, Z.S., et al., HPeak: an HMM-based algorithm for defining read-enriched regionsin ChIP-Seq data. BMC Bioinformatics,2010.11: p.369.
35. Zang, C., et al., A clustering approach for identification of enriched domains fromhistone modification ChIP-Seq data. Bioinformatics,2009.25(15): p.1952-1958.
36. Johnson, D.S., et al., Genome-Wide Mapping of in Vivo Protein-DNA Interactions.Science,2007.316(5830): p.1497-1502.
37. Laajala, T.D., et al., A practical comparison of methods for detecting transcriptionfactor binding sites in ChIP-seq experiments. BMC Genomics,2009.10: p.618.
38. Cai, C., et al., Androgen receptor gene expression in prostate cancer is directlysuppressed by the androgen receptor through recruitment of lysine-specificdemethylase1. Cancer Cell,2011.20(4): p.457-71.
39. Massie, C.E., et al., The androgen receptor fuels prostate cancer by regulating centralmetabolism and biosynthesis. EMBO J,2011.30(13): p.2719-33.
40. Choudhary, V., et al., Novel role of androgens in mitochondrial fission and apoptosis.Mol Cancer Res,2011.9(8): p.1067-77.
41. Sahu, B., et al., Dual role of FoxA1in androgen receptor binding to chromatin,androgen signalling and prostate cancer. EMBO J,2011.30(19): p.3962-76.
42. Quinlan, A.R. and I.M. Hall, BEDTools: a flexible suite of utilities for comparinggenomic features. Bioinformatics,2010.26(6): p.841-842.
43. Hinrichs, A.S., et al., The UCSC Genome Browser Database: update2006. NucleicAcids Res,2006.34(Database issue): p. D590-8.
44. Salmon-Divon, M., et al., PeakAnalyzer: Genome-wide annotation of chromatinbinding and modification loci. BMC Bioinformatics,2010.11(1): p.415.
45. Thomas-Chollier, M., et al., RSAT peak-motifs: motif analysis in full-size ChIP-seqdatasets. Nucleic Acids Res,2012.40(4): p. e31.
46. Bailey, T.L., et al., MEME SUITE: tools for motif discovery and searching. NucleicAcids Res,2009.37(Web Server issue): p. W202-8.
47. Portales-Casamar, E., et al., JASPAR2010: the greatly expanded open-access databaseof transcription factor binding profiles. Nucleic Acids Res,2010.38(Database issue):p. D105-10.
48. Wang, Y., et al., Identifying novel prostate cancer associated pathways based onintegrative microarray data analysis. Comput Biol Chem,2011.35(3): p.151-8.
49. Tang, Y., et al., A practical comparison and application of heterogeneity consideredoutlier detection algorithms for prostate cancer driven microRNA expression data. Tobe submitted.
50. Wilson, A.C., et al., Leuprolide acetate: a drug of diverse clinical applications. ExpertOpin Investig Drugs,2007.16(11): p.1851-63.
51.丁红梅,邵根宝,徐银学,内含子与基因表达调控. Animal husbandry&VeterinaryMedicine,2006.38(3): p.8.