潜在的胚胎干细胞自我更新与多能性的调控基因的鉴定: 基于随机森林算法

Identification of potential regulatory genes for embryonic stem cell self-renewal and pluripotency by random forest

曾彭归航 , ^1, * 唐秀晓 , ² 吴庭芩 , ² 田奇 , ² 李茫茫 , ^*, ¹ and 丁俊军 ^*, ²

曾彭归航

南方医科大学基础医学院, 广东广州 510515, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, China

Find articles by 曾彭归航

唐秀晓

中山大学中山医学院, 广东广州 510080, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China

Find articles by 唐秀晓

吴庭芩

中山大学中山医学院, 广东广州 510080, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China

Find articles by 吴庭芩

田奇

中山大学中山医学院, 广东广州 510080, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China

Find articles by 田奇

李茫茫

南方医科大学基础医学院, 广东广州 510515, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, China

Find articles by 李茫茫

丁俊军

中山大学中山医学院, 广东广州 510080, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China 南方医科大学基础医学院, 广东广州 510515, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, China 中山大学中山医学院, 广东广州 510080, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China moc.qq@ehcues

Funding Statement

国家重点研发计划（2017YFA0102800，2016YFA0101700）；国家自然科学基金（31970811，31771639，32170798，31671420，81602482）；广州再生医学与健康广东省实验室前沿研究项目（2018GZR110105007）；广东省引进创新创业团队项目（2016ZT06S029）

Supported by National Natural Science Foundation of China (31970811, 31771639, 32170798, 31671420, 81602482)

References

1. De Luca M, Aiuti A, Cossu G, et al Advances in stem cell research and therapeutic development. Nat Cell Biol. 2019; 21 (7):801–11. doi: 10.1038/s41556-019-0344-z.
[De Luca M, Aiuti A, Cossu G, et al. Advances in stem cell research and therapeutic development[J]. Nat Cell Biol, 2019, 21(7): 801-11.] [ PubMed ] [ CrossRef ] [ Google Scholar ]

2. Ivanova N, Dobrin R, Lu R, et al Dissecting self-renewal in stem cells with RNAinterference. Nature. 2006; 442 (7102):533–8. doi: 10.1038/nature04915.
[Ivanova N, Dobrin R, Lu R, et al. Dissecting self-renewal in stem cells with RNAinterference[J]. Nature, 2006, 442(7102): 533-8.] [ PubMed ] [ CrossRef ] [ Google Scholar ]

3. Hu G, Kim J, Xu Q, et al A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev. 2009; 23 (7):837–48. doi: 10.1101/gad.1769609.
[Hu G, Kim J, Xu Q, et al. A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal[J]. Genes Dev, 2009, 23(7): 837-48.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

4. Ding L, Paszkowski-Rogacz M, Nitzsche A, et al A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Cell Stem Cell. 2009; 4 (5):403–15. doi: 10.1016/j.stem.2009.03.009.
[Ding L, Paszkowski-Rogacz M, Nitzsche A, et al. A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity[J]. Cell Stem Cell, 2009, 4(5): 403-15.] [ PubMed ] [ CrossRef ] [ Google Scholar ]

5. Zhang JZ, Gao W, Yang HB, et al Screening for genes essential for mouse embryonic stem cell self-renewal using a subtractive RNA interference library. Stem Cells. 2006; 24 (12):2661–8. doi: 10.1634/stemcells.2006-0017.
[Zhang JZ, Gao W, Yang HB, et al. Screening for genes essential for mouse embryonic stem cell self-renewal using a subtractive RNA interference library[J]. Stem Cells, 2006, 24(12): 2661-8.] [ PubMed ] [ CrossRef ] [ Google Scholar ]

6. Xu H, Lemischka IR, Ma'ayan A SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst Biol. 2010; 4 :173. doi: 10.1186/1752-0509-4-173.
[Xu H, Lemischka IR, Ma'ayan A. SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells[J]. BMC Syst Biol, 2010, 4: 173.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

7. Scheubert L, Schmidt R, Repsilber D, et al Learning biomarkers of pluripotent stem cells in mouse. http://europepmc.org/abstract/med/21658760 . DNARes. 2011; 18 (4):233–51.
[Scheubert L, Schmidt R, Repsilber D, et al. Learning biomarkers of pluripotent stem cells in mouse[J]. DNARes, 2011, 18(4): 233-51.] [ PMC free article ] [ PubMed ] [ Google Scholar ]

8. Mandal SD, Saha S PluriPred: a Web server for predicting proteins involved in pluripotent network. J Biosci. 2016; 41 (4):743–50. doi: 10.1007/s12038-016-9649-2.
[Mandal SD, Saha S. PluriPred: a Web server for predicting proteins involved in pluripotent network[J]. J Biosci, 2016, 41(4): 743-50.] [ PubMed ] [ CrossRef ] [ Google Scholar ]

9. Weintraub AS, Li CH, Zamudio AV, et al YY1 is a structural regulator of enhancer-promoter loops. http://www.onacademic.com/detail/journal_1000040134570010_b5d9.html . Cell. 2017; 171 (7)
[Weintraub AS, Li CH, Zamudio AV, et al. YY1 is a structural regulator of enhancer-promoter loops[J]. Cell, 2017, 171(7): .] [ PMC free article ] [ PubMed ] [ Google Scholar ]

10. Heurtier V, Owens N, Gonzalez I, et al The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells. Nat Commun. 2019; 10 (1):1109. doi: 10.1038/s41467-019-09041-z.
[Heurtier V, Owens N, Gonzalez I, et al. The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells[J]. Nat Commun, 2019, 10(1): 1109.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

11. Mansour MR, Abraham BJ, Anders L, et al Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science. 2014; 346 (6215):1373–7. doi: 10.1126/science.1259037.
[Mansour MR, Abraham BJ, Anders L, et al. Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element[J]. Science, 2014, 346(6215): 1373-7.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

12. Whyte WA, Orlando DA, Hnisz D, et al Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013; 153 (2):307–19. doi: 10.1016/j.cell.2013.03.035. doi: 10.1016/j.cell.2013.03.035.
[Whyte WA, Orlando DA, Hnisz D, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes[J]. Cell, 2013, 153(2): 307-19.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ CrossRef ] [ Google Scholar ]

13. Buenrostro JD, Giresi PG, Zaba LC, et al Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013; 10 (12):1213–8. doi: 10.1038/nmeth.2688.
[Buenrostro JD, Giresi PG, Zaba LC, et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position[J]. Nat Methods, 2013, 10(12): 1213-8.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

14. Li D, Liu J, Yang X, et al Chromatin accessibility dynamics during iPSC reprogramming. Cell Stem Cell. 2017; 21 (6):819–33.e6. doi: 10.1016/j.stem.2017.10.012.
[Li D, Liu J, Yang X, et al. Chromatin accessibility dynamics during iPSC reprogramming[J]. Cell Stem Cell, 2017, 21(6): 819-33.e6.] [ PubMed ] [ CrossRef ] [ Google Scholar ]

15. Beagan JA, Duong MT, Titus KR, et al YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. Genome Res. 2017; 27 (7):1139–52. doi: 10.1101/gr.215160.116.
[Beagan JA, Duong MT, Titus KR, et al. YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment[J]. Genome Res, 2017, 27(7): 1139-52.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

16. Dekker J, Mirny L The 3D genome as moderator of chromosomal communication. Cell. 2016; 164 (6):1110–21. doi: 10.1016/j.cell.2016.02.007.
[Dekker J, Mirny L. The 3D genome as moderator of chromosomal communication[J]. Cell, 2016, 164(6): 1110-21.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

17. Wang J, Wu X, Wei C, et al YY1 positively regulates transcription by targeting promoters and super-enhancers through the BAF complex in embryonic stem cells. Stem Cell Reports. 2018; 10 (4):1324–39. doi: 10.1016/j.stemcr.2018.02.004.
[Wang J, Wu X, Wei C, et al. YY1 positively regulates transcription by targeting promoters and super-enhancers through the BAF complex in embryonic stem cells[J]. Stem Cell Reports, 2018, 10(4): 1324-39.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

18. Madeira F, Park YM, Lee J, et al The EMBL-EBI search and sequence analysis toolsAPIs in 2019. NucleicAcids Res. 2019; 47 (w1):W636–41. doi: 10.1093/nar/gkz268.
[Madeira F, Park YM, Lee J, et al. The EMBL-EBI search and sequence analysis toolsAPIs in 2019[J]. NucleicAcids Res, 2019, 47(w1): W636-41.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

19. Anders S, Pyl PT, Huber W HTSeq: a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015; 31 (2):166–9. doi: 10.1093/bioinformatics/btu638.
[Anders S, Pyl PT, Huber W. HTSeq: a Python framework to work with high-throughput sequencing data[J]. Bioinformatics, 2015, 31(2): 166-9.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

20. Langmead B, Salzberg SL Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9 (4):357–9. doi: 10.1038/nmeth.1923.
[Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2[J]. Nat Methods, 2012, 9(4): 357-9.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

21. Quinlan AR BEDTools: the Swiss-army tool for genome feature analysis. http://ucgd.genetics.utah.edu/wp-content/uploads/2014/09/nihms628461.pdf . Curr Protoc Bioinformatics. 2014; 47 :11.12.1–34.
[Quinlan AR. BEDTools: the Swiss-army tool for genome feature analysis [J]. Curr Protoc Bioinformatics, 2014, 47: 11.12.1-34.] [ PMC free article ] [ PubMed ] [ Google Scholar ]

22. Ramírez F, Ryan DP, Grüning B, et al deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016; 44 (w1):W160–5. doi: 10.1093/nar/gkw257.
[Ramírez F, Ryan DP, Grüning B, et al. deepTools2: a next generation web server for deep-sequencing data analysis[J]. Nucleic Acids Res, 2016, 44(w1): W160-5.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

23. Li DF, Hsu S, Purushotham D, et al WashU epigenome browser update 2019. NucleicAcids Res. 2019; 47 (W1):W158–65. doi: 10.1093/nar/gkz348.
[Li DF, Hsu S, Purushotham D, et al. WashU epigenome browser update 2019[J]. NucleicAcids Res, 2019, 47(W1): W158-65.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

24. Shen Y, Yue F, McCleary DF, et al A map of the Cis-regulatory sequences in the mouse genome. Nature. 2012; 488 (7409):116–20. doi: 10.1038/nature11243.
[Shen Y, Yue F, McCleary DF, et al. A map of the Cis-regulatory sequences in the mouse genome[J]. Nature, 2012, 488(7409): 116-20.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

25. Kagey MH, Newman JJ, Bilodeau S, et al Mediator and cohesin connect gene expression and chromatin architecture. Nature. 2010; 467 (7314):430–5. doi: 10.1038/nature09380.
[Kagey MH, Newman JJ, Bilodeau S, et al. Mediator and cohesin connect gene expression and chromatin architecture[J]. Nature, 2010, 467(7314): 430-5.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

26. Cho SW, Xu J, Sun R, et al Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element. http://www.onacademic.com/detail/journal_1000040321187310_be80.html . Cell. 2018; 173 (6):1242.
[Cho SW, Xu J, Sun R, et al. Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element[J]. Cell, 2018, 173(6): 1242.] [ PMC free article ] [ PubMed ] [ Google Scholar ]

27. Das PP, Shao Z, Beyaz S, et al Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Mol Cell. 2014; 53 (1):32–48. doi: 10.1016/j.molcel.2013.11.011.
[Das PP, Shao Z, Beyaz S, et al. Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity[J]. Mol Cell, 2014, 53(1): 32-48.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

28. Sabari BR, Dall'Agnese A, Boija A, et al Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018; 361 (6400):eaar3958. doi: 10.1126/science.aar3958.
[Sabari BR, Dall'Agnese A, Boija A, et al. Coactivator condensation at super-enhancers links phase separation and gene control[J]. Science, 2018, 361(6400): eaar3958.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

29. Chen X, Xu H, Yuan P, et al Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008; 133 (6):1106–17. doi: 10.1016/j.cell.2008.04.043.
[Chen X, Xu H, Yuan P, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells[J]. Cell, 2008, 133(6): 1106-17.] [ PubMed ] [ CrossRef ] [ Google Scholar ]

30. Bonev B, Mendelson Cohen N, Szabo Q, et al Multiscale 3D genome rewiring during mouse neural development. Cell. 2017; 171 (3):557–72.e24. doi: 10.1016/j.cell.2017.09.043.
[Bonev B, Mendelson Cohen N, Szabo Q, et al. Multiscale 3D genome rewiring during mouse neural development[J]. Cell, 2017, 171(3): 557-72.e24.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

31. Mumbach MR, Rubin AJ, Flynn RA, et al HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat Methods. 2016; 13 (11):919–22. doi: 10.1038/nmeth.3999.
[Mumbach MR, Rubin AJ, Flynn RA, et al. HiChIP: efficient and sensitive analysis of protein-directed genome architecture[J]. Nat Methods, 2016, 13(11): 919-22.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

32. Xu H, Baroukh C, Dannenfelser R, et al ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. http://www.onacademic.com/detail/journal_1000037596860110_9083.html . Database: Oxford. 2013:bat045.
[Xu H, Baroukh C, Dannenfelser R, et al. ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells[J]. Database: Oxford, 2013: bat045.] [ PMC free article ] [ PubMed ] [ Google Scholar ]

33. Pedregosa F, Varoquaux G, Gramfort A, et al. Scikit-learn: machine learning in Python[EB/OL]. 2012: arXiv: 1201.0490[cs. LG].<a href="https://arxiv.org/abs/1201.0490" target="_blank">https://arxiv.org/abs/1201.0490</a>.

34. Baştanlar Y, Ozuysal M Introduction to machine learning. http://www.zentralblatt-math.org/ioport/en/?q=an%3A05654348 . Methods Mol Biol. 2014; 1107 :105–28.
[Baştanlar Y, Ozuysal M. Introduction to machine learning[J]. Methods Mol Biol, 2014, 1107: 105-28.] [ PubMed ] [ Google Scholar ]

35. Li YF, Wu FX, Ngom A A review on machine learning principles for multi-view biological data integration. http://www.researchgate.net/profile/Yifeng_Li/publication/309152315_A_Review_on_Machine_Learning_Principles_for_Multi-View_Biological_Data_Integration/links/5800e83f08ae1d2d72eae236.pdf . Brief Bioinform. 2018; 19 (2):325–40.
[Li YF, Wu FX, Ngom A. A review on machine learning principles for multi-view biological data integration[J]. Brief Bioinform, 2018, 19(2): 325-40.] [ PubMed ] [ Google Scholar ]

36. Raudvere U, Kolberg L, Kuzmin I, et al G: Profiler: a web server for functional enrichment analysis and conversions of gene lists(2019 update) NucleicAcids Res. 2019; 47 (w1):W191–8. doi: 10.1093/nar/gkz369.
[Raudvere U, Kolberg L, Kuzmin I, et al. G: Profiler: a web server for functional enrichment analysis and conversions of gene lists(2019 update)[J]. NucleicAcids Res, 2019, 47(w1): W191-8.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

37. Stewart SA, Dykxhoorn DM, Palliser D, et al Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA. 2003; 9 (4):493–501. doi: 10.1261/rna.2192803.
[Stewart SA, Dykxhoorn DM, Palliser D, et al. Lentivirus-delivered stable gene silencing by RNAi in primary cells[J]. RNA, 2003, 9(4): 493-501.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

38. Huang G, Ye S, Zhou X, et al Molecular basis of embryonic stem cell self-renewal: from signaling pathways to pluripotency network. Cell Mol Life Sci. 2015; 72 (9):1741–57. doi: 10.1007/s00018-015-1833-2.
[Huang G, Ye S, Zhou X, et al. Molecular basis of embryonic stem cell self-renewal: from signaling pathways to pluripotency network[J]. Cell Mol Life Sci, 2015, 72(9): 1741-57.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

39. Fudenberg G, Imakaev M, Lu C, et al Formation of chromosomal domains by loop extrusion. Cell Rep. 2016; 15 (9):2038–49. doi: 10.1016/j.celrep.2016.04.085.
[Fudenberg G, Imakaev M, Lu C, et al. Formation of chromosomal domains by loop extrusion[J]. Cell Rep, 2016, 15(9): 2038-49.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

40. Davidson IF, Bauer B, Goetz D, et al DNA loop extrusion by human cohesin. Science. 2019; 366 (6471):1338–45. doi: 10.1126/science.aaz3418.
[Davidson IF, Bauer B, Goetz D, et al. DNA loop extrusion by human cohesin[J]. Science, 2019, 366(6471): 1338-45.] [ PubMed ] [ CrossRef ] [ Google Scholar ]

41. Kim Y, Shi Z, Zhang H, et al Human cohesin compacts DNA by loop extrusion. Science. 2019; 366 (6471):1345–9. doi: 10.1126/science.aaz4475.
[Kim Y, Shi Z, Zhang H, et al. Human cohesin compacts DNA by loop extrusion[J]. Science, 2019, 366(6471): 1345-9.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

42. Ying Z, Tian H, Li Y, et al CCT6A suppresses SMAD2 and promotes prometastatic TGF-β signaling. J Clin Invest. 2017; 127 (5):1725–40. doi: 10.1172/JCI90439.
[Ying Z, Tian H, Li Y, et al. CCT6A suppresses SMAD2 and promotes prometastatic TGF-β signaling[J]. J Clin Invest, 2017, 127(5): 1725-40.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

43. Sakaki-Yumoto M, Liu J, Ramalho-Santos M, et al Smad2 is essential for maintenance of the human and mouse primed pluripotent stem cell state. J Biol Chem. 2013; 288 (25):18546–60. doi: 10.1074/jbc.M112.446591.
[Sakaki-Yumoto M, Liu J, Ramalho-Santos M, et al. Smad2 is essential for maintenance of the human and mouse primed pluripotent stem cell state[J]. J Biol Chem, 2013, 288(25): 18546-60.] [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]

Articles from Journal of Southern Medical University are provided here courtesy of Editorial Department of Journal of Southern Medical University

潜在的胚胎干细胞自我更新与多能性的调控基因的鉴定: 基于随机森林算法

Identification of potential regulatory genes for embryonic stem cell self-renewal and pluripotency by random forest

曾 彭归航

唐 秀晓

吴 庭芩

田 奇

李 茫茫

丁 俊军

Funding Statement

References

曾彭归航

唐秀晓

吴庭芩

田奇

李茫茫

丁俊军