Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Guo, Zhiyun ^a   Maki, Miranda ^b   Ding, Ruofan ^a   Yang, Yalan ^a   Zhang, Bao ^a   Xiong, Lili ^a  

^a SOUTHWEST JIAOTONG UNIVERSITY   (China)

^b LAKEHEAD UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTION FACTOR;

ANTIBODY SPECIFICITY; CHROMOSOME MAP; GENE REGULATORY NETWORK; GENETICS; HUMAN; HUMAN GENOME; METABOLISM; VISCERA;

CHROMOSOME MAPPING; GENE REGULATORY NETWORKS; GENOME, HUMAN; HUMANS; MICRORNAS; ORGAN SPECIFICITY; TRANSCRIPTION FACTORS; VISCERA;

EID: 84901952075     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep05150     Document Type: Article

References (58)

1. Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 298, 799-804 (2002). (Pubitemid 35231527)
2. Yu, H. & Gerstein,M. Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A. 103, 14724-14731 (2006). (Pubitemid 44527797)
3. Hobert, O. Gene regulation by transcription factors andmicroRNAs. Science. 319, 1785-1786 (2008). (Pubitemid 351451553)
4. Saito, Y., Suzuki, H. & Hibi, T. The role of microRNAs in gastrointestinal cancers. J Gastroenterol. 44 Suppl 19, 18-22 (2009).
5. Baek, D. et al. The impact of microRNAs on protein output. Nature. 455, 64-71 (2008).
6. Farh, K. K. et al. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science. 310, 1817-1821 (2005). (Pubitemid 41814382)
7. Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 116, 281-297 (2004).
8. Filipowicz, W., Bhattacharyya, S. N. & Sonenberg, N. Mechanisms of posttranscriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet. 9, 102-114 (2008).
9. Niehrs, C. & Pollet, N. Synexpression groups in eukaryotes. Nature. 402, 483-487 (1999).
10. Ambros, V. The functions of animal microRNAs. Nature. 431, 350-355 (2004). (Pubitemid 39265675)
11. Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 129, 1401-1414 (2007). (Pubitemid 46970709)
12. Calin, G. A. et al. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A. 101, 2999-3004 (2004). (Pubitemid 38327724)
13. van Rooij, E. et al. A signature pattern of stress-responsive microRNAs that can evoke cardiac hypertrophy and heart failure. Proc Natl Acad Sci U S A. 103, 18255-18260 (2006). (Pubitemid 44871645)
14. Esquela-Kerscher, A. & Slack, F. J. Oncomirs-microRNAs with a role in cancer. Nat Rev Cancer. 6, 259-269 (2006).
15. Odom, D. T. et al. Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol. 2, 2006 0017 (2006).
16. Tan, K., Tegner, J. & Ravasi, T. Integrated approaches to uncovering transcription regulatory networks in mammalian cells. Genomics. 91, 219-231 (2008).
17. Liao, Y. L. et al. Transcriptional regulation of miR-196b by ETS2 in gastric cancer cells. Carcinogenesis. 33, 760-769 (2012).
18. Re, A., Cora, D., Taverna, D. & Caselle, M. Genome-wide survey of microRNAtranscription factor feed-forward regulatory circuits in human. Mol Biosyst. 5, 854-867 (2009).
19. Shalgi, R., Lieber, D., Oren, M. & Pilpel, Y. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol. 3, e131 (2007).
20. Saini, H. K., Griffiths-Jones, S. & Enright, A. J. Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci U S A. 104, 17719-17724 (2007). (Pubitemid 350210901)
21. Gerstein,M. B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 489, 91-100 (2012).
22. Hsu, S. D. et al. miRNAMap 2. 0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res. 36, D165-169 (2008).
23. Megraw, M. et al. MicroRNA promoter element discovery in Arabidopsis. RNA. 12, 1612-1619 (2006). (Pubitemid 44316025)
24. Chien, C. H. et al. Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res. 39, 9345-9356 (2011).
25. Corcoran, D. L. et al. Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One. 4, e5279 (2009).
26. Ozsolak, F. et al. Chromatin structure analyses identifymiRNA promoters. Genes Dev. 22, 3172-3183 (2008).
27. Alexiou, P. et al. miRGen 2. 0: a database of microRNA genomic information and regulation. Nucleic Acids Res. 38, D137-141 (2010).
28. McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 28, 495-501 (2010).
29. Bi, Y., Kim, H., Gupta, R. & Davuluri, R. V. Tree-based position weight matrix approach to model transcription factor binding site profiles. PLoS One. 6, e24210 (2011).
30. Johnson, D. S., Mortazavi, A.,Myers, R. M. &Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science. 316, 1497-1502 (2007). (Pubitemid 46906620)
31. Tabach, Y. et al. Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS One. 2, e807 (2007).
32. Franco, L. O., de, O. M. C. L., Hamdi, S., Sachetto-Martins, G. & de Oliveira, D. E. Distal regulatory regions restrict the expression of cis-linked genes to the tapetal cells. FEBS Lett. 517, 13-18 (2002). (Pubitemid 34327622)
33. Jelinic, P., Stehle, J. C. & Shaw, P. The testis-specific factor CTCFL cooperates with the protein methyltransferase PRMT7 in H19 imprinting control region methylation. PLoS Biol. 4, e355 (2006).
34. Virtue, A.,Wang, H. & Yang, X. F. MicroRNAs and toll-like receptor/interleukin-1 receptor signaling. J Hematol Oncol. 5, 66 (2012).
35. Yu, X., Lin, J., Zack, D. J. & Qian, J. Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res. 34, 4925-4936 (2006). (Pubitemid 44605635)
36. Lagos-Quintana, M. et al. Identification of tissue-specific microRNAs from mouse. Curr Biol. 12, 735-739 (2002). (Pubitemid 34455427)
37. Chen, J. F. et al. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet. 38, 228-233 (2006).
38. Wienholds, E. et al. MicroRNA expression in zebrafish embryonic development. Science. 309, 310-311 (2005). (Pubitemid 40967869)
39. Liang, Y., Ridzon, D., Wong, L. & Chen, C. Characterization of microRNA expression profiles in normal human tissues. BMC Genomics. 8, 166 (2007).
40. Lee, E. J. et al. Systematic evaluation of microRNA processing patterns in tissues, cell lines, and tumors. RNA. 14, 35-42 (2008).
41. Beuvink, I. et al. A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs. Nucleic Acids Res. 35, e52 (2007).
42. Bostjancic, E., Zidar, N., Stajer, D. & Glavac, D. MicroRNAs miR-1, miR-133a, miR-133b and miR-208 are dysregulated in human myocardial infarction. Cardiology. 115, 163-169 (2010).
43. Fu, H. et al. Identification of human fetal liver miRNAs by a novel method. FEBS Lett. 579, 3849-3854 (2005). (Pubitemid 40903114)
44. Bargaje, R., Hariharan, M., Scaria, V. & Pillai, B. Consensus miRNA expression profiles derived from interplatform normalization of microarray data. RNA. 16, 16-25 (2010).
45. Townley-Tilson, W. H., Callis, T. E. & Wang, D. MicroRNAs 1, 133, and 206: critical factors of skeletal and cardiac muscle development, function, and disease. Int J Biochem Cell Biol. 42, 1252-1255 (2010).
46. Liu, C. G. et al. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci U S A. 101, 9740-9744 (2004).
47. Barad, O. et al. MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res. 14, 2486-2494 (2004). (Pubitemid 40012232)
48. Ramkissoon, S. H. et al. Hematopoietic-specific microRNA expression in human cells. Leuk Res. 30, 643-647 (2006). (Pubitemid 43374593)
49. Mestdagh, P. et al. The microRNA body map: dissecting microRNA function through integrative genomics. Nucleic Acids Res. 39, e136 (2011).
50. Baskerville, S. & Bartel, D. P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA. 11, 241-247 (2005). (Pubitemid 40270816)
51. Sempere, L. F. et al. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol. 5, R13 (2004).
52. Ravasi, T. et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 140, 744-752 (2010).
53. Hsu, S. D. et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res. 39, D163-169 (2011).
54. Xiao, F. et al. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res. 37, D105-110 (2009).
55. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 27, 91-105 (2007). (Pubitemid 46991392)
56. Liu, X., Yu, X., Zack, D. J., Zhu, H. & Qian, J. TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics. 9, 271 (2008).
57. Stark,C. et al. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 34, D535-539 (2006).
58. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003). (Pubitemid 37428274)