Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon γ-stimulated HeLa cells

PLoS ONE

Volumn 5, Issue 7, 2010, Pages

  Wang, Guohua ^a   Wang, Yadong ^a   Teng, Mingxiang ^a,b,c   Zhang, Denan ^a   Li, Lang ^b,c   Liu, Yunlong ^b,c  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CCAAT ENHANCER BINDING PROTEIN; GAMMA INTERFERON; MICRORNA; RNA POLYMERASE II; STAT1 PROTEIN; TRANSCRIPTION FACTOR AP 1;

ARTICLE; BINDING SITE; BIOINFORMATICS; CELL STIMULATION; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DATA BASE; FEEDBACK SYSTEM; GENE REGULATORY NETWORK; HELA CELL; HUMAN; HUMAN CELL; PROMOTER REGION; PROTEIN RNA BINDING; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; BIOLOGICAL MODEL; BIOLOGY; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM;

CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; INTERFERON-GAMMA; MICRORNAS; MODELS, BIOLOGICAL; PROMOTER REGIONS, GENETIC; STAT1 TRANSCRIPTION FACTOR;

EID: 77955597990     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0011794     Document Type: Article

References (49)

1. Ambros V (2001) microRNAs: tiny regulators with great potential. Cell 107: 823-826.
2. Kim VN (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6: 376-385.
3. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34: D140-144.
4. Shalgi R, Lieber D, Oren M, Pilpel Y (2007) Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol 3: e131.
5. Zhou Y, Ferguson J, Chang JT, Kluger Y (2007) Inter- and intra-combinatorial regulation by transcription factors and microRNAs. BMC Genomics 8: 396.
6. Tsang J, Zhu J, van Oudenaarden A (2007) MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 26: 753-767.
7. Coller HA, Forman JJ, Legesse-Miller A (2007) ';';Myc'ed messages'': myc induces transcription of E2F1 while inhibiting its translation via a microRNA polycistron. PLoS Genet 3: e146.
8. Saini HK, Griffiths-Jones S, Enright AJ (2007) Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci U S A 104: 17719-17724.
9. Zhou X, Ruan J, Wang G, Zhang W (2007) Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol 3: e37.
10. Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, et al. (2008) Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134: 521-533.
11. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, et al. (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 27: 66-75.
12. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, et al. (2007) Genomewide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651-657.
13. Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, et al. (2008) Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res 36: 4549-4564.
14. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) Highresolution profiling of histone methylations in the human genome. Cell 129: 823-837.
15. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genomewide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560. STAT1 Regulates microRNA PLoS ONE www.plosone.org 7 July 2010 Volume 5 Issue 7 e11794
16. Baugh LR, Demodena J, Sternberg PW (2009) RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science 324: 92-94.
17. Gray PW, Goeddel DV (1982) Structure of the human immune interferon gene. Nature 298: 859-863.
18. Aaronson DS, Horvath CM (2002) A road map for those who don't know JAKSTAT. Science 296: 1653-1655.
19. Gregersen LH, Jacobsen AB, Frankel LB, Wen J, Krogh A, et al. (2010) MicroRNA-145 targets YES and STAT1 in colon cancer cells. PLoS ONE 5: e8836.
20. Tang Y, Luo X, Cui H, Ni X, Yuan M, et al. (2009) MicroRNA-146A contributes to abnormal activation of the type I interferon pathway in human lupus by targeting the key signaling proteins. Arthritis Rheum 60: 1065-1075.
21. Jiang S, Zhang HW, Lu MH, He XH, Li Y, et al. (2010) MicroRNA-155 functions as an OncomiR in breast cancer by targeting the suppressor of cytokine signaling 1 gene. Cancer Res 70: 3119-3127.
22. Wang G, Wang Y, Shen C, Huang Y, Huang T, et al. (In revision) RNA Polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. PLoS ONE.
23. Mense SM, Sengupta A, Zhou M, Lan C, Bentsman G, et al. (2006) Gene expression profiling reveals the profound upregulation of hypoxia-responsive genes in primary human astrocytes. Physiol Genomics 25: 435-449.
24. Affymetrix (2001) Affymetrix Microarray Suite Users Guide, version 5.0. Technote. Affymetrix, Santa Clara, CA.
25. Lee Y, Ahn C, Han J, Choi H, Kim J, et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415-419.
26. Yi R, Qin Y, Macara IG, Cullen BR (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17: 3011-3016.
27. Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, et al. (2008) The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 36: D773-779.
28. Wingender E, Dietze P, Karas H, Knuppel R (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 24: 238-241.
29. Liu Y, Taylor MW, Edenberg HJ (2006) Model-based identification of cis-acting elements from microarray data. Genomics 88: 452-461.
30. Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450-461.
31. Horvai AE, Xu L, Korzus E, Brard G, Kalafus D, et al. (1997) Nuclear integration of JAK/STAT and Ras/AP-1 signaling by CBP and p300. Proc Natl Acad Sci U S A 94: 1074-1079.
32. Do H, Pyo S, Sohn EH (2009) Suppression of iNOS expression by fucoidan is mediated by regulation of p38 MAPK, JAK/STAT, AP-1 and IRF-1, and depends on up-regulation of scavenger receptor B1 expression in TNF-alphaand IFN-gamma-stimulated C6 glioma cells. J Nutr Biochem.
33. Xu W, Comhair SA, Zheng S, Chu SC, Marks-Konczalik J, et al. (2003) STAT- 1 and c-Fos interaction in nitric oxide synthase-2 gene activation. Am J Physiol Lung Cell Mol Physiol 285: L137-148.
34. Lo RK, Wong YH (2006) Transcriptional activation of c-Fos by constitutively active Galpha(16)QL through a STAT1-dependent pathway. Cell Signal 18: 2143-2153.
35. Jiang Q, Wang Y, Hao Y, Juan L, Teng M, et al. (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease.Nucleic Acids Res 37: D 98-104.
36. Ciafre SA, Galardi S, Mangiola A, Ferracin M, Liu CG, et al. (2005) Extensive modulation of a set of microRNAs in primary glioblastoma. Biochem Biophys Res Commun 334: 1351-1358.
37. Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, et al. (2006) Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9: 189-198.
38. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, et al. (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103: 2257-2261.
39. Lee EJ, Gusev Y, Jiang J, Nuovo GJ, Lerner MR, et al. (2007) Expression profiling identifies microRNA signature in pancreatic cancer. Int J Cancer 120: 1046-1054.
40. Bloomston M, Frankel WL, Petrocca F, Volinia S, Alder H, et al. (2007) MicroRNA expression patterns to differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis. JAMA 297: 1901-1908.
41. He H, Jazdzewski K, Li W, Liyanarachchi S, Nagy R, et al. (2005) The role of icroRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A 102: 19075-19080.
42. Calin GA, Liu CG, Sevignani C, Ferracin M, Felli N, et al. (2004) MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci U S A 101: 11755-11760.
43. Huang S, He X, Ding J, Liang L, Zhao Y, et al. (2008) Upregulation of miR-23a approximately 27a approximately 24 decreases transforming growth factor-betainduced tumor-suppressive activities in human hepatocellular carcinoma cells. Int J Cancer 123: 972-978.
44. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
45. Liu XS, Brutlag DL, Liu JS (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 20: 835-839.
46. Hu M, Yu J, Taylor JM, Chinnaiyan AM, Qin ZS (2010) On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Res 38: 2154-2167.
47. Bhat-Nakshatri P, Wang G, Appaiah H, Luktuke N, Carroll JS, et al. (2008) AKT alters genome-wide estrogen receptor alpha binding and impacts estrogen signaling in breast cancer. Mol Cell Biol 28: 7487-7503.
48. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
49. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.