MER41 repeat sequences contain inducible STAT1 binding sites

PLoS ONE

Volumn 5, Issue 7, 2010, Pages

  Schmid, Christoph D ^a,b,c   Bucher, Philipp ^a  

^a EPFL   (Switzerland)

^b SWISS TROPICAL AND PUBLIC HEALTH INSTITUTE   (Switzerland)

^c UNIVERSITY OF BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

GAMMA INTERFERON; PROTEIN P53; STAT1 PROTEIN;

ARTICLE; BINDING SITE; CELL TYPE; CHROMATIN IMMUNOPRECIPITATION; GENE CONTROL; GENE SEQUENCE; GENETIC CONSERVATION; GENOME; HELA CELL; LONG TERMINAL REPEAT; REGULATORY MECHANISM; DRUG EFFECT; GENETICS; HUMAN; METABOLISM; NUCLEOTIDE REPEAT; PROTEIN BINDING;

PRIMATES; RODENTIA;

BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; HELA CELLS; HUMANS; INTERFERON-GAMMA; PROTEIN BINDING; REPETITIVE SEQUENCES, NUCLEIC ACID; STAT1 TRANSCRIPTION FACTOR;

EID: 77955342465     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0011425     Document Type: Article

References (49)

1. Tompa M, Li N, Bailey TL, Church GM, De Moor B, et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 23: 137-144.
2. Hu J, Li B, Kihara D (2005) Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res 33: 4899-4913.
3. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651-657.
4. Schmid CD, Bucher P (2007) ChlP-Seq Data Reveal Nucleosome Architecture of Human Promoters. Cell 131: 831-832.
5. Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, et al. (2008) Find Peaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24: 1729-1730.
6. Ji H, Jiang H, Ma W, Johnson DS, Myers RM, et al. (2008) An integrated software system for analyzing ChlP-chip and ChlP-seq data. Nat Biotechnol 26: 1293-1300.
7. Jothi R, Cuddapah S, Barski A, Cui K, Zhao K (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChlP-Seq data. Nucleic Acids Res 36: 5221-5231.
8. Kharchenko PV, Tolstorukov MY, Park PJ (2008) Design and analysis of ChlP-seq experiments for DNA-binding proteins. Nat Biotechnol 26: 1351-1359.
9. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, et al. (2008) Genome-wide analysis of transcription factor binding sites based on ChlP-Seq data. Nat Methods 5: 829-834.
10. Xu H, Wei CL, Lin F, Sung WK (2008) An HMM approach to genome-wide identification of differential histone modification sites from ChlP-seq data. Bioinformatics 24: 2344-2349.
11. Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M (2008) Modeling ChIP sequencing in silico with applications. PLoS Comput Biol 4: e1000158.
12. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, et al. (2009) Peak Seq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 27: 66-75.
13. Darnell JE, Jr., Kerr IM, Stark GR (1994) Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins. Science 264: 1415-1421.
14. Ehret GB, Reichenbach P, Schindler U, Horvath CM, Fritz S, et al. (2001) DNA binding specificity ofdifferent STAT proteins. Comparison ofin vitro specificity with natural target sites. J Biol Chem 276: 6675-6688.
15. Levy DE, Kessler DS, Pine R, Reich N, Darnell JE, Jr. (1988) Interferon-induced nuclear factors that bind a shared promoter element correlate with positive and negative transcriptional control. Genes Dev 2: 383-393.
16. Polak P, Domany E (2006) Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics 7: 133.
17. Mortazavi A, Leeper Thompson EC, Garcia ST, Myers RM, Wold B (2006) Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genome Res 16: 1208-1221.
18. Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, et al. (2007) Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A 104: 18613-18618.
19. Laperriere D, Wang TT, White JH, Mader S (2007) Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. BMC Genomics 8: 23.
20. Johnson R, Gamblin RJ, Ooi L, Bruce AW, Donaldson IJ, et al. (2006) Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic Acids Res 34: 3862-3877.
21. Bourque G, Leong B, Vega VB, Chen X, Lee YL, et al. (2008) Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 18: 1752-1762.
22. Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, et al. (2006) ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 22: 637-640.
23. Stormo GD (2000) DNA binding sites: representation and discovery. Bioinfor-matics 16: 16-23.
24. Schutz F, Delorenzi M (2008) MAMOT: hidden Markov modeling tool. Bioinformatics 24: 1399-1400.
25. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, California. pp 28-36.
26. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324: 1720-1723.
27. Bailey TL, Gribskov M (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14: 48-54.
28. van Nimwegen E (2007) Finding regulatory elements and regulatory motifs: a general probabilistic framework. BMC Bioinformatics 8 Suppl 6: S4.
29. Berg OG, von Hippel PH (1987) Selection ofDNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol 193: 723-750.
30. Platanias LC (2005) Mechanisms of type-I- and type-II-interferon-mediated signalling. Nat Rev Immunol 5: 375-386.
31. 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.
32. Yoder JA, Walsh CP, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13: 335-340.
33. Jurka J (2000) Repbase update: a database and an electronic journal of repetitive elements. Trends Genet 16: 418-420.
34. Li X, Leung S, Burns C, Stark GR (1998) Cooperative binding of Stat1-2 heterodimers and ISGF3 to tandem DNA elements. Biochimie 80: 703-710.
35. Lecine P, Algarte M, Rameil P, Beadling C, Bucher P, et al. (1996) Elf-1 and Stat5 bind to a critical element in a new enhancer ofthe human interleukin-2 receptor alpha gene. Mol Cell Biol 16: 6829-6840.
36. Vinkemeier U, Cohen SL, Moarefi I, Chait BT, Kuriyan J, et al. (1996) DNA binding of in vitro activated Stat1 alpha, Stat1 beta and truncated Stat1: interaction between NH2-terminal domains stabilizes binding oftwo dimers to tandem DNA sites. Embo J 15: 5616-5626.
37. Stark GR, Kerr IM, Williams BR, Silverman RH, Schreiber RD (1998) How cells respond to interferons. Annu Rev Biochem 67: 227-264.
38. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
39. Tanay A (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res 16: 962-972.
40. Ward LD, Bussemaker HJ (2008) Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics 24: i165-171.
41. Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, et al. (2008) Genome wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res 18: 1906-1917.
42. Kaplan N, Moore IK, Fondufe-MittendorfY, Gossett AJ, Tillo D, et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
43. Whitington T, Perkins AC, Bailey TL (2009) High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Res 37: 14-25.
44. Sepp T, Tong-Starksen SE (1997) STAT1 pathway is involved in activation of caprine arthritis-encephalitis virus long terminal repeat in monocytes. J Virol 71: 771-777.
45. Johnson R, Samuel J, Ng CKL, Jauch R, Stanton LW, et al. (2009) Evolution of the vertebrate gene regulatory network controlled by the transcriptional repressor REST. Mol. Biol. Evol 26: 1491-1507.
46. Ackermann-Liebrich U, Kuna-Dibbert B, Probst-Hensch NM, Schindler C, Felber Dietrich D, et al. (2005) Follow-up of the Swiss Cohort Study on Air Pollution and Lung Diseases in Adults (SAPALDIA 2) 1991-2003: methods and characterization of participants. Soz Praventivmed 50: 245-263.
47. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, et al. (2002) Large-scale analysis ofthe human and mouse transcriptomes. Proc Natl Acad Sci U S A 99: 4465-4470.
48. Wormald S, Hilton DJ, Smyth GK, Speed TP (2006) Proximal genomic localization of STAT1 binding and regulated transcriptional activity. BMC Genomics 7: 254.
49. Iseli C, Ambrosini G, Bucher P, Jongeneel CV (2007) Indexing strategies for rapid searches ofshort words in genome sequences. PLoS ONE 2: e579.