Systematic classification of non-coding RNAs by epigenomic similarity

BMC Bioinformatics

Volumn 14, Issue SUPPL.14, 2013, Pages

  Dozmorov, Mikhail G ^a   Giles, Cory B ^a   Koelsch, Kristi A ^a   Wren, Jonathan D ^a,b  

^a OKLAHOMA MEDICAL RESEARCH FOUNDATION   (United States)

^b UNIVERSITY OF OKLAHOMA HEALTH SCIENCES CENTER   (United States)

Author keywords

ENCODE; epigenetics; genome; GenomeRunner; ncRNA; non coding RNA

Indexed keywords

ENCODE; EPIGENETICS; GENOMERUNNER; NCRNA; NON-CODING RNAS;

ACETYLATION; BIOCHEMISTRY; GENES; PROTEINS; STATISTICAL TESTS; TRANSCRIPTION;

NUCLEIC ACIDS;

HISTONE; TRANSCRIPTION FACTOR; UNTRANSLATED RNA; CHROMATIN;

ALGORITHM; ARTICLE; BINDING SITE; CHEMISTRY; CHROMATIN; CLASSIFICATION; EPIGENETICS; GENETICS; HUMAN; HUMAN GENOME; METABOLISM;

ALGORITHMS; BINDING SITES; CHROMATIN; EPIGENOMICS; GENOME, HUMAN; HISTONES; HUMANS; RNA, UNTRANSLATED; TRANSCRIPTION FACTORS;

EID: 84885215226     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S14-S2     Document Type: Article

References (45)

1. GEO ftp data archive., ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/
2. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al. Landscape of transcription in human cells. Nature 2012, 489(7414):101-108. 10.1038/nature11233, 3684276, 22955620.
3. ENCODE Project Consortium The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306(5696):636-640. ENCODE Project Consortium.
4. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447(7146):799-816. 10.1038/nature05874, 2212820, 17571346, ENCODE Project Consortium.
5. Mattick JS. The genetic signatures of noncoding RNAs. PLoS Genet 2009, 5(4):e1000459. 10.1371/journal.pgen.1000459, 2667263, 19390609.
6. Mattick JS. The functional genomics of noncoding RNA. Science 2005, 309(5740):1527-1528. 10.1126/science.1117806, 16141063.
7. Mattick JS, Makunin IV. Non-coding RNA. Hum Mol Genet 2006, 15(Spec No 1):R17-29.
8. Amaral PP, Mattick JS. Noncoding RNA in development. Mamm Genome 2008, 19(78):454-492.
9. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Solda G, Simons C, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008, 18(9):1433-1445. 10.1101/gr.078378.108, 2527704, 18562676.
10. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet 2009, 10(3):155-159. 10.1038/nrg2521, 19188922.
11. Nagano T, Fraser P. No-nonsense functions for long noncoding RNAs. Cell 2011, 145(2):178-181. 10.1016/j.cell.2011.03.014, 21496640.
12. Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009, 136(4):629-641. 10.1016/j.cell.2009.02.006, 19239885.
13. Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 2007, 17(6):746-759. 10.1101/gr.5660607, 1891335, 17567994.
14. Horiuchi T, Aigaki T. Alternative trans-splicing: a novel mode of pre-mRNA processing. Biol Cell 2006, 98(2):135-140. 10.1042/BC20050002, 16417469.
15. Lipovich L, Johnson R, Lin CY. MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA. Biochim Biophys Acta 2010, 1799(9):597-615. 10.1016/j.bbagrm.2010.10.001, 20951849.
16. St Laurent G, Shtokalo D, Tackett MR, Yang Z, Eremina T, Wahlestedt C, Urcuqui-Inchima S, Seilheimer B, McCaffrey TA, Kapranov P. Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. BMC Genomics 2012, 13:504. 10.1186/1471-2164-13-504, 3507791, 23006825.
17. De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 2010, 8(5):e1000384. 10.1371/journal.pbio.1000384, 2867938, 20485488.
18. Kurokawa R. Promoter-associated long noncoding RNAs repress transcription through a RNA binding protein TLS. Adv Exp Med Biol 2011, 722:196-208. 10.1007/978-1-4614-0332-6_12, 21915790.
19. Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A. An operational definition of epigenetics. Genes Dev 2009, 23(7):781-783. 10.1101/gad.1787609, 19339683.
20. Hardison RC. Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies. J Biol Chem 2012, 287(37):30932-30940. 10.1074/jbc.R112.352427, 3438926, 22952232.
21. Bird A. Perceptions of epigenetics. Nature 2007, 447(7143):396-398. 10.1038/nature05913, 17522671.
22. Leung A, Schones DE, Natarajan R. Using epigenetic mechanisms to understand the impact of common disease causing alleles. Curr Opin Immunol 2012, 24(5):558-563. 10.1016/j.coi.2012.07.004, 22857822.
23. Inbar-Feigenberg M, Choufani S, Butcher DT, Roifman M, Weksberg R. Basic concepts of epigenetics. Fertil Steril 2013, 99(3):607-15. 10.1016/j.fertnstert.2013.01.117, 23357459.
24. Ptashne M. Epigenetics: Core misconcept. Proc Natl Acad Sci USA 2013, 110(18):7101-7103. 10.1073/pnas.1305399110, 3645541, 23584020.
25. Wren JD, Johnson D, Gruenwald L. Automating genomic data mining via a sequence-based matrix format and associative rule set. BMC Bioinformatics 2005, 6(Suppl 2):S2. 10.1186/1471-2105-6-S2-S2, 1866388, 16351746.
26. Dozmorov MG, Wren JD. High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses. BMC Bioinformatics 2011, 12(Suppl 10):S2. 10.1186/1471-2105-12-S10-S2, 3278836, 22373013.
27. Dozmorov MG, Giles CB, Wren JD. Predicting gene ontology from a global meta-analysis of 1-color microarray experiments. BMC Bioinformatics 2011, 12(Suppl 10):S14. 10.1186/1471-2105-12-S10-S14, 3278830, 22479706.
28. Dozmorov MG, Cara LR, Giles CB, Wren JD. GenomeRunner: Automating genome exploration. Bioinformatics 2012, 28(3):419-20. 10.1093/bioinformatics/btr666, 3268239, 22155868.
29. Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, et al. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res 2013, 41(Database):D56-63. 3531152, 23193274.
30. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921. 10.1038/35057062, 11237011.
31. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing. J R Stat Soc Series B 1995, 57(1):289-300.
32. Ward JH. Hierarchical Grouping to Optimize an Objective Function. J Am Stat Assoc 1963, 58(301):236-244.
33. R Core Team R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing 2013, R Core Team., http://www.R-project.org
34. Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 2010, 28(8):817-825. 10.1038/nbt.1662, 2919626, 20657582.
35. Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell 2009, 137(7):1194-1211. 10.1016/j.cell.2009.06.001, 3040116, 19563753.
36. Huet J, Sentenac A. The TATA-binding protein participates in TFIIIB assembly on tRNA genes. Nucleic Acids Res 1992, 20(24):6451-6454. 10.1093/nar/20.24.6451, 334556, 1480467.
37. Ablasser A, Bauernfeind F, Hartmann G, Latz E, Fitzgerald KA, Hornung V. RIG-I-dependent sensing of poly(dA:dT) through the induction of an RNA polymerase III-transcribed RNA intermediate. Nat Immunol 2009, 10(10):1065-1072. 10.1038/ni.1779, 19609254.
38. Chiu YH, Macmillan JB, Chen ZJ. RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway. Cell 2009, 138(3):576-591. 10.1016/j.cell.2009.06.015, 2747301, 19631370.
39. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004, 23(20):4051-4060. 10.1038/sj.emboj.7600385, 524334, 15372072.
40. Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigo R, Birney E, et al. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol 2012, 13(9):R53. 10.1186/gb-2012-13-9-r53, 3491397, 22950368.
41. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 2009, 106(28):11667-11672. 10.1073/pnas.0904715106, 2704857, 19571010.
42. Kanhere A, Viiri K, Araujo CC, Rasaiyaah J, Bouwman RD, Whyte WA, Pereira CF, Brookes E, Walker K, Bell GW, et al. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol Cell 2010, 38(5):675-688. 10.1016/j.molcel.2010.03.019, 2886029, 20542000.
43. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res 2004, 14(10A):1902-1910. 10.1101/gr.2722704, 524413, 15364901.
44. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 2012, 22(9):1798-1812. 10.1101/gr.139105.112, 3431495, 22955990.
45. RFAM., ftp://ftp.sanger.ac.uk/pub/databases/Rfam/CURRENT/USERMAN