Systematic study of human long intergenic non-coding RNAs and their impact on cancer

Science China Life Sciences

Volumn 56, Issue 4, 2013, Pages 324-334

  Sun, Liang ^a   Luo, HaiTao ^b   Liao, Qi ^c   Bu, DeChao ^b   Zhao, GuoGuang ^b   Liu, ChangNing ^b   Liu, YuanNing ^a   Zhao, Yi ^b  

^a JILIN UNIVERSITY   (China)

^b INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^c NINGBO UNIVERSITY   (China)

Author keywords

cancer; functional annotation; identification; lincRNA

Indexed keywords

EID: 84876152425     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-013-4460-x     Document Type: Article

References (45)

1. Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 2009, 458: 223-227.
2. Khalil A M, Guttman M, Huarte M, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA, 2009, 106: 11667-11672.
3. Cabili M N, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev, 2011, 25: 1915-1927.
4. Trapnell C, Williams B A, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol, 2010, 28: 511-515.
5. Guttman M, Garber M, Levin J Z, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol, 2010, 28: 503-510.
6. Sone M, Hayashi T, Tarui H, et al. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci, 2007, 120: 2498-2506.
7. Mercer T R, Dinger M E, Sunkin S M, et al. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA, 2008, 105: 716-721.
8. Mercer T R, Dinger M E, Mattick J S. Long non-coding RNAs: insights into functions. Nat Rev Genet, 2009, 10: 155-159.
9. Wilusz J E, Sunwoo H, Spector D L. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev, 2009, 23: 1494-1504.
10. Yamasaki C, Murakami K, Fujii Y, et al. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res, 2008, 36: D793-799.
11. Harrow J, Denoeud F, Frankish A, et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol, 2006, 7: S41-49.
12. Pruitt K D, Tatusova T, Maglott D R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res, 2007, 35: D61-65.
13. Bono H, Kasukawa T, Furuno M, et al. FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones. Nucleic Acids Res, 2002, 30: 116-118.
14. Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 2009, 458: 223-227.
15. Khalil A, Guttman M, Huarte M, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA, 2009, 106: 11667.
16. Guttman M, Garber M, Levin J Z, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol, 2010, 28: 503-510.
17. Cabili M N, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev, 2011, 25: 1915-1927.
18. Rinn J, Kertesz M, Wang J, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 2007, 129: 1311-1323.
19. Nagano T, Mitchell J A, Sanz L A, et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science, 2008, 322: 1717-1720.
20. Pandey R R, Mondal T, Mohammad F, et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell, 2008, 32: 232-246.
21. Huarte M, Guttman M, Feldser D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell, 2010, 142: 409-419.
22. Liao Q, Liu C, Yuan X, et al. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res, 2011, 39: 3864-3878.
23. Gupta R A, Shah N, Wang K C, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 2010, 464: 1071-1076.
24. Huarte M, Rinn J L. Large non-coding RNAs: missing links in cancer? Hum Mol Genet, 2010, 19: R152-161.
25. Chen G, Wang Z, Wang D, et al. LncRNADisease: a database for long noncoding RNA associated diseases. Nucleic Acids Res, 2013, 41: D983-986.
26. Bernstein B E, Birney E, Dunham I, et al. An integrated encyclopedia of DNA elements in the human genome. Nature, 2012, 489: 57-74.
27. Fejes A P, Robertson G, Bilenky M, et al. FindPeaks 3. 1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics, 2008, 24: 1729-1730.
28. Kong L, Zhang Y, Ye Z Q, et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res, 2007, 35: W345-349.
29. Dunham I, Kundaje A, Aldred S F, et al. An integrated encyclopedia of DNA elements in the human genome. Nature, 2012, 489: 57-74.
30. Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol, 2005, 4: Article17.
31. Nayak R R, Kearns M, Spielman R S, et al. Coexpression network based on natural variation in human gene expression reveals gene interactions and functions. Genome Res, 2009, 19: 1953-1962.
32. Berkofsky-Fessler W, Nguyen T Q, Delmar P, et al. Preclinical biomarkers for a cyclin-dependent kinase inhibitor translate to candidate pharmacodynamic biomarkers in phase I patients. Mol Cancer Ther, 2009, 8: 2517-2525.
33. Ergun A, Lawrence C A, Kohanski M A, et al. A network biology approach to prostate cancer. Mol Syst Biol, 2007, 3: 82.
34. di Bernardo D, Thompson M J, Gardner T S, et al. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol, 2005, 23: 377-383.
35. Ding L, Getz G, Wheeler D A, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature, 2008, 455: 1069-1075.
36. Segal E, Friedman N, Koller D, et al. A module map showing conditional activity of expression modules in cancer. Nat Genet, 2004, 36: 1090-1098.
37. Saijo T, Ishii G, Ochiai A, et al. Eg5 expression is closely correlated with the response of advanced non-small cell lung cancer to antimitotic agents combined with platinum chemotherapy. Lung Cancer, 2006, 54: 217-225.
38. Okazaki Y, Furuno M, Kasukawa T, et al. Analysis of the mouse transcriptome based on functional annotation of 60770 full-length cDNAs. Nature, 2002, 420: 563-573.
39. Metzker M L. Sequencing technologies-the next generation. Nat Rev Genet, 2010, 11: 31-46.
40. Wang E T, Sandberg R, Luo S, et al. Alternative isoform regulation in human tissue transcriptomes. Nature, 2008, 456: 470-476.
41. Mortazavi A, Williams B A, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods, 2008, 5: 621-628.
42. Maher C A, Kumar-Sinha C, Cao X, et al. Transcriptome sequencing to detect gene fusions in cancer. Nature, 2009, 458: 97-101.
43. Pan Q, Shai O, Lee L J, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet, 2008, 40: 1413-1415.
44. Orom U A, Derrien T, Beringer M, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell, 2010, 143: 46-58.
45. Tripathi V, Ellis J D, Shen Z, et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell, 2010, 39: 925-938.