Physiological roles of long noncoding RNAs: Insight from knockout mice

Trends in Cell Biology

Volumn 24, Issue 10, 2014, Pages 594-602

  Li, Lingjie ^a   Chang, Howard Y ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Gene targeting; Genetic study; Knockout; lncRNA; Phenotype

Indexed keywords

LONG UNTRANSLATED RNA;

GENE; GENE EXPRESSION; GENE SEQUENCE; GROWTH REGULATION; HEART DEVELOPMENT; HUMAN; IMMUNITY; KNOCKOUT MOUSE; LUNG DEVELOPMENT; NONHUMAN; ORGANOGENESIS; PHYSIOLOGY; PROMOTER REGION; REVIEW; RNA TRANSCRIPTION; ANIMAL; GENE INACTIVATION; GENE TARGETING; MOUSE; PROCEDURES; TRENDS;

ANIMALS; GENE KNOCKOUT TECHNIQUES; GENE TARGETING; HUMANS; MICE; MICE, KNOCKOUT; RNA, LONG NONCODING;

EID: 84908482957     PISSN: 09628924     EISSN: 18793088     Source Type: Journal    
DOI: 10.1016/j.tcb.2014.06.003     Document Type: Review

References (66)

1. Djebali S., et al. Landscape of transcription in human cells. Nature 2012, 489:101-108.
2. Mattick J.S. RNA regulation: a new genetics?. Nat. Rev. Genet. 2004, 5:316-323.
3. Gutschner T., Diederichs S. The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol. 2012, 9:703-719.
4. Fatica A., Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat. Rev. Genet. 2014, 15:7-21.
5. Rinn J.L., Chang H.Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 2012, 81:145-166.
6. Wang K.C., Chang H.Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 2011, 43:904-914.
7. Kung J.T., et al. Long noncoding RNAs: past, present, and future. Genetics 2013, 193:651-669.
8. Derrien T., et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012, 22:1775-1789.
9. Cabili M.N., et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011, 25:1915-1927.
10. Ulitsky I., et al. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 2011, 147:1537-1550.
11. Ulitsky I., Bartel D.P. lincRNAs: genomics, evolution, and mechanisms. Cell 2013, 154:26-46.
12. Wapinski O., Chang H.Y. Long noncoding RNAs and human disease. Trends Cell Biol. 2011, 21:354-361.
13. Batista P.J., Chang H.Y. Long noncoding RNAs: cellular address codes in development and disease. Cell 2013, 152:1298-1307.
14. Sigova A.A., et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:2876-2881.
15. Grote P., et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev. Cell 2013, 24:206-214.
16. Grote P., Herrmann B.G. The long non-coding RNA Fendrr links epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis. RNA Biol. 2013, 10:1579-1585.
17. Gutschner T., et al. Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases. Genome Res. 2011, 21:1944-1954.
18. Latos P.A., et al. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 2012, 338:1469-1472.
19. Sauvageau M., et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife 2013, 2:e01749.
20. Rinn J.L., et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007, 129:1311-1323.
21. Tsai M.C., et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010, 329:689-693.
22. Chu C., et al. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 2011, 44:667-678.
23. Gupta R.A., et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464:1071-1076.
24. Kim K., et al. HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene 2013, 32:1616-1625.
25. Kogo R., et al. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 2011, 71:6320-6326.
26. Schorderet P., Duboule D. Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet. 2011, 7:e1002071.
27. Li L., et al. Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Rep. 2013, 5:3-12.
28. Suemori H., Noguchi S. Hox C cluster genes are dispensable for overall body plan of mouse embryonic development. Dev. Biol. 2000, 220:333-342.
29. Szafranski P., et al. Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder. Genome Res. 2013, 23:23-33.
30. Lee J.T., Bartolomei M.S. X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 2013, 152:1308-1323.
31. Yildirim E., et al. Xist RNA is a potent suppressor of hematologic cancer in mice. Cell 2013, 152:727-742.
32. Marahrens Y., et al. Xist-deficient mice are defective in dosage compensation but not spermatogenesis. Genes Dev. 1997, 11:156-166.
33. Penny G.D., et al. Requirement for Xist in X chromosome inactivation. Nature 1996, 379:131-137.
34. Tian D., et al. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 2010, 143:390-403.
35. Sun S., et al. Jpx RNA activates Xist by evicting CTCF. Cell 2013, 153:1537-1551.
36. Lee J.T. Disruption of imprinted X inactivation by parent-of-origin effects at Tsix. Cell 2000, 103:17-27.
37. Sado T., et al. Regulation of imprinted X-chromosome inactivation in mice by Tsix. Development 2001, 128:1275-1286.
38. Sleutels F., et al. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 2002, 415:810-813.
39. Nagano T., et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 2008, 322:1717-1720.
40. Mancini-Dinardo D., et al. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev. 2006, 20:1268-1282.
41. Pandey R.R., et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 2008, 32:232-246.
42. Fitzpatrick G.V., et al. Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1. Nat. Genet. 2002, 32:426-431.
43. Valenzuela D.M., et al. High-throughput engineering of the mouse genome coupled with high-resolution expression analysis. Nat. Biotechnol. 2003, 21:652-659.
44. Gomez J.A., et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus. Cell 2013, 152:743-754.
45. Latiano A., et al. Investigation of multiple susceptibility loci for inflammatory bowel disease in an Italian cohort of patients. PLoS ONE 2011, 6:e22688.
46. Silverberg M.S., et al. Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. Nat. Genet. 2009, 41:216-220.
47. Collier S.P., et al. Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells. J. Immunol. 2012, 189:2084-2088.
48. Kawakami T., et al. Characterization of loss-of-inactive X in Klinefelter syndrome and female-derived cancer cells. Oncogene 2004, 23:6163-6169.
49. McDonald H.L., et al. Involvement of the X chromosome in non-Hodgkin lymphoma. Genes Chromosomes Cancer 2000, 28:246-257.
50. Gutschner T., et al. MALAT1 - a paradigm for long noncoding RNA function in cancer. J. Mol. Med. (Berl.) 2013, 91:791-801.
51. Eissmann M., et al. Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol. 2012, 9:1076-1087.
52. Zhang B., et al. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep. 2012, 2:111-123.
53. Nakagawa S., et al. Malat1 is not an essential component of nuclear speckles in mice. Rna 2012, 18:1487-1499.
54. Miska E.A., et al. Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet. 2007, 3:e215.
55. Abbott A.L. Uncovering new functions for microRNAs in Caenorhabditis elegans. Curr. Biol. 2011, 21:R668-R671.
56. Gutschner T., et al. The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res. 2013, 73:1180-1189.
57. Kornienko A.E., et al. Gene regulation by the act of long non-coding RNA transcription. BMC Biol. 2013, 11:59.
58. Meller V.H., Rattner B.P. The roX genes encode redundant male-specific lethal transcripts required for targeting of the MSL complex. EMBO J. 2002, 21:1084-1091.
59. Franke A., Baker B.S. The rox1 and rox2 RNAs are essential components of the compensasome, which mediates dosage compensation in Drosophila. Mol. Cell 1999, 4:117-122.
60. Liu G., et al. A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle 2013, 12:2061-2072.
61. Modarresi F., et al. Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat. Biotechnol. 2012, 30:453-459.
62. Wheeler T.M., et al. Targeting nuclear RNA for in vivo correction of myotonic dystrophy. Nature 2012, 488:111-115.
63. Nakagawa S., et al. Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J. Cell Biol. 2011, 193:31-39.
64. Gabory A., et al. The H19 locus: role of an imprinted non-coding RNA in growth and development. Bioessays 2010, 32:473-480.
65. Lyon M.F. Some milestones in the history of X-chromosome inactivation. Ann. Rev. Genet. 1992, 26:16-28.
66. Ilik I., Akhtar A. roX RNAs: non-coding regulators of the male X chromosome in flies. RNA Biol. 2009, 6:113-121.