Age-dependent differential expression profile of a novel intergenic long noncoding RNA in rat brain

International Journal of Developmental Neuroscience

Volumn 46, Issue , 2015, Pages 55-66

  Kour, Sukhleen ^a   Rath, Pramod C ^a  

^a JAWAHARLAL NEHRU UNIVERSITY   (India)

Author keywords

Aging; Brain; Hippocampus; In situ RNA hybridization; Long noncoding RNA

Indexed keywords

LONG UNTRANSLATED RNA; RNA; TRANSCRIPTION FACTOR; MESSENGER RNA;

ADULT; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BINDING SITE; BRAIN DEVELOPMENT; CELL GROWTH; CELL SURVIVAL; CELLS BY BODY ANATOMY; CENTRAL NERVOUS SYSTEM; CONTROLLED STUDY; DNA SEQUENCE; DOWNSTREAM PROCESSING; GENE SEQUENCE; IN SITU HYBRIDIZATION; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA TRANSCRIPTION; AGING; ANIMAL; BIOLOGY; BRAIN; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; NEWBORN; PHYSIOLOGY; WISTAR RAT;

MAMMALIA; RATTUS;

AGING; ANIMALS; ANIMALS, NEWBORN; BINDING SITES; BRAIN; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MALE; RATS; RATS, WISTAR; RNA, LONG NONCODING; RNA, MESSENGER;

EID: 84939818239     PISSN: 07365748     EISSN: 1873474X     Source Type: Journal    
DOI: 10.1016/j.ijdevneu.2015.07.011     Document Type: Article

References (55)

1. Abdelmohsen K., Panda A., Kang M.J., Xu J., Selimyan R., Yoon J.H., Martindale J.L., De S., Wood W.H., 3rd B., Becker K.G., Gorospe M. Senescence-associated lncRNAs: senescence-associated long noncoding RNAs. Aging Cell 2013, 12:890-900.
2. Adler A.S., Sinha S., Kawahara T.L., Zhang J.Y., Segal E., Chang H.Y. Motif module map reveals enforcement of aging by continual NF-kappaB activity. Genes Dev. 2007, 21:3244-3257.
3. Bernard D., Prasanth K.V., Tripathi V., Colasse S., Nakamura T., Xuan Z., Zhang M.Q., Sedel F., Jourdren L., Coulpier F., Triller A., Spector D.L., Bessis A. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J. 2010, 29:3082-3093.
4. Bernstein B.E., Birney E., Dunham I., Green E.D., Gunter C., Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
5. Berretta J., Morillon A. Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep. 2009, 10:973-982.
6. Bertani S., Sauer S., Bolotin E., Sauer F. The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. Mol. Cell 2011, 43:1040-1046.
7. Broadbent H.M., Peden J.F., Lorkowski S., Goel A., Ongen H., Green F., Clarke R., Collins R., Franzosi M.G., Tognoni G., Seedorf U., Rust S., Eriksson P., Hamsten A., Farrall M., Watkins H. Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Hum. Mol. Genet. 2008, 17:806-814.
8. Cesana M., Cacchiarelli D., Legnini I., Santini T., Sthandier O., Chinappi M., Tramontano A., Bozzoni I. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 2011, 147:358-369.
9. Chodroff R.A., Goodstadt L., Sirey T.M., Oliver P.L., Davies K.E., Green E.D., Molnar Z., Ponting C.P. Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol. 2010, 11:R72.
10. Chow J.C., Ciaudo C., Fazzari M.J., Mise N., Servant N., Glass J.L., Attreed M., Avner P., Wutz A., Barillot E., Greally J.M., Voinnet O., Heard E. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 2010, 141:956-969.
11. Chu C., Qu K., Zhong F.L., Artandi S.E., Chang H.Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 2011, 44:667-678.
12. Clark B.S., Blackshaw S. Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease. Front. Genet. 2014, 5. 164.
13. Clark M.B., Mercer T.R., Bussotti G., Leonardi T., Haynes K.R., Crawford J., Brunck M.E., Cao K.A., Thomas G.P., Chen W.Y., Taft R.J., Nielsen L.K., Enright A.J., Mattick J.S., Dinger M.E. Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nat. Methods 2015, 12:339-342.
14. Cusanelli E., Romero C.A., Chartrand P. Telomeric noncoding RNA TERRA is induced by telomere shortening to nucleate telomerase molecules at short telomeres. Mol. Cell 2013, 51:780-791.
15. de Koning A.P., Gu W., Castoe T.A., Batzer M.A., Pollock D.D. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011, 7:e1002384.
16. Denas O., Sandstrom R., Cheng Y., Beal K., Herrero J., Hardison R.C., Taylor J. Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution. BMC Genom. 2015, 16:87.
17. Derrien T., Johnson R., Bussotti G., Tanzer A., Djebali S., Tilgner H., Guernec G., Martin D., Merkel A., Knowles D.G., Lagarde J., Veeravalli L., Ruan X., Ruan Y., Lassmann T., Carninci P., Brown J.B., Lipovich L., Gonzalez J.M., Thomas M., Davis C.A., Shiekhattar R., Gingeras T.R., Hubbard T.J., Notredame C., Harrow J., Guigo R. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012, 22:1775-1789.
18. Dey I., Rath P.C. A novel rat genomic simple repeat DNA with RNA-homology shows triplex (H-DNA)-like structure and tissue-specific RNA expression. Biochem. Biophys. Res. Commun. 2005, 327:276-286.
19. ElSharawy A., Keller A., Flachsbart F., Wendschlag A., Jacobs G., Kefer N., Brefort T., Leidinger P., Backes C., Meese E., Schreiber S., Rosenstiel P., Franke A., Nebel A. Genome-wide miRNA signatures of human longevity. Aging Cell 2012, 11:607-616.
20. Faghihi M.A., Modarresi F., Khalil A.M., Wood D.E., Sahagan B.G., Morgan T.E., Finch C.E., St Laurent G., Kenny P.J., Wahlestedt C. Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat. Med. 2008, 14:723-730.
21. Feng J., Bi C., Clark B.S., Mady R., Shah P., Kohtz J.D. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev. 2006, 20:1470-1484.
22. Girard A., Sachidanandam R., Hannon G.J., Carmell M.A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 2006, 442:199-202.
23. Guo L., Zhao Y., Yang S., Zhang H., Wu Q., Chen F. An integrated evolutionary analysis of miRNA-lncRNA in mammals. Mol. Biol. Rep. 2014, 41:201-207.
24. Guttman M., Amit I., Garber M., French C., Lin M.F., Feldser D., Huarte M., Zuk O., Carey B.W., Cassady J.P., Cabili M.N., Jaenisch R., Mikkelsen T.S., Jacks T., Hacohen N., Bernstein B.E., Kellis M., Regev A., Rinn J.L., Lander E.S. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458:223-227.
25. Johnsson P., Lipovich L., Grander D., Morris K.V. Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim. Biophys. Acta 2014, 1840:1063-1071.
26. Kapusta A., Kronenberg Z., Lynch V.J., Zhuo X., Ramsay L., Bourque G., Yandell M., Feschotte C. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet. 2013, 9:e1003470.
27. Khalil A.M., Guttman M., Huarte M., Garber M., Raj A., Rivea Morales D., Thomas K., Presser A., Bernstein B.E., van Oudenaarden A., Regev A., Lander E.S., Rinn J.L. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:11667-11672.
28. Lau N.C., Seto A.G., Kim J., Kuramochi-Miyagawa S., Nakano T., Bartel D.P., Kingston R.E. Characterization of the piRNA complex from rat testes. Science 2006, 313:363-367.
29. Lee J.T. Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control. Nat. Rev. Mol. Cell Biol. 2011, 12:815-826.
30. Mattick J.S., Rinn J.L. Discovery and annotation of long noncoding RNAs. Nat. Struct. Mol. Biol. 2015, 22:5-7.
31. McHugh C.A., Chen C.K., Chow A., Surka C.F., Tran C., McDonel P., Pandya-Jones A., Blanco M., Burghard C., Moradian A., Sweredoski M.J., Shishkin A.A., Su J., Lander E.S., Hess S., Plath K., Guttman M. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 2015, 21:232-236.
32. Mercer T.R., Dinger M.E., Sunkin S.M., Mehler M.F., Mattick J.S. Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:716-721.
33. Mercer T.R., Gerhardt D.J., Dinger M.E., Crawford J., Trapnell C., Jeddeloh J.A., Mattick J.S., Rinn J.L. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol. 2012, 30:99-104.
34. Mercer T.R., Mattick J.S. Structure and function of long noncoding RNAs in epigenetic regulation. Nat. Struct. Mol. Biol. 2013, 20:300-307.
35. Milligan M.J., Lipovich L. Pseudogene-derived lncRNAs: emerging regulators of gene expression. Front. Genet. 2014, 5:476.
36. Modarresi F., Faghihi M.A., Patel N.S., Sahagan B.G., Wahlestedt C., Lopez-Toledano M.A. Knockdown of BACE1-AS nonprotein-coding transcript modulates Beta-Amyloid-related hippocampal neurogenesis. Int. J. Alzheimers Dis. 2011, 929042-929053.
37. Ng S.Y., Johnson R., Stanton L.W. Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J. 2012, 31:522-533.
38. Ponjavic J., Ponting C.P. The long and the short of RNA maps. Bioessays 2007, 29:1077-1080.
39. Quek X.C., Thomson D.W., Maag J.L., Bartonicek N., Signal B., Clark M.B., Gloss B.S., Dinger M.E. lncRNAdb v2. 0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res. 2015, 43:D168-D173.
40. Rapicavoli N.A., Qu K., Zhang J., Mikhail M., Laberge R.M., Chang H.Y. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. Elife 2013, 2:e00762.
41. Redon S., Zemp I., Lingner J. A three-state model for the regulation of telomerase by TERRA and hnRNPA1. Nucleic Acids Res. 2013, 41:9117-9128.
42. Roberts T.C., Morris K.V., Wood M.J. The role of long non-coding RNAs in neurodevelopment, brain function and neurological disease. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2014, 369:1652.
43. Rossi M.N., Antonangeli F. LncRNAs: new players in apoptosis control. Int. J. Cell Biol. 2014, 473857.
44. Scheele C., Petrovic N., Faghihi M.A., Lassmann T., Fredriksson K., Rooyackers O., Wahlestedt C., Good L., Timmons J.A. The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function. BMC Genom. 2007, 8:74-87.
45. St Laurent G., Wahlestedt C., Kapranov P. The Landscape of long noncoding RNA classification. Trends Genet. 2015, 31:239-251.
46. Tissenbaum H.A. Genetics, life span, health span, and the aging process in Caenorhabditis elegans. J. Gerontol. A. Biol. Sci. Med. Sci. 2012, 67:503-510.
47. Tripathi V., Ellis J.D., Shen Z., Song D.Y., Pan Q., Watt A.T., Freier S.M., Bennett C.F., Sharma A., Bubulya P.A., Blencowe B.J., Prasanth S.G., Prasanth K.V. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 2010, 39:925-938.
48. Tripathi V., Shen Z., Chakraborty A., Giri S., Freier S.M., Wu X., Zhang Y., Gorospe M., Prasanth S.G., Lal A., Prasanth K.V. Long noncoding RNA MALAT1 controls cell cycle progression by regulating the expression of oncogenic transcription factor B-MYB. PLoS Genet. 2013, 9:e1003368.
49. van Almen G.C., Verhesen W., van Leeuwen R.E., van de Vrie M., Eurlings C., Schellings M.W., Swinnen M., Cleutjens J.P., van Zandvoort M.A., Heymans S., Schroen B. MicroRNA-18 and microRNA-19 regulate CTGF and TSP-1 expression in age-related heart failure. Aging Cell 2011, 10:769-779.
50. van Balkom B.W., de Jong O.G., Smits M., Brummelman J., den Ouden K., de Bree P.M., van Eijndhoven M.A., Pegtel D.M., Stoorvogel W., Wurdinger T., Verhaar M.C. Endothelial cells require miR-214 to secrete exosomes that suppress senescence and induce angiogenesis in human and mouse endothelial cells. Blood 2013, 121:3997-4006. S3991-3915.
51. Vucicevic D., Corradin O., Ntini E., Scacheri P.C., Orom U.A. Long ncRNA expression associates with tissue-specific enhancers. Cell Cycle 2015, 14:253-260.
52. Wang Y., Xu Z., Jiang J., Xu C., Kang J., Xiao L., Wu M., Xiong J., Guo X., Liu H. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev. Cell 2013, 25:69-80.
53. Willingham A.T., Orth A.P., Batalov S., Peters E.C., Wen B.G., Aza-Blanc P., Hogenesch J.B., Schultz P.G. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 2005, 309:1570-1573.
54. Xue Y., Gu D., Ma G., Zhu L., Hua Q., Chu H., Tong N., Chen J., Zhang Z., Wang M. Genetic variants in lncRNA HOTAIR are associated with risk of colorectal cancer. Mutagenesis 2015, 30:303-310.
55. Yang G., Lu X., Yuan L. LncRNA: a link between RNA and cancer. Biochim. Biophys. Acta 2014, 1839:1097-1109.