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Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome

Jalali, Saakshi, Singh, Amrita, Maiti, Souvik, Scaria, Vinod·2017·Journal of Translational Medicine
DOI 10.1186/s12967-017-1282-9PMC PMC7670996
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  1. Carninci P. Tagging mammalian transcription complexity. Trends Genet. 2006;22:501–10. · DOI
  2. Mercer TR, Dinger ME. M attick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009;10:155–9. · DOI · Paper page
  3. Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009;136:629–41. · DOI · Paper page
  4. Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell. 2011;43:904–14. · DOI
  5. Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 2009;23:1494–504. · DOI
  6. Braconi C, Kogure T, Valeri N, Huang N, Nuovo G, Costinean S, et al. microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene. 2011;30:4750–6. · DOI · Paper page
  7. Jalali S, Kapoor S, Sivadas A, Bhartiya D, Scaria V. Computational approaches towards understanding human long non-coding RNA biology. Bioinformatics. 2015;31:2241–51. · DOI
  8. Kirsebom LA, Virtanen A, Mikkelsen NE. Aminoglycoside interactions with RNAs and nucleases. Handb Exp Pharmacol. 2006;173:73–96. · DOI
  9. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563–73. · DOI
  10. Tsai M-C, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science [Internet]. 2010;329:689–93. · DOI · Paper page
  11. Bhartiya D, Kapoor S, Jalali S, Sati S, Kaushik K, Sachidanandan C, et al. Conceptual approaches for lncRNA drug discovery and future strategies. Expert Opin Drug Discov. 2012;7:503–13. · DOI
  12. Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S, Scaria V. Systematic transcriptome wide analysis of lncRNA-miRNA interactions. PLoS One. 2013;8:e53823. · DOI
  13. Li Y, Syed J, Sugiyama H. RNA-DNA triplex formation by long noncoding RNAs. Cell Chem Biol. 2016;6:7743.
  14. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell. 2011;44:667–78. · DOI
  15. Jeon Y, Lee JT. YY1 tethers Xist RNA to the inactive X nucleation center. Cell. 2011;146:119–33. · DOI
  16. Grote P, Herrmann BG. The long non-coding RNA Fendrr links epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis. RNA Biol. 2013;10:1579–85. · DOI
  17. Blume SW, Meng Z, Shrestha K, Snyder RC, Emanuel PD. The 5′-untranslated RNA of the human dhfr minor transcript alters transcription pre-initiation complex assembly at the major (core) promoter. J Cell Biochem. 2003;88:165–80. · DOI
  18. Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature. 2007;445:666–70. · DOI
  19. O’Leary VB, Ovsepian SV, Carrascosa LG, Buske FA, Radulovic V, Niyazi M, et al. PARTICLE, a triplex-forming long ncRNA, Regulates locus-specific methylation in response to low-dose irradiation. Cell Rep. 2015;11:474–85. · DOI
  20. Mondal T, Subhash S, Vaid R, Enroth S, Uday S, Reinius B, et al. MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures. Nat Commun. 2015;6:7743. · DOI
  21. Postepska-Igielska A, Giwojna A, Gasri-Plotnitsky L, Schmitt N, Dold A, Ginsberg D, et al. LncRNA Khps1 regulates expression of the proto-oncogene SPHK1 via triplex-mediated changes in chromatin structure. Mol Cell. 2015;60:626–36. · DOI
  22. Roberts RW, Crothers DM. Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition. Science. 1992;258:1463–6. · DOI
  23. Buske FA, Mattick JS, Bailey TL. Potential in vivo roles of nucleic acid triple-helices. RNA Biol. 2011;8:427–39. · DOI
  24. Hoyne PR, Gacy AM, McMurray CT, Maher LJ. Stabilities of intrastrand pyrimidine motif DNA and RNA triple helices. Nucleic Acids Res. 2000;28:770–5. · DOI
  25. Chu C, Quinn J, Chang HY. Chromatin isolation by RNA purification (ChIRP). J Vis Exp. 2012;61:4–9.
  26. Simon MD. Capture hybridization analysis of RNA targets (CHART). Curr Protoc Mol Biol. 2013;21:21–5.
  27. Buske FA, Bauer DC, Mattick JS, Bailey TL. Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data. Genome Res. 2012;22:1372–81. · DOI
  28. Wongsurawat T, Jenjaroenpun P, Kwoh CK, Kuznetsov V. Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity. Nucleic Acids Res. 2012;40:e16. · DOI
  29. Buske FA, Bauer DC, Mattick JS, Bailey TL. Triplex-inspector: an analysis tool for triplex-mediated targeting of genomic loci. Bioinformatics. 2013;29:1895–7. · DOI
  30. Chang C-W, Cheng W-C, Chen C-R, Shu W-Y, Tsai M-L, Huang C-L, et al. Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis. PLoS ONE. 2011;6:e22859. · DOI
  31. Shannon P. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504. · DOI · Paper page
  32. Xodo LE, Manzini G, Quadrifoglio F. Spectroscopic and calorimetric investigation on the DNA triplex formed by d(CTCTTCTTTCTTTTCTTTCTTCTC) and d(GAGAAGAAAGA) at acidic pH. Nucleic Acids Res. 1990;18:3557–64. · DOI
  33. Manzini G, Xodo LE, Gasparotto D, Quadrifoglio F, van der Marel GA, van Boom JH. Triple helix formation by oligopurine–oligopyrimidine DNA fragments. Electrophoretic and thermodynamic behavior. J Mol Biol [Internet]. 1990;213:833–43. · DOI
  34. Scaria PV, Will S, Levenson C, Shafer RH. Physicochemical studies of the d(G3T4G3)*d(G3A4G3).d(C3T4C3) triple helix. J Biol Chem. 1995;270:7295–303. · DOI
  35. Ziebarth JD, Bhattacharya A, Cui Y. CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization. Nucleic Acids Res. 2013;41:D188–94. · DOI
  36. Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, et al. CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell. 2015;163:1611–27. · DOI · Paper page
  37. Ong C-T, Corces VG. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet. 2014;15:234–46. · DOI
  38. Guardavaccaro D, Frescas D, Dorrello NV, Peschiaroli A, Multani AS, Cardozo T, et al. Control of chromosome stability by the β-TrCP–REST–Mad2 axis. Nat Nat Publ Group. 2008;452:365–9.
  39. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22:1760–74. · DOI · Paper page
  40. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25:1915–27. · DOI
  41. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009;458:223–7. · DOI · Paper page
  42. Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012;81:145–66. · DOI
  43. Quek XC, Thomson DW, Maag JLV, Bartonicek N, Signal B, Clark MB, et al. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res. 2015;43:D168–73. · DOI
  44. Vinogradova S, Mironov A. HOTAIR expression and its role in chromatin modifications. In: Information technology and systems - 2013 conference for young scientists and engineers, 1–6 September, Kaliningrad, Russia. ISBN 978-5-901158-23-4
  45. Schlumbrecht MP, Xie S-S, Shipley GL, Urbauer DL, Broaddus RR. Molecular clustering based on ERα and EIG121 predicts survival in high-grade serous carcinoma of the ovary/peritoneum. Mod Pathol [Internet]. 2011;24:453–62. · DOI
  46. Deng L, Feng J, Broaddus RR. The novel estrogen-induced gene EIG121 regulates autophagy and promotes cell survival under stress. Cell Death Dis. 2010;1:e32. · DOI

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Metadata

Authors
Jalali, S., Singh, A., Maiti, S., & Scaria, V.
ORCID
Scaria, Vinod
Venue
Journal of Translational Medicine
Publisher
Springer Science and Business Media LLC
Published
2017-09-02
Volume
15
Issue
1
ISSN
1479-5876
DOI
10.1186/s12967-017-1282-9
PMC
PMC7670996
Cited by
37
References
0
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (tdm)
Funders
Council of Scientific and Industrial Research (BSC0123)

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