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Volumn 15, Issue 1, 2014, Pages

Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals

Author keywords

Bidirectional promoter; CpG island; Directional RNA Seq; Gene activation; Non coding RNA

Indexed keywords

MESSENGER RNA; UNTRANSLATED RNA;

EID: 84892465462     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-35     Document Type: Article
Times cited : (89)

References (39)
  • 3
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • 10.1038/nature11247, 3439153, 22955616, The ENCODE Project Consortium
    • The ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74. 10.1038/nature11247, 3439153, 22955616, The ENCODE Project Consortium.
    • (2012) Nature , vol.489 , pp. 57-74
  • 4
    • 58749097426 scopus 로고    scopus 로고
    • Small RNAs in transcriptional gene silencing and genome defence
    • 10.1038/nature07756, 3246369, 19158787
    • Moazed D. Small RNAs in transcriptional gene silencing and genome defence. Nature 2009, 457:413-420. 10.1038/nature07756, 3246369, 19158787.
    • (2009) Nature , vol.457 , pp. 413-420
    • Moazed, D.1
  • 5
    • 58749096360 scopus 로고    scopus 로고
    • On the road to reading the RNA-interference code
    • 10.1038/nature07754, 19158785
    • Siomi H, Siomi MC. On the road to reading the RNA-interference code. Nature 2009, 457:396-404. 10.1038/nature07754, 19158785.
    • (2009) Nature , vol.457 , pp. 396-404
    • Siomi, H.1    Siomi, M.C.2
  • 6
    • 0011823131 scopus 로고
    • A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs
    • 10.1073/pnas.86.8.2647, 286974, 2704740
    • Wagner RW, Smith JE, Cooperman BS, Nishikura K. A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs. Proc Natl Acad Sci USA 1989, 86:2647-2651. 10.1073/pnas.86.8.2647, 286974, 2704740.
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 2647-2651
    • Wagner, R.W.1    Smith, J.E.2    Cooperman, B.S.3    Nishikura, K.4
  • 7
    • 41149112564 scopus 로고    scopus 로고
    • A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition
    • 10.1101/gad.455708, 2275429, 18347095
    • Beltran M, Puig I, Peña C, García JM, Alvarez AB, Peña R, Bonilla F, de Herreros AG. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 2008, 22:756-769. 10.1101/gad.455708, 2275429, 18347095.
    • (2008) Genes Dev , vol.22 , pp. 756-769
    • Beltran, M.1    Puig, I.2    Peña, C.3    García, J.M.4    Alvarez, A.B.5    Peña, R.6    Bonilla, F.7    de Herreros, A.G.8
  • 8
    • 0025721986 scopus 로고
    • Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA
    • Munroe SH, Lazar MA. Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J Biol Chem 1991, 266:22083-22086.
    • (1991) J Biol Chem , vol.266 , pp. 22083-22086
    • Munroe, S.H.1    Lazar, M.A.2
  • 9
    • 0024424453 scopus 로고
    • An antisense mRNA directs the covalent modification of the transcript encoding fibroblast growth factor in Xenopus oocytes
    • 10.1016/0092-8674(89)90015-9, 2479482
    • Kimelman D, Kirschner MW. An antisense mRNA directs the covalent modification of the transcript encoding fibroblast growth factor in Xenopus oocytes. Cell 1989, 59:687-696. 10.1016/0092-8674(89)90015-9, 2479482.
    • (1989) Cell , vol.59 , pp. 687-696
    • Kimelman, D.1    Kirschner, M.W.2
  • 10
    • 0034646647 scopus 로고    scopus 로고
    • Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA
    • 10.1074/jbc.275.15.11507, 10753970
    • Hastings ML, Ingle HA, Lazar MA, Munroe SH. Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA. J Biol Chem 2000, 275:11507-11513. 10.1074/jbc.275.15.11507, 10753970.
    • (2000) J Biol Chem , vol.275 , pp. 11507-11513
    • Hastings, M.L.1    Ingle, H.A.2    Lazar, M.A.3    Munroe, S.H.4
  • 12
    • 77952514762 scopus 로고    scopus 로고
    • Regulation of Emx2 expression by antisense transcripts in murine cortico-cerebral precursors
    • 10.1371/journal.pone.0008658, 2799550, 20066053
    • Spigoni G, Gedressi C, Mallamaci A. Regulation of Emx2 expression by antisense transcripts in murine cortico-cerebral precursors. PLoS One 2010, 5:e8658. 10.1371/journal.pone.0008658, 2799550, 20066053.
    • (2010) PLoS One , vol.5
    • Spigoni, G.1    Gedressi, C.2    Mallamaci, A.3
  • 15
    • 4644309196 scopus 로고    scopus 로고
    • The functions of animal microRNAs
    • 10.1038/nature02871, 15372042
    • Ambros V. The functions of animal microRNAs. Nature 2004, 431:350-355. 10.1038/nature02871, 15372042.
    • (2004) Nature , vol.431 , pp. 350-355
    • Ambros, V.1
  • 16
    • 10644237968 scopus 로고    scopus 로고
    • RNAi-mediated pathways in the nucleus
    • 10.1038/nrg1500, 15630419
    • Matzke MA, Birchler JA. RNAi-mediated pathways in the nucleus. Nat Rev Genet 2005, 6:24-35. 10.1038/nrg1500, 15630419.
    • (2005) Nat Rev Genet , vol.6 , pp. 24-35
    • Matzke, M.A.1    Birchler, J.A.2
  • 18
    • 4344705410 scopus 로고    scopus 로고
    • Small interfering RNA-induced transcriptional gene silencing in human cells
    • 10.1126/science.1101372, 15297624
    • Morris KV, Chan SW-L, Jacobsen SE, Looney DJ. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 2004, 305:1289-1292. 10.1126/science.1101372, 15297624.
    • (2004) Science , vol.305 , pp. 1289-1292
    • Morris, K.V.1    Chan, S.W.-L.2    Jacobsen, S.E.3    Looney, D.J.4
  • 20
    • 84860885909 scopus 로고    scopus 로고
    • A Long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy
    • 10.1016/j.cell.2012.03.035, 3350859, 22541069
    • Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D. A Long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 2012, 149:819-831. 10.1016/j.cell.2012.03.035, 3350859, 22541069.
    • (2012) Cell , vol.149 , pp. 819-831
    • Cabianca, D.S.1    Casa, V.2    Bodega, B.3    Xynos, A.4    Ginelli, E.5    Tanaka, Y.6    Gabellini, D.7
  • 21
    • 0042329754 scopus 로고    scopus 로고
    • Structure, function and evolution of CpG island promoters
    • 10.1007/s00018-003-3088-6, 14504655
    • Antequera F. Structure, function and evolution of CpG island promoters. Cell Mol Life Sci 2003, 60:1647-1658. 10.1007/s00018-003-3088-6, 14504655.
    • (2003) Cell Mol Life Sci , vol.60 , pp. 1647-1658
    • Antequera, F.1
  • 22
    • 0023402842 scopus 로고
    • Coincident start sites for divergent transcripts at a randomly selected CpG-rich island of mouse
    • 553702, 2445562
    • Lavia P, Macleod D, Bird A. Coincident start sites for divergent transcripts at a randomly selected CpG-rich island of mouse. EMBO J 1987, 6:2773-2779. 553702, 2445562.
    • (1987) EMBO J , vol.6 , pp. 2773-2779
    • Lavia, P.1    Macleod, D.2    Bird, A.3
  • 23
  • 24
    • 80053428353 scopus 로고    scopus 로고
    • Single-stranded noncoding RNAs mediate local epigenetic alterations at gene promoters in rat cell lines
    • 10.1074/jbc.M111.275750, 3186369, 21844201
    • Tomikawa J, Shimokawa H, Uesaka M, Yamamoto N, Mori Y, Tsukamura H, Maeda K, Imamura T. Single-stranded noncoding RNAs mediate local epigenetic alterations at gene promoters in rat cell lines. J Biol Chem 2011, 286:34788-34799. 10.1074/jbc.M111.275750, 3186369, 21844201.
    • (2011) J Biol Chem , vol.286 , pp. 34788-34799
    • Tomikawa, J.1    Shimokawa, H.2    Uesaka, M.3    Yamamoto, N.4    Mori, Y.5    Tsukamura, H.6    Maeda, K.7    Imamura, T.8
  • 29
    • 0023216891 scopus 로고
    • CpG islands in vertebrate genomes
    • 10.1016/0022-2836(87)90689-9, 3656447
    • Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987, 196:261-282. 10.1016/0022-2836(87)90689-9, 3656447.
    • (1987) J Mol Biol , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1    Frommer, M.2
  • 31
    • 84859087611 scopus 로고    scopus 로고
    • R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters
    • 10.1016/j.molcel.2012.01.017, 3319272, 22387027
    • Ginno PA, Lott PL, Christensen HC, Korf I, Chédin F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell 2012, 45:814-825. 10.1016/j.molcel.2012.01.017, 3319272, 22387027.
    • (2012) Mol Cell , vol.45 , pp. 814-825
    • Ginno, P.A.1    Lott, P.L.2    Christensen, H.C.3    Korf, I.4    Chédin, F.5
  • 32
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • 10.1093/bioinformatics/btp120, 2672628, 19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 35
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • 10.1038/nbt.1621, 3146043, 20436464
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28:511-515. 10.1038/nbt.1621, 3146043, 20436464.
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    van Baren, M.J.6    Salzberg, S.L.7    Wold, B.J.8    Pachter, L.9
  • 36
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: the European molecular biology open software suite
    • 10.1016/S0168-9525(00)02024-2, 10827456
    • Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet 2000, 16:276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 37
    • 84892868953 scopus 로고    scopus 로고
    • RGADEM: de novo motif discovery (R package version 2.8.0)
    • rGADEM: de novo motif discovery (R package version 2.8.0). [http://www.bioconductor.org/packages/release/bioc/html/rGADEM.html].
  • 39
    • 59649113226 scopus 로고    scopus 로고
    • GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery
    • 10.1089/cmb.2008.16TT, 2756050,2756050, 19193149
    • Li L. GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. J Comput Biol 2009, 16:317-329. 10.1089/cmb.2008.16TT, 2756050,2756050, 19193149.
    • (2009) J Comput Biol , vol.16 , pp. 317-329
    • Li, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.