非编码DNA序列的功能及其鉴定
收稿日期: 2013-06-07
修回日期: 2013-07-31
网络出版日期: 2013-10-23
基金资助
国家重点基础研究发展计划项目(973计划)(编号：2012CB722304)和河南省基础与前沿技术研究计划项目(编号：102300413213)资助
Characterization and identification of functional elements in non-coding DNA sequences
Received date: 2013-06-07
Revised date: 2013-07-31
Online published: 2013-10-23
秦丹 徐存拴 . 非编码DNA序列的功能及其鉴定[J]. 遗传, 2013 , 35(11) : 1253 -1264 . DOI: 10.3724/SP.J.1005.2013.01253
The non-coding DNA sequences refer to non-protein-coding DNA sequences in genome. These sequences can bind with transcription factors or be transcribed as functional RNAs, thus participating in the regulation of many physiological activities and pathological processes. Aiming at gene expression regulation, this review focuses on the recent progress of non-coding DNA and illustrates their structures, functions and potential acting mechanisms. Meanwhile, some computational and experimental methods of identifying functional elements in the non-coding DNAs are introduced. Finally, further studies in this field are proposed.
[1] Ponting CP, Belgard TG. Transcribed dark matter: meaning or myth? Hum Mol Gene, 2010, 19(R2): R162–R168.<\p>
[2] ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature, 2012, 489(7414): 57–74.<\p>
[3] Vickers KC, Palmisano BT, Remaley AT. Remaley. The role of noncoding "junk DNA" in cardiovascular disease. Clin Chem, 2010, 56(10): 1518–1520.<\p>
[4] Xie C, Zhang YE, Chen JY, Liu CJ, Zhou WZ, Li Y, Zhang M, Zhang R, Wei L, Li CY. Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genet, 2012, 8(9): e1002942.<\p>
[5] Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB. Annotating non-coding regions of the genome. Nat Rev Genet, 2010, 11(8): 559–571.<\p>
[6] Lander ES. Initial sequencing and analysis of the human genome. Nature, 2001, 409(6822): 860–921.<\p>
[7] Gangwal K, Lessnick SL. Microsatellites are EWS/FLI response elements: genomic "junk" is EWS/FLI's treasure. Cell Cycle, 2008, 7(20): 3127–3132.<\p>
[8] Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Ir-vine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. The regulated retrotrans-poson transcriptome of mammalian cells. Nat Genet, 2009, 41(5): 563–571.<\p>
[9] Zuckerkandl E, Cavalli G. Combinatorial epigenetics, "junk DNA", and the evolution of complex organisms. Gene, 2007, 390(1-2): 232–242.<\p>
[10] Zheng DY, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu YT, Denoeud F, Antonarakis SE, Snyder M, Ruan YJ, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. Pseudogenes in the ENCODE regions: con-sensus annotation, analysis of transcription, and evolution. Genome Res, 2007, 17(6): 839–851.<\p>
[11] Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, Hannon GJ. Pseudogene-derived small inter-fering RNAs regulate gene expression in mouse oocytes. Nature, 2008, 453(7194): 534–538.<\p>
[12] Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramo-chi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H. Endogenous siRNAs from naturally formed dsRNAs regulate tran-scripts in mouse oocytes. Nature, 2008, 453(7194): 539– 543.<\p>
[13] Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Ta-naka Y, Gabellini D. A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell, 2012, 149(4): 819–831.<\p>
[14] Tsai MC, Spitale RC, Chang HY. Long intergenic non-coding RNAs: new links in cancer progression. Cancer Res, 2011, 71(1): 3–7.<\p>
[15] Hemberg M, Gray JM, Cloonan N, Kuersten S, Grimmond S, Greenberg ME, Kreiman G. Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites. Nucleic Acids Res, 2012, 40(16): 7858–7869.<\p>
[16] Mullapudi N, Joseph SJ, Kissinger JC. Identification and functional characterization of cis-regulatory elements in the apicomplexan parasite Toxoplasma gondii. Genome Biol, 2009, 10(4): R34.<\p>
[17] Narlikar L, Ovcharenko I. Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic, 2009, 8(4): 215–230.<\p>
[18] Lee JT. Epigenetic regulation by long noncoding RNAs. Science, 2012, 338(6113): 1435–1439.<\p>
[19] Ogbourne S, Antalis TM. Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes. Biochem J, 1998, 331 (Pt 1): 1–14.<\p>
[20] Noonan JP, McCallion AS. Genomics
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