长链非编码RNA及其在畜禽生长调控中的研究进展

doi:10.16431/j.cnki.1671-7236.2016.01.029

摘要/Abstract

摘要： 长链非编码RNA(long non-coding RNA,lncRNA)是一类长度大于200个核苷酸、没有编码蛋白能力的RNA,通常被认为是一类异构体RNA。近年来,越来越多的研究表明,lncRNA在许多重要的生物作用及人类疾病发展中起关键作用。lncRNA作为调节因子参与基因表达调控的各个层次,在表观遗传、转录调控及转录后调控等方面有着广泛功能。研究结果已表明,lncRNA表达水平的紊乱与人类各种癌症及其他疾病有很大的关系。作为基因调控网络的调控因子,lncRNA被越来越多的研究者所关注。相较于人类医学,lncRNA在畜禽上的研究尚处于起步阶段。作者对lncRNA的特点、分类、作用机制、研究方法及其在畜禽生长调控方面的研究进展进行了综述,并对其在畜禽养殖中的应用进行了展望,以期为lncRNA在畜禽生长调控方面开展深入研究提供理论基础。

关键词: 长链非编码RNA; 基因调控; 作用机制; 畜禽; 研究进展

Abstract: Long non-coding RNA(lncRNA) are non-protein coding transcripts longer than 200 nucleotides that are usually considered collectively as a heterogeneous class of RNA.Recently, an increasing number of studies have shown that lncRNA have a pivotal role in various critical biological processes and a number of complex human diseases.lncRNA act as regulators at different levels of gene expression including chromatin organization, transcriptional regulation, and post-transcriptional control.lncRNA expression disorder has been found to be associated to cancer and other human disease.As functional molecules, lncRNA have attracted more and more researchers attention.Compared to human medicine, it is still at the initial stage of lncRNA application in livestock studies.In the present study, the characteristics, classification, acting mechanisms, methods for lncRNA analysis, as well as research progress in growth regulation of livestock of lncRNA are reviewed, and prospect the application of lncRNA in livestock breeding, in order to provide the theory foundation for thorough study of lncRNA in growth regulation of livestock.

Key words: long non-coding RNA(lncRNA); gene regulation; acting mechanism; livestock; research progress

中图分类号:

Q527

苏晓娜, 谢靑梅, 陈峰. 长链非编码RNA及其在畜禽生长调控中的研究进展[J]. , 2016, 43(1): 197-203.

SU Xiao-na, XIE Qing-mei, CHEN Feng. Research Progress on Long Non-coding RNA in Growth Regulation of Livestock[J]. , 2016, 43(1): 197-203.

参考文献

[1] Hattori M.Finishing the euchromatic sequence of the human genome[J]. Tanpakushitsu Kakusan Koso,2005,50(2):162-168.
[2] Okazaki Y,Furuno M,Kasukawa T,et al.Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs[J]. Nature,2002,420(6915):563-573.
[3] Kapranov P,Cheng J,Dike S,et al.RNA maps reveal new RNA classes and a possible function for pervasive transcription[J]. Science,2007,316(5830):1484-1488.
[4] Ponting C P,Oliver P L,Reik W.Evolution and functions of long noncoding RNAs[J]. Cell,2009,136(4):629-641.
[5] Mattick J S,Makunin I V.Non-coding RNA[J]. Human Molecular Genetics,2006,15(1):R17-R29.
[6] Mercer T R,Dinger M E,Mattick J S.Long non-coding RNAs:Insights into functions[J]. Nat Rev Genet,2009,10(3):155-159.
[7] Wang K C,Chang H Y.Molecular mechanisms of long noncoding RNAs[J]. Mol Cell,2011,43(6):904-914.
[8] Birney E,Stamatoyannopoulos J A,Dutta A,et al.Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project[J]. Nature,2007,447(7146):799-816.
[9] Ravasi T,Suzuki H,Pang K C,et al.Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome[J]. Genome Res,2006,16(1):11-19.
[10] Derrien T,Johnson R,Bussotti G,et al.The GENCODE v7 catalogof human long noncoding RNAs:Analysis of their gene,structure,evolution,and expression[J]. Genome Res,2012,22(9):1775-1789.
[11] Lipovich L,Johnson R,Lin C Y.microRNA underdogs in a microRNA world:Evolutionary,regulatory,and biomedical significance of mammalian long non-protein-coding RNA[J]. Biochim Biophys Acta,2010,1799(9):597-615.
[12] Guttman M,Amit I,Garber M,et al.Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals[J]. Nature,2009,458(7235):223-227.
[13] Salmena L,Poliseno L,Tay Y,et al.A ceRNA hypothesis:The Rosetta stone of a hidden RNA language[J]. Cell,2011,146(3):353-358.
[14] Chen L L,Carmichael G G.Decoding the function of nuclear long non-coding RNAs[J]. Curr Opin Cell Biol,2010,22(3):357-364.
[15] Holdt L M,Teupser D.Long noncoding RNA-microRNA pathway controlling nuclear factor IA,a novel atherosclerosis modifier gene[J]. Arterioscler Thromb Vasc Biol,2015,35(1):7-8.
[16] Tsai M C,Manor O,Wan Y,et al.Long non-coding RNA as modular scaffold of histone modification complexes[J]. Science,2010,329(5992):689-693.
[17] Zhou S,Wang J,Zhang Z.An emerging understanding of long noncoding RNAs in kidney cancer[J]. J Cancer Res Clin Oncol,2014,140(12):1989-1995.
[18] Bhan A,Mandal S S.Long non-coding RNAs:Emerging stars in gene regulation,epigenetics and human disease[J]. Chem Med Chem,2014,9(9):1932-1956.
[19] Zhi H,Ning S,Li X,et al.A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non-coding RNAs in cancers[J]. Nucleic Acids Res,2014,42(13):8258-8270.
[20] Rinn J L,Kertesz M,Wang J K,et al.Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs[J]. Cell,2007,129(7):1311-1323.
[21] Zhang K,Sun X,Zhou X,et al.Long non-coding RNA HOTAIR promotes glioblastoma cell cycle progression in an EZH2 dependent manner[J]. Oncotarget,2015,6(1):537-546.
[22] Xiang J F,Yin Q F,Chen T,et al.Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus[J]. Cell Res,2014,24(5):513-531.
[23] Lee J T,Bartolomei M S.X-inactivation,imprinting,and long noncoding RNAs in health and disease[J]. Cell,2013,152(6):1308-1323.
[24] Mohammad F,Mondal T,Kanduri C.Epigenetics of imprinted long noncoding RNAs[J]. Epigenetics,2009,4(5):277-286.
[25] Pandey R R,Mondal T,Mohammad F,et al.Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation[J]. Mol Cell,2008,32(2):232-246.
[26] Lee J T.The X as model for RNA's niche in epigenomic regulation[J]. Cold Spring Harb Perspect Biol,2010,2(9):a3749.
[27] Zhao J,Sun B K,Erwin J A,et al.Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome[J]. Science,2008,322(5902):750-756.
[28] Orom U A,Derrien T,Beringer M,et al.Long noncoding RNAs with enhancer-like function in human cells[J]. Cell,2010,143(1):46-58.
[29] Pruneski J A,Hainer S J,Petrov K O,et al.The Paf1 complex represses SER3 transcription in Saccharomyces cerevisiae by facilitating intergenic transcription-dependent nucleosome occupancy of the SER3 promoter[J]. Eukaryot Cell,2011,10(10):1283-1294.
[30] Wang X,Arai S,Song X,et al.Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription[J]. Nature,2008,454:126-130
[31] Shi X,Sun M,Liu H,et al.Long non-coding RNAs:A new frontier in the study of human diseases[J]. Cancer Lett,2013,339(2):159-166.
[32] Johnson R.Long non-coding RNAs in Huntington's disease neurodegeneration[J]. Neurobiol Dis,2012,46(2):245-254.
[33] Hainer S J,Martens J A.Transcription of ncDNA:Many roads lead to local gene regulation[J]. Transcription,2011,2(3):120-123.
[34] Beltran M,Puig I,Pena C,et al.A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition[J]. Genes Dev,2008,22(6):756-769.
[35] Ying L,Chen Q,Wang Y,et al.Upregulated MALAT-1 contributes to bladder cancer cell migration by inducing epithelial-to-mesenchymal transition[J]. Mol Biosyst,2012,8(9):2289-2294.
[36] Trimarchi T,Bilal E,Ntziachristos P,et al.Genome-wide mapping and characterization of Notch-regulated long non-coding RNAs in acute leukemia[J]. Cell,2014,158(3):593-606.
[37] Rother S,Meister G.Small RNAs derived from longer non-coding RNAs[J]. Biochimie,2011,93(11):1905-1915.
[38] Gong C,Maquat L E."Alu"strious long ncRNAs and their role in shortening mRNA half-lives[J]. Cell Cycle,2011,10(12):1882-1883.
[39] Wu X,Brewer G.The regulation of mRNA stability in mammalian cells:2.0[J]. Gene,2012,500(1):10-21.
[40] Faghihi M A,Modarresi F,Khalil A M,et al.Expression of a non-coding RNA is elevated in Alzheimer's disease and drives rapid feedforward regulation of β-secretase[J]. Nat Med,2008,14:723-730.
[41] Kretz M,Siprashvili Z,Chu C,et al.Control of somatic tissue differentiation by the long non-coding RNA TINCR[J]. Nature,2013,493:231-235.
[42] Kim Y K,Furic L,Parisien M,et al.Staufen1 regulates diverse classes of mammalian transcripts[J]. EMBO J,2007,26(11):2670-2681.
[43] Guo G,Kang Q,Zhu X,et al.A long noncoding RNA critically regulates Bcr-Abl-mediated cellular transformation by acting as a competitive endogenous RNA[J]. Oncogene,2015,34(14):1768-1779.
[44] Angrand P O,Vennin C,Le Bourhis X,et al.The role of long non-coding RNAs in genome formatting and expression[J]. Front Genet,2015,6:165.
[45] Yan B,Wang Z H,Guo J T.The research strategies for probing the function of long noncoding RNAs[J]. Genomics,2012,99(2):76-80.
[46] Shao Y,Ye M,Jiang X,et al.Gastric juice long noncoding RNA used as a tumor marker for screening gastric cancer[J]. Cancer,2014,120(21):3320-3328.
[47] Guo G,Kang Q,Chen Q,et al.High expression of long non-coding RNA H19 is required for efficient tumorigenesis induced by Bcr-Abl oncogene[J]. FEBS Lett, 2014,588(9):1780-1786.
[48] Matouk I J,Degroot N,Mezan S,et al.The H19 non-coding RNA is essential for human tumor growth[J]. PLoS One,2007,2(9):e845.
[49] Emmrich S,Streltsov A,Schmidt F,et al.lincRNAs MONC and MIR100HG act as oncogenes in acute megakaryoblastic leukemia[J]. Mol Cancer,2014,13:171.
[50] Han L,Zhang K,Chen L,et al.lncRNA profile of glioblastoma reveals the potential role of lncRNA in contributing to Glioblastoma pathogenesis[J]. Neutron-oncology,2013,151:46.
[51] Ren H,Li Y,Tang Z,et al.Genomic structure,chromosomal localization and expression profile of a porcine long non-coding RNA isolated from long SAGE libraries[J]. Anim Genet,2009,40(4):499-508.
[52] 赵为民.猪胚胎骨骼肌中基因间长非编码RNA的鉴定、特征及功能的初步分析[D].北京:中国农业科学院,2013.
[53] Li T,Wang S,Wu R,et al.Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing[J]. Genomics,2012,99(5):292-298.
[54] 张淑平,陈文,鲁卫卫,等.鸡一个新非编码长链RNA基因的克隆及表达分析[A].中国畜牧兽医学会家禽学分会第九次代表会议暨第十六次全国家禽学术讨论会论文集[C].2013.