全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...

利用转录组数据鉴定和分析小鼠非编码RNA

DOI: 10.1007/s11427-015-4929-x, PP. 845-859

Keywords: 非编码RNA,RNA-seq,转录组,lincRNA,小鼠

Full-Text   Cite this paper   Add to My Lib

Abstract:

基因转录表达是一个复杂、精确并具有时空特异性的过程.目前对转录组的研究主要集中在蛋白编码基因上.近几年,一个新的转录组研究工具—大规模并行cDNA测序技术(RNA-seq)为更深入地研究转录组带来了希望.利用RNA-seq数据,鉴定出大量的非编码RNA,特别是lincRNA,并且发现这些非编码RNA是多个生物学过程中重要的调控因子.利用深度测序获得的15个小鼠组织RNA-seq数据探索非编码RNA在小鼠不同组织中的多样性和动态变化.依据自定的标准,在这15个组织中共鉴定出16249个非编码基因(对应21569个非编码RNA).研究这些非编码RNA的多种特征,可以发现与蛋白编码基因相比,非编码RNA通常比较短,外显子个数少,表达量低,组织特异性强.而且,这些非编码RNA有明显的转录起始和转录延伸信号(H3K4me3,H3K27me3,H3K36me3修饰,RNAPⅡ结合位点以及CAGE)的富集.基因集富集分析结果表明,lincRNA与多个生物学过程相关,如免疫反应、肌肉发育和有性生殖等.本研究提供了更加全面的对小鼠非编码RNA的注释信息,为小鼠非编码RNA的功能和进化研究奠定了基础.

References

[1]  64 周媛媛, 龚未, 肖景发, 等. 小鼠乳腺发育的转录组学研究—怀孕哺乳周期乳腺的关键调控基因. 中国科学: 生命科学, 2014, 57: 340-355
[2]  65 Pan L, Gong W, Zhou Y, et al. A comprehensive transcriptomic analysis of infant and adult mouse ovary. Genomics Proteomics Bioinformatics, 2014, 12: 239-248
[3]  66 Sauvageau M, Goff L A, Lodato S, et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. ELife, 2013, 2: e01749
[4]  41 Wang K C, Chang H Y. Molecular mechanisms of long noncoding RNAs. Mol Cell, 2011, 43: 904-914
[5]  42 Sasaki Y T, Ideue T, Sano M, et al. MENe/b noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci USA, 2009, 106: 2525-2530
[6]  43 Brown J B, Boley N, Eisman R, et al. Diversity and dynamics of the Drosophila transcriptome. Nature, 2014, 512: 393-399
[7]  44 Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res, 2012, 22: 1775-1789
[8]  45 Consortium E P. An integrated encyclopedia of DNA elements in the human genome. Nature, 2012, 489: 57-74
[9]  46 Stamatoyannopoulos J A, Snyder M, Hardison R, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol, 2012, 13: 418
[10]  47 Pervouchine D D, Djebali S, Breschi A, et al. Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nat Commun, 2015, 6: 5903
[11]  55 Lv J, Liu H, Huang Z, et al. Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. Nucleic Acids Res, 2013, 41: 10044-10061
[12]  56 Li G, Ruan X, Auerbach R K, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell, 2012, 148: 84-98
[13]  57 Faulkner G J, Forrest A R, Chalk A M, et al. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics, 2008, 91: 281-288
[14]  58 Hüttenhofer A, Vogel J. Experimental approaches to identify non-coding RNAs. Nucleic Acids Res, 2006, 34: 635-646
[15]  59 Werner A. Biological functions of natural antisense transcripts. BMC Biol, 2013, 11: 31
[16]  60 Qu Z, Adelson D L. Identification and comparative analysis of ncRNAs in human, mouse and zebrafish indicate a conserved role in regulation of genes expressed in brain. PLoS One, 2012, 7: e52275
[17]  61 Ulitsky I, Bartel D P. lincRNAs: genomics, evolution, and mechanisms. Cell, 2013, 154: 26-46
[18]  62 Kuhn R M, Karolchik D, Zweig A S, et al. The UCSC genome browser database: update 2009. Nucleic Acids Res, 2009, 37: D755-D761
[19]  63 Yang L, Duff M O, Graveley B R, et al. Genomewide characterization of non-polyadenylated RNAs. Genome Biol, 2011, 12: R16
[20]  1 Clark M B, Amaral P P, Schlesinger F J, et al. The reality of pervasive transcription. PLoS Biol, 2011, 9: e1000625
[21]  2 Ewan Birney J A S, Anindya Dutta R G, Thomas R G, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 2007, 447: 799-816
[22]  3 Djebali S, Davis C A, Merkel A, et al. Landscape of transcription in human cells. Nature, 2012, 489: 101-108
[23]  4 Okazaki Y, Furuno M, Kasukawa T, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 2002, 420: 563-573
[24]  5 Katayama S, Tomaru Y, Kasukawa T, et al. Antisense transcription in the mammalian transcriptome. J Biol Chem, 2005, 309: 1564-1566
[25]  6 Carninci P, Kasukawa T, Katayama S, et al. The transcriptional landscape of the mammalian genome. Science, 2005, 309: 1559
[26]  7 Yue F, Cheng Y, Breschi A, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature, 2014, 515: 355-364
[27]  8 Zheng D, Frankish A, Baertsch R, et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res, 2007, 17: 839-851
[28]  9 Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 2009, 458: 223-227
[29]  10 Sati S, Ghosh S, Jain V, et al. Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. Nucleic Acids Res, 2012, 40: 10018-10031
[30]  11 Pauli A, Rinn J L, Schier A F. Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet, 2011, 12: 136-149
[31]  12 Hu W, Alvarez-Dominguez J R, Lodish H F. Regulation of mammalian cell differentiation by long non-coding RNAs. EMBO Rep, 2012, 13: 971-983
[32]  13 Pauli A, Valen E, Lin M F, et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res, 2012, 22: 577-591
[33]  14 Brown C J, Hendrich B D, Rupert J L, et al. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell, 1992, 71: 527-542
[34]  15 Heard E, Disteche C M. Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev, 2006, 20: 1848-1867
[35]  16 Yang P K, Kuroda M I. Noncoding RNAs and intranuclear positioning in monoallelic gene expression. Cell, 2007, 128: 777-786
[36]  17 Dinger M E, Amaral P P, Mercer T R, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res, 2008, 18: 1433-1445
[37]  18 Hawkins P G, Morris K V. Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription, 2010, 1: 165-175
[38]  19 Guttman M, Donaghey J, Carey B W, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature, 2011, 477: 295-300
[39]  20 Haas B J, Zody M C. Advancing RNA-seq analysis. Nat Biotechnol, 2010, 28: 421
[40]  21 Cloonan N, Forrest A R, Kolle G, et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods, 2008, 5: 613-619
[41]  22 Yassour M, Kaplan T, Fraser H B, et al. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci USA, 2009, 106: 3264-3269
[42]  23 Cui P, Lin Q, Ding F, et al. A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics, 2010, 96: 259-265
[43]  24 Guttman M, Garber M, Levin J Z, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol, 2010, 28: 503-510
[44]  25 Sigova A A, Mullen A C, Molinie B, et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci USA, 2013, 110: 2876-2881
[45]  26 Luo H, Sun S, Li P, et al. Comprehensive characterization of 10,571 mouse large intergenic noncoding RNAs from whole transcriptome sequencing. PLoS One, 2013, 8: e70835
[46]  27 Liu W, Zhao Y, Cui P, et al. Thousands of novel transcripts identified in mouse cerebrum, testis, and ES cells based on ribo-minus RNA sequencing. Front Genet, 2011, 2: 93
[47]  28 Cabili M N, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev, 2011, 25: 1915-1927
[48]  29 Hangauer M J, Vaughn I W, Mcmanus M T. Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet, 2013, 9: e1003569
[49]  30 Wetterbom A, Ameur A, Feuk L, et al. Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing. Genome Biol, 2010, 11: R78
[50]  31 Ulitsky I, Shkumatava A, Jan C H, et al. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell, 2011, 147: 1537-1550
[51]  32 Tan M H, Au K F, Yablonovitch A L, et al. RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. Genome Res, 2013, 23: 201-216
[52]  33 Nam J W, Bartel D. Long non-coding RNAs in C. elegans. Genome Res, 2012, 22: 2529-2540
[53]  34 Liu J, Jung C, Xu J, et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell, 2012, 24: 4333-4345
[54]  35 Maamar H, Cabili M N, Rinn J, et al. linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes Dev, 2013, 27: 1260-1271
[55]  36 ?rom U A, Derrien T, Beringer M, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell, 2010, 143: 46-58
[56]  37 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. Cell, 2007, 129: 1311-1323
[57]  38 Gupta R A, Shah N, Wang K C, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 2010, 464: 1071-1076
[58]  39 mattick J S. The genetic signatures of noncoding RNAs. PLoS Genet, 2009, 5: e1000459
[59]  40 Mercer T R, Dinger M E, Mattick J S. Long non-coding RNAs: insights into functions. Nat Rev Genet, 2009, 10: 155-159
[60]  48 Karolchik D, Barber G P, Casper J, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res, 2014, 42: D764-D770
[61]  49 Barbosa-Morais N L, Irimia M, Pan Q, et al. The evolutionary landscape of alternative splicing in verterbrate species. Science, 2012, 338: 1587-1593
[62]  50 FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, et al. A promoter-level mammalian expression atlas. Nature, 2014, 507: 462-470
[63]  51 Meyer L R, Zweig A S, Hinrichs A S, et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res, 2013, 41: D64-D69
[64]  52 Subramanian A, Tamayo P, Mootha V K, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA, 2005, 102: 15545-15550
[65]  53 Ramskold D, Wang E T, Burge C B, et al. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol, 2009, 5: e1000598
[66]  54 Nakaya H I, Amaral P P, Louro R, et al. Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol, 2007, 8: R43

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133