Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs.
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs.
复制标题
DOI：
10.1186/gb-2013-14-11-r131
复制
发表时间：
2013-11-29
期刊：
影响因子：
12.3
通讯作者：
Ponting CP
中科院分区：
文献类型：
--
作者：
Marques AC;Hughes J;Graham B;Kowalczyk MS;Higgs DR;Ponting CP
哺乳动物转录组包含数以千计的长链非编码rna （lncrna）。一些lncrna起源于基因内增强子，当这些增强子活跃时，作为替代启动子产生转录本，这些转录本使用宿主基因的规范信号进行处理。我们通过分析基因间lncrna来跟踪这一观察结果，以确定它们在多大程度上也可能起源于基因间增强子。我们整合了转录起始和转录的高分辨率图谱，以注释小鼠红母细胞中表达的一组保守的基因间lncrna。我们根据转录起始区染色质状态对基因间lncrna进行亚分类，由组蛋白H3K4单甲基化和三甲基化的相对水平定义。这些转录本几乎平均分为增强子相关（elncRNA）或启动子相关（plncRNA）元件。这两类5 '封顶和聚腺苷化的RNA转录本在其长度、外显子数量或相对于其最近的邻近基因的转录方向方面是无法区分的。然而，在进化过程中，elncrna受到更多的组织限制，表达水平较低，保守性较差。令人感兴趣的是，我们发现elncRNAs的表达与红细胞生成过程中邻近蛋白编码基因的表达增强有关，而不是plncRNAs。我们已经在全球范围内确定了红系细胞中基因间lncrna的起始位点，使我们能够区分两种相似的丰富转录本。elncrna、plncrna水平与邻近基因表达的不同相关性表明，这两类功能性lncrna可能在调节局部或远端位点的转录丰度方面发挥不同的作用。
Mammalian transcriptomes contain thousands of long noncoding RNAs (lncRNAs). Some lncRNAs originate from intragenic enhancers which, when active, behave as alternative promoters producing transcripts that are processed using the canonical signals of their host gene. We have followed up this observation by analyzing intergenic lncRNAs to determine the extent to which they might also originate from intergenic enhancers. We integrated high-resolution maps of transcriptional initiation and transcription to annotate a conservative set of intergenic lncRNAs expressed in mouse erythroblasts. We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. These transcripts are almost evenly divided between those arising from enhancer-associated (elncRNA) or promoter-associated (plncRNA) elements. These two classes of 5′ capped and polyadenylated RNA transcripts are indistinguishable with regard to their length, number of exons or transcriptional orientation relative to their closest neighboring gene. Nevertheless, elncRNAs are more tissue-restricted, less highly expressed and less well conserved during evolution. Of considerable interest, we found that expression of elncRNAs, but not plncRNAs, is associated with enhanced expression of neighboring protein-coding genes during erythropoiesis. We have determined globally the sites of initiation of intergenic lncRNAs in erythroid cells, allowing us to distinguish two similarly abundant classes of transcripts. Different correlations between the levels of elncRNAs, plncRNAs and expression of neighboring genes suggest that functional lncRNAs from the two classes may play contrasting roles in regulating the transcript abundance of local or distal loci.
登录
查看更多内容
影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
9.8
作者：
Church DM;Goodstadt L;Hillier LW;Zody MC;Goldstein S;She X;Bult CJ;Agarwala R;Cherry JL;DiCuccio M;Hlavina W;Kapustin Y;Meric P;Maglott D;Birtle Z;Marques AC;Graves T;Zhou S;Teague B;Potamousis K;Churas C;Place M;Herschleb J;Runnheim R;Forrest D;Amos-Landgraf J;Schwartz DC;Cheng Z;Lindblad-Toh K;Eichler EE;Ponting CP;Mouse Genome Sequencing Consortium
通讯作者：
Mouse Genome Sequencing Consortium
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
10.7
作者：
de Souza FS;Franchini LF;Rubinstein M
通讯作者：
Rubinstein M