Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification.
Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification.
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DOI：
10.1371/journal.pone.0011779
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发表时间：
2010-07-26
期刊：
影响因子：
3.7
通讯作者：
Raymond CK
中科院分区：
文献类型：
--
作者：
Castle JC;Armour CD;Löwer M;Haynor D;Biery M;Bouzek H;Chen R;Jackson S;Johnson JM;Rohl CA;Raymond CK
非编码RNA（ncRNA）是一类重要的分子种类，由于经常缺乏多聚腺苷酸化，难以在高通量平台上监测。使用多聚腺苷酸化中性扩增方案和下一代测序，我们探索ncRNA在11种人体组织中的表达。ncRNA 7SL、U2、7SK和HBII-52的表达水平远远超过mRNA。C/D和H/ACA盒snoRNA分别与rRNA甲基化和假尿苷化相关：脾脏表达两者，下丘脑主要表达C/D盒snoRNA，睾丸显示H/ACA盒snoRNA和RNA端粒酶TERC的富集表达。在snoRNA 14 q簇内，14 q（I-6）的表达水平比其他簇成员高得多。与线粒体比对的读段比与核tRNA比对的读段多。许多lincRNA被活跃地转录，特别是那些重叠的已知ncRNA。在Prader-Willi综合征基因座内，snoRNA HBII-85（组I）簇在下丘脑中高度表达，高于其他组织，并且高于组II或III。此外，在疾病基因座内，我们在卵巢中发现了跨越400，000 nt跨度的新转录。这个全基因组polyA中性表达纲要展示了ncRNA表达的丰富性、其高表达模式、其功能特异性表达模式，并且是公开可用的。
Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. ncRNAs 7SL, U2, 7SK, and HBII-52 are expressed at levels far exceeding mRNAs. C/D and H/ACA box snoRNAs are associated with rRNA methylation and pseudouridylation, respectively: spleen expresses both, hypothalamus expresses mainly C/D box snoRNAs, and testes show enriched expression of both H/ACA box snoRNAs and RNA telomerase TERC. Within the snoRNA 14q cluster, 14q(I-6) is expressed at much higher levels than other cluster members. More reads align to mitochondrial than nuclear tRNAs. Many lincRNAs are actively transcribed, particularly those overlapping known ncRNAs. Within the Prader-Willi syndrome loci, the snoRNA HBII-85 (group I) cluster is highly expressed in hypothalamus, greater than in other tissues and greater than group II or III. Additionally, within the disease locus we find novel transcription across a 400,000 nt span in ovaries. This genome-wide polyA-neutral expression compendium demonstrates the richness of ncRNA expression, their high expression patterns, their function-specific expression patterns, and is publicly available.
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影响因子：
14.9
作者：
Griffiths-Jones, S;Bateman, A;Eddy, SR
通讯作者：
Eddy, SR
DOI：
10.1073/pnas.250426397
发表时间：
2000-12-19
影响因子：
11.1
作者：
Cavaillé, J;Buiting, K;Hüttenhofer, A
通讯作者：
Hüttenhofer, A
影响因子：
4.4
作者：
Hutchinson, John N;Ensminger, Alexander W;Clemson, Christine M;Lynch, Christopher R;Lawrence, Jeanne B;Chess, Andrew
通讯作者：
Chess, Andrew
影响因子：
48
作者：
Armour, Christopher D.;Castle, John C.;Raymond, Christopher K.
通讯作者：
Raymond, Christopher K.
影响因子：
7.3
作者：
Kino T;Hurt DE;Ichijo T;Nader N;Chrousos GP
通讯作者：
Chrousos GP