Novel microRNA discovery using small RNA sequencing in post-mortem human brain.
Novel microRNA discovery using small RNA sequencing in post-mortem human brain.
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DOI：
10.1186/s12864-016-3114-3
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发表时间：
2016-10-04
期刊：
影响因子：
4.4
通讯作者：
Myers RH
中科院分区：
文献类型：
--
作者：
Wake C;Labadorf A;Dumitriu A;Hoss AG;Bregu J;Albrecht KH;DeStefano AL;Myers RH
microRNA（miRNAs）是一类短的非编码RNA，主要通过翻译抑制靶mRNA分子来调控基因表达。已经鉴定了超过2700种人类miRNA，并且已知一些与疾病表型相关并显示组织特异性表达模式。我们使用高通量小RNA测序在93个人类死后前额叶皮质样本中发现了新的miRNA，这些样本来自患有亨廷顿病（n = 28）或帕金森病（n = 29）的个体和没有神经功能障碍的对照组（n = 36）。构建了一个自定义的miRNA鉴定分析管道，该管道利用miRDeep* miRNA鉴定和基于假阳性率估计的结果过滤。鉴定了99种新的候选miRNA，假阳性率低于5%。34个候选miRNA与已知成熟miRNA序列具有序列相似性，可能是已知miRNA家族的新成员，而其余65个可能构成以前未发现的miRNA家族。99个候选miRNAs中的19个使用独立的、公开可用的人脑RNA测序样品进行了复制，7个使用qPCR进行了实验验证。我们已经使用小RNA测序来鉴定存在于人脑样品中的99种推定的新型miRNA。本文的在线版本（doi：10.1186/s12864-016-3114-3）包含补充材料，可供授权用户使用。
MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known to be associated with disease phenotypes and to display tissue-specific patterns of expression. We used high-throughput small RNA sequencing to discover novel miRNAs in 93 human post-mortem prefrontal cortex samples from individuals with Huntington’s disease (n = 28) or Parkinson’s disease (n = 29) and controls without neurological impairment (n = 36). A custom miRNA identification analysis pipeline was built, which utilizes miRDeep* miRNA identification and result filtering based on false positive rate estimates. Ninety-nine novel miRNA candidates with a false positive rate of less than 5 % were identified. Thirty-four of the candidate miRNAs show sequence similarity with known mature miRNA sequences and may be novel members of known miRNA families, while the remaining 65 may constitute previously undiscovered families of miRNAs. Nineteen of the 99 candidate miRNAs were replicated using independent, publicly-available human brain RNA-sequencing samples, and seven were experimentally validated using qPCR. We have used small RNA sequencing to identify 99 putative novel miRNAs that are present in human brain samples. The online version of this article (doi:10.1186/s12864-016-3114-3) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
14.9
作者：
Li N;You X;Chen T;Mackowiak SD;Friedländer MR;Weigt M;Du H;Gogol-Döring A;Chang Z;Dieterich C;Hu Y;Chen W
通讯作者：
Chen W
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
14.9
作者：
Ritchie ME;Phipson B;Wu D;Hu Y;Law CW;Shi W;Smyth GK
通讯作者：
Smyth GK
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