Comparison of Poly-A(+) Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq.
Comparison of Poly-A(+) Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq.
复制标题
DOI：
10.3390/ncrna6030032
复制
发表时间：
2020-08-21
期刊：
影响因子：
4.3
通讯作者：
Finno CJ
中科院分区：
文献类型：
--
作者：
Dahlgren AR;Scott EY;Mansour T;Hales EN;Ross PJ;Kalbfleisch TS;MacLeod JN;Petersen JL;Bellone RR;Finno CJ
长链非编码RNA（longnon-codingRNA，lncRNA）是一类长度超过200个核苷酸的非翻译调控转录物，在转录、翻译后和表观遗传调控中发挥重要作用。传统上，RNA测序（RNA-seq）文库是通过poly-A+选择分离转录组RNA来创建的。在过去的10年中，已经开发了进行总RNA的核糖体RNA（rRNA）消耗的方法作为替代方案，旨在更好地覆盖全转录组RNA，包括多聚腺苷酸化和非多聚腺苷酸化转录物。本研究的目的是确定哪种文库制备方法是马中lncRNA研究的最佳方法。使用来自两只健康纯种马的肝脏和大脑顶叶组织，使用标准聚A+选择和rRNA耗尽方法制备RNA-seq文库。对两个生物学重复进行平均，聚A+选择分别产生了327和773个肝脏和顶叶的独特lncRNA转录本。发现更多的lncRNA是poly-A+选择的文库所特有的，并且rRNA耗尽鉴定出小核仁RNA（snoRNA）具有比在poly-A+选择的文库中更高的相对表达。总的来说，多聚-A+选择提供了马组织中总lncRNA的更彻底的鉴定，而rRNA耗尽可以允许更容易地检测snoRNA。
Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A+ selection. In the past 10 years, methods to perform ribosomal RNA (rRNA) depletion of total RNA have been developed as an alternative, aiming for better coverage of whole transcriptomic RNA, both polyadenylated and non-polyadenylated transcripts. The purpose of this study was to determine which library preparation method is optimal for lncRNA investigations in the horse. Using liver and cerebral parietal lobe tissues from two healthy Thoroughbred mares, RNA-seq libraries were prepared using standard poly-A+ selection and rRNA-depletion methods. Averaging the two biologic replicates, poly-A+ selection yielded 327 and 773 more unique lncRNA transcripts for liver and parietal lobe, respectively. More lncRNA were found to be unique to poly-A+ selected libraries, and rRNA-depletion identified small nucleolar RNA (snoRNA) to have a higher relative expression than in the poly-A+ selected libraries. Overall, poly-A+ selection provides a more thorough identification of total lncRNA in equine tissues while rRNA-depletion may allow for easier detection of snoRNAs.
登录
查看更多内容
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：
56.9
作者：
Cheng, J;Kapranov, P;Gingeras, TR
通讯作者：
Gingeras, TR
影响因子：
3.7
作者：
Capomaccio S;Vitulo N;Verini-Supplizi A;Barcaccia G;Albiero A;D'Angelo M;Campagna D;Valle G;Felicetti M;Silvestrelli M;Cappelli K
通讯作者：
Cappelli K
影响因子：
4.4
作者：
Chao, Hsueh-Ping;Chen, Yueping;Shen, Jianjun
通讯作者：
Shen, Jianjun
lncRNA H19 在结直肠癌中充当 miRNA 海绵，促进上皮细胞向间质细胞的转变。
影响因子：
--
作者：
Liang WC;Fu WM;Wong CW;Wang Y;Wang WM;Hu GX;Zhang L;Xiao LJ;Wan DC;Zhang JF;Waye MM
通讯作者：
Waye MM