Wang Feng, Li Liping, Xu Haiming, Liu Yong, Yang Chun, Cowley Allen W, Wang Niansong, Liu Pengyuan, Liang Mingyu
1] Department of Nephrology and Rheumatology, Shanghai JiaoTong University Affiliated Sixth People's Hospital, Shanghai, China [2] Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA [3] Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310029, China.
Sci Rep. 2014 Nov 21;4:7146. doi: 10.1038/srep07146.
Long non-coding RNAs (lncRNAs) are potentially important mediators of genomic regulation. lncRNAs, however, remain poorly characterized in the rat model organism widely used in biomedical research. Using poly(A)-independent and strand-specific RNA-seq, we identified 1,500 to 1,800 lncRNAs expressed in each of the following tissues of Brown Norway rats: the renal cortex, renal outer medulla, liver, cardiac left ventricle, adrenal gland, and hypothalamus. Expression and the binding of histone H3K4me3 to promoter regions were confirmed for several lncRNAs. Rat lncRNA expression appeared to be more tissue-specific than mRNA. Rat lncRNAs had 4.5 times fewer exons and 29% shorter transcripts than mRNA. The median cumulative abundance of rat lncRNAs was 53% of that of mRNA. Approximately 28% of the lncRNAs identified in the renal outer medulla appeared to lack a poly(A) tail. Differential expression of 74 lncRNAs was detected in the renal outer medulla between Dahl SS rats, a model of salt-sensitive hypertension, and salt-insensitive, congenic SS.13(BN26) rats fed a high-salt diet. Two of the differentially expressed lncRNAs, which were confirmed, were located within the congenic region and contained several sequence variants. The study identified genome-wide characteristics of lncRNAs in the rat model and suggested a role of lncRNAs in hypertension.
长链非编码RNA（lncRNAs）可能是基因组调控的重要介质。然而，在生物医学研究中广泛使用的大鼠模式生物中，lncRNAs的特征仍不清楚。利用不依赖于聚腺苷酸（poly(A)）和链特异性的RNA测序技术，我们在以下棕色挪威大鼠组织中分别鉴定出1500至1800个lncRNAs：肾皮质、肾外髓质、肝脏、心脏左心室、肾上腺和下丘脑。对几种lncRNAs的表达以及组蛋白H3K4me3与启动子区域的结合进行了确认。大鼠lncRNA的表达似乎比mRNA更具组织特异性。大鼠lncRNAs的外显子数量比mRNA少4.5倍，转录本比mRNA短29%。大鼠lncRNAs的中位累积丰度是mRNA的53%。在肾外髓质中鉴定出的lncRNAs中，约28%似乎缺乏聚腺苷酸尾巴。在盐敏感性高血压模型Dahl SS大鼠和喂食高盐饮食的盐不敏感同基因SS.13(BN26)大鼠的肾外髓质中，检测到74个lncRNAs的差异表达。经确认的两个差异表达的lncRNAs位于同基因区域内，并包含几个序列变体。该研究确定了大鼠模型中lncRNAs的全基因组特征，并提示lncRNAs在高血压中的作用。
