A Computational Framework to Infer Human Disease-Associated Long Noncoding RNAs

As a major class of noncoding RNAs, long noncoding RNAs (lncRNAs) have been implicated in various critical biological processes. Accumulating researches have linked dysregulations and mutations of lncRNAs to a variety of human disorders and diseases. However, to date, only a few human lncRNAs have been associated with diseases. Therefore, it is very important to develop a computational method to globally predict potential associated diseases for human lncRNAs. In this paper, we developed a computational framework to accomplish this by combining human lncRNA expression profiles, gene expression profiles, and human disease-associated gene data. Applying this framework to available human long intergenic noncoding RNAs (lincRNAs) expression data, we showed that the framework has reliable accuracy. As a result, for non-tissue-specific lincRNAs, the AUC of our algorithm is 0.7645, and the prediction accuracy is about 89%. This study will be helpful for identifying novel lncRNAs for human diseases, which will help in understanding the roles of lncRNAs in human diseases and facilitate treatment. The corresponding codes for our method and the predicted results are all available at http://asdcd.amss.ac.cn/MingXiLiu/lncRNA-disease.html.     

非编码长链RNA与基因表达调控

近年来,在小鼠全长cDNA文库大规模测序中发现一类新的转录物——非编码长链RNA(long noncoding RNA,lncRNA),引起了科学界的关注.lncRNA长度大于200个核苷酸,无蛋白质编码功能,在真核细胞基因组中被普遍转录.lncRNA种类繁多,数量庞大,占哺乳动物基因组转录物的绝大部分.相对于研究较多的非编码小RNA,lncRNA的功能目前尚不完全清楚.但越来越多的研究发现,lncRNA在多个水平调控基因的表达,在胚胎发育、物种进化、细胞分化和某些疾病如神经退行性疾病及肿瘤的发生过程中起着重要作用.本文在简要介绍lncRNA基本概念的基础上,结合当前研究成果,就lncRNA在转录水平、转录后水平和表观遗传水平调控基因表达的机制作一综述.     

长链非编码RNA在心血管疾病发病中的研究进展

心血管疾病是一种威胁人类,特别是中老年人健康的常见疾病。每年死于心血管疾病的人数位居全球榜首。长链非编码RNA是长度大于200个核苷酸且不编码蛋白质的RNA,也是体内表达数量最多的RNA。越来越多的研究发现长链非编码RNA在心血管疾病的发生、发展中有重要的调节作用。本文将就长链非编码RNA和心血管疾病的最新研究进展进行综述。     

长链非编码RNA调节缺血性脑卒中损伤和修复的研究进展

长链非编码RNA(long noncoding RNA,lnc RNA)是一组在转录、转录后和表观遗传水平发挥作用的调控序列,其在中枢神经系统中特异性高表达,对中枢神经系统发育和疾病发展具有重要调控作用。缺血性脑卒中诱导脑内大量lnc RNA表达改变,提示lnc RNA与缺血性脑卒中复杂的病理过程有关,这将有利于全面认识缺血性脑卒中的病理机制及脑缺血损伤后的分子调控网络,并提供新的治疗方向。尽管有少数研究报道lnc RNA在缺血性心脏病中的作用,但目前对于其在缺血性脑卒中病理发展中的作用知之甚少。综述目前已知的lnc RNA在脑缺血再灌注损伤、细胞凋亡与抗凋亡及损伤后神经再生与修复中的作用,并提出了未来可能的lnc RNA在缺血性脑卒中损伤与修复中的研究方向。     

Isolation of Small Noncoding RNAs from Human Serum

The analysis of RNA and its expression is a common feature in many laboratories. Of significance is the emergence of small RNAs like microRNAs, which are found in mammalian cells. These small RNAs are potent gene regulators controlling vital pathways such as growth, development and death and much interest has been directed at their expression in bodily fluids. This is due to their dysregulation in human diseases such as cancer and their potential application as serum biomarkers. However, the analysis of miRNA expression in serum may be problematic. In most cases the amount of serum is limiting and serum contains low amounts of total RNA, of which small RNAs only constitute 0.4-0.5%¹. Thus the isolation of sufficient amounts of quality RNA from serum is a major challenge to researchers today. In this technical paper, we demonstrate a method which uses only 400 µl of human serum to obtain sufficient RNA for either DNA arrays or qPCR analysis. The advantages of this method are its simplicity and ability to yield high quality RNA. It requires no specialized columns for purification of small RNAs and utilizes general reagents and hardware found in common laboratories. Our method utilizes a Phase Lock Gel to eliminate phenol contamination while at the same time yielding high quality RNA. We also introduce an additional step to further remove all contaminants during the isolation step. This protocol is very effective in isolating yields of total RNA of up to 100 ng/µl from serum but can also be adapted for other biological tissues.     

Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer

Recently, large numbers of normal human tissues have been profiled for non-coding RNAs and more than fourteen thousand long intergenic non-coding RNAs (lincRNAs) are found expressed in normal human tissues. The functional roles of these normal lincRNAs (nlincRNAs) in the regulation of protein coding genes in normal and disease biology are yet to be established. Here, we have profiled two RNA-seq datasets including cancer and matched non-neoplastic tissues from 12 individuals from diverse demography for both coding genes and nlincRNAs. We find 130 nlincRNAs significantly regulated in cancer, with 127 regulated in the same direction in the two datasets. Interestingly, according to Illumina Body Map, significant numbers of these nlincRNAs display baseline null expression in normal prostate tissues but are specific to other tissues such as thyroid, kidney, liver and testis. A number of the regulated nlincRNAs share loci with coding genes, which are either co-regulated or oppositely regulated in all cancer samples studied here. For example, in all cancer samples i) the nlincRNA, TCONS_00029157, and a neighboring tumor suppressor factor, SIK1, are both down regulated; ii) several thyroid-specific nlincRNAs in the neighborhood of the thyroid-specific gene TPO, are both up-regulated; and iii) the TCONS_00010581, an isoform of HEIH, is down-regulated while the neighboring EZH2 gene is up-regulated in cancer. Several nlincRNAs from a prostate cancer associated chromosomal locus, 8q24, are up-regulated in cancer along with other known prostate cancer associated genes including PCAT-1, PVT1, and PCAT-92. We observe that there is significant bias towards up-regulation of nlincRNAs with as high as 118 out of 127 up-regulated in cancer, even though regulation of coding genes is skewed towards down-regulation. Considering that all reported cancer associated lincRNAs (clincRNAs) are biased towards up-regulation, we conclude that this bias may be functionally relevant.