An expanded landscape of human long noncoding RNA

Abstract

Long noncoding RNAs (lncRNAs) are emerging as key regulators of multiple essential biological processes involved in physiology and pathology. By analyzing the largest compendium of 14,166 samples from normal and tumor tissues, we significantly expand the landscape of human long noncoding RNA with a high-quality atlas: RefLnc (Reference catalog of LncRNA). Powered by comprehensive annotation across multiple sources, RefLnc helps to pinpoint 275 novel intergenic lncRNAs correlated with sex, age or race as well as 369 novel ones associated with patient survival, clinical stage, tumor metastasis or recurrence. Integrated in a user-friendly online portal, the expanded catalog of human lncRNAs provides a valuable resource for investigating lncRNA function in both human biology and cancer development.

LncRNA FGD5‐AS1 can be predicted as therapeutic target in oral cancer

“…Long non‐coding RNAs (lncRNAs) are those genes longer than 200 nucleotides (nt) in length but without the ability to encode proteins . LncRNAs have been reported to be aberrantly expressed in many diseases, including cancer, and plays a vital role in tumor growth and progression . Furthermore, lncRNAs have been discovered to be participated in various biological and pathological activities, such as cell growth, apoptosis, invasion, and migration …”

“…4 LncRNAs have been reported to be aberrantly expressed in many diseases, including cancer, and plays a vital role in tumor growth and progression. [5][6][7][8] Furthermore, lncRNAs have been discovered to be participated in various biological and pathological activities, such as cell growth, apoptosis, invasion, and migration. [9][10][11] MicroRNAs (miRNAs) are another type of non-coding RNAs characterized by short length.…”

Long non-coding RNA gene regulation and trait associations across human tissues

“…Not only do these analyses highlight the differences between lncRNA and protein-coding genes, but they can also be used to interrogate lncRNA genes of interest and systematically identify lncRNAs associated with certain cell types or traits. There are other resources that 10 provide lncRNA gene networks, conservation data, or expression-based assessments (11,(40)(41)(42)(43); our analyses examine several of these characteristics, and also provide trait association information. Searching for convergence of evidence across multiple lncRNA resources here enabled identification of the most compelling candidate genes for further study.…”

“…Many of these physical differences likely informed the more complex regulatory differences we saw throughout these analyses. 15 The well-established tissue-specificity of lncRNA gene expression (1,5,6,8,11), was apparent across the 49 analyzed tissues. At an expression threshold of TPM ≥0.5 in at least 20% of samples, most of the genes in both the total lncRNA and the high-confidence non-coding lncRNA gene groups are either not expressed, or only expressed in 1-5 tissues (Fig.…”

“…Despite these differences, many lncRNA genes have been demonstrated to have important roles in gene regulation from epigenetic reprogramming to posttranscriptional regulation (4,9). Although the number of annotated lncRNA genes is increasing as a result of more sensitive transcriptomic profiling in a wide range of contexts (1,5,10,11), it is not known how many of these lncRNAs have important functional consequences. 25 In this study, we used the Genotype-Tissue Expression (GTEx) project v8 data to profile genetic regulation of lncRNA genes across 49 human tissues.…”