A comprehensive overview of lncRNA annotation resources

Abstract

Long noncoding RNAs (lncRNAs) are emerging as a class of important regulators participating in various biological functions and disease processes. With the widespread application of next-generation sequencing technologies, large numbers of lncRNAs have been identified, producing plenty of lncRNA annotation resources in different contexts. However, at present, we lack a comprehensive overview of these lncRNA annotation resources. In this study, we reviewed 24 currently available lncRNA annotation resources referring to > 205 000 lncRNAs in over 50 tissues and cell lines. We characterized these annotation resources from different aspects, including exon structure, expression, histone modification and function. We found many distinct properties among these annotation resources. Especially, these resources showed diverse chromatin signatures, remarkable tissue and cell type dependence and functional specificity. Our results suggested the incompleteness and complementarity of current lncRNA annotations and the necessity of integration of multiple resources to comprehensively characterize lncRNAs. Finally, we developed 'LNCat' (lncRNA atlas, freely available at http://biocc.hrbmu.edu.cn/LNCat/), a user-friendly database that provides a genome browser of lncRNA structures, visualization of different resources from multiple angles and download of different combinations of lncRNA annotations, and supports rapid exploration, comparison and integration of lncRNA annotation resources. Overall, our study provides a comprehensive comparison of numerous lncRNA annotations, and can facilitate understanding of lncRNAs in human disease.

A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease

“…Using RNA-seq, the Illumina Human BodyMap and Genotype-Tissue Expression Project (GTEx, (30)) has reported a median count of less than 5000 lncRNA genes across a large number of human tissue and cell types (123), often with only a few hundred per tissue-type. The present analysis, which relies on a probe-level signal filter (study specificity), a secondary transcript-level ‘noise’ filter and confirmation that the low-end of the dynamic expression range equates to known low-expressed RNA and proteins (Supplemental data S10 and raw data), demonstrates the advantages of our new approach to customising array processing to tissue/study specific patterns of RNA detection.…”

Long Noncoding RNAs in the Heart

“…9 This study represents the first in-depth analysis of lncRNAs in cardiac development in humans. Although this approach naturally represented a snapshot of lncRNA profiles in time, and prevented a thorough analysis of lnRNAs expression at each stage of cardiac development or identification of contributing cell types to the same degree as what can be accomplished in mice, these data provide a unique resource for the future study of lncRNAs that may functionally contribute …”

LNCediting: a database for functional effects of RNA editing in lncRNAs

“…The annotation of more than 300 000 human lncRNAs (hg19) was obtained from LNCat (6), the most comprehensive annotation resources for human lncRNAs. The lncRNA annotation of mouse (mm10) was downloaded from NONCODE (version 2016) (3) and GENCODE (M10) (34), while the lncRNA annotations of rhesus (mac3) and fly (dm6) were downloaded from NONCODE (version 2016).…”

“…Therefore, several databases have been developed to annotate lncRNAs, such as NONCODE (3), LNCipedia (4) and GENCODE (5). The most comprehensive lncRNA database, LNCat, combined 24 lncRNA annotation resources and annotated >300 000 lncRNA transcripts in over 50 tissues and cell lines in the human genome (6). LncRNAs play key roles in various biological processes, such as imprinting control, cell differentiation, immune response and chromatin modification (7,8).…”