An atlas of human long non-coding RNAs with accurate 5′ ends

By C. Hon, Jordan A. Ramilowski, J. Harshbarger, Nicolas Bertin, O. Rackham, Julian Gough, E. Denisenko, S. Schmeier, Thomas M. Poulsen, Jessica Severin and 29 more. Nature, 2017

934 citations recorded by the source corpus.

Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5′ ends and expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters. Incorporating genetic and expression data, we show that lncRNAs overlapping trait-associated single nucleotide polymorphisms are specifically expressed in cell types relevant to the traits, implicating these lncRNAs in multiple diseases. We further demonstrate that lncRNAs overlapping expression quantitative trait loci (eQTL)-associated single nucleotide polymorphisms of messenger RNAs are co-expressed with the corresponding messenger RNAs, suggesting their potential roles in transcriptional regulation. Combining these findings with conservation data, we identify 19,175 potentially functional lncRNAs in the human genome.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/353ccbf8dae807a9d59976d2e3ce12f083a6162f

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Citations in the corpus

The multidimensional mechanisms of long noncoding RNA function (2017, background): “The efforts to generate a comprehensive atlas of the transcripts expressed in cells have revealed an extremely large collection of lncRNAs [1, 2].”
Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. (2018, methodology): “Because the roles of lncRNAs (Hon et al., 2017; Nguyen and Carninci, 2016) in UM largely remain to be clarified, we compared correlations of lncRNA abundance with PARADIGM pathway activities and MARINa regulator activities in the M3/ BAP1-abberant lncRNA transcriptional clusters 3 and 4 (Figure 6 an”
LNCipedia 5: towards a reference set of human long non-coding RNAs (2018, methodology): “LNCipedia 5 content and filtering New lncRNA annotation in LNCipedia 5 (Table 1) originates from Ensembl (22), RefSeq (23) and FANTOM CAT (21).”
GENCODE 2021 (2020, neutral): “miTranscriptome (28), NONCODE (29), FANTOM CAT (30)).”