The Landscape of Long Noncoding RNAs in the Human Transcriptome

By Matthew K. Iyer, Y. Niknafs, Rohit Malik, Udit Singhal, Anirban Sahu, Yasuyuki Hosono, T. Barrette, John R. Prensner, Joseph R Evans, Shuang G Zhao and 9 more. Nature Genetics, 2015

2,524 citations recorded by the source corpus.

Long noncoding RNAs (lncRNAs) are emerging as important regulators of tissue physiology and disease processes including cancer. To delineate genome-wide lncRNA expression, we curated 7,256 RNA sequencing (RNA-seq) libraries from tumors, normal tissues and cell lines comprising over 43 Tb of sequence from 25 independent studies. We applied ab initio assembly methodology to this data set, yielding a consensus human transcriptome of 91,013 expressed genes. Over 68% (58,648) of genes were classified as lncRNAs, of which 79% were previously unannotated. About 1% (597) of the lncRNAs harbored ultraconserved elements, and 7% (3,900) overlapped disease-associated SNPs. To prioritize lineage-specific, disease-associated lncRNA expression, we employed non-parametric differential expression testing and nominated 7,942 lineage- or cancer-associated lncRNA genes. The lncRNA landscape characterized here may shed light on normal biology and cancer pathogenesis and may be valuable for future biomarker development.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c9f8f7995253057b5509aca1a3f898155c6f8846

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Citations in the corpus

Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, background): “[149] Iyer MK, Niknafs YS, Malik R: The landscape of long noncoding RNAs in the human transcriptome.”
NONCODE 2016: an informative and valuable data source of long non-coding RNAs (2015, background): “miRNAs and snoRNAs), several reports have suggested that lncRNAs are modestly conserved (11).”
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Comprehensive Genomic Characterization of Long Non-Coding RNAs across Human Cancers (2015, background): “In addition to the fact that they are highly deregulated in tumors (Akrami et al., 2013; Calin et al., 2007; Du et al., 2013; Iyer et al., 2015; Kim et al., 2014; Li et al., 2015; Ling et al., 2013; Prensner et al., 2011; Trimarchi et al., 2014; Xing et al., 2014), lncRNAs have been found to act as…”
GENCODE: reference annotation for the human and mouse genomes in 2023 (2022, background): “These panels target a large number of GENCODE-unannotated elements in external ncRNA catalogues such as Bigtranscriptome (31), FANTOMCat (32) and miTranscriptome (33) and computational predictions.”
Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers (2015, background): “In addition, several recent large-scale RNA-sequencing datasets have generated a large number of lncRNA-cancer associations (34).”
An atlas of human long non-coding RNAs with accurate 5′ ends (2017, methodology): “scenarios: (1) both TIR and exon conserved, (2) TIR conserved only, (3) exon conserved”
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Long Non-Coding RNA in the Pathogenesis of Cancers (2019, background): “It has been estimated that there are more than 60,000 lncRNAs in humans, and the number of lncRNAs is still increasing quickly [13].”
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