RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

By Philipp Kapranov, Jill Cheng, S. Dike, D. Nix, R. Duttagupta, A. Willingham, Peter F. Stadler, Jana Hertel, Jörg Hackermüller, Ivo L. Hofacker and 12 more. Science, 2007

2,532 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/96624f8bfa7b7ef7c705b6e0b22cca25606fc8eb

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In Molecular Biology

Citations in the corpus

Transcriptome analysis by strand-specific sequencing of complementary DNA (2009, background): “Antisense transcription is characteristic for eukaryotic genes and is thought to play an important regulatory role (2,12).”
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. (2008, background): “Given the tissue- and cell-type specific (Kapranov et al. 2007; Mercer et al. 2008; Nakaya et al. 2007) and dynamically regulated expression (Ravasi et al.”
Non‐coding RNAs: regulators of disease (2010, background): “Genome-wide transcriptomic studies have now shown that the mammalian genome is abundantly transcribed [2–10] and that at least 80% of this transcription is exclusively associated with long non-coding RNAs (lncRNAs) [9].”
Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs (2013, background): “In contrast to the limited reach of prior tiling array studies [2–5], we analyzed the much larger portion (83.”
Long non-coding RNAs: a new frontier in the study of human diseases. (2013, background): “This length is a convenient cut-off to exclude small RNAs in RNA purification protocols [6,7].”
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers (2014, neutral): “In mammalian cells, transcription initiation at promoters of annotated genes is accompanied by upstream antisense transcription initiation 1–3 .”
The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. (2013, background): “Most studies investigating metastasis mechanisms focused on protein-coding genes, although recent transcriptome-wide analyses have revealed an overwhelming amount of transcribed but not translated genes (4, 5).”
Ribosome profiling provides evidence that large non-coding RNAs do not encode proteins (2013, background): “If classical ncRNAs and lincRNAs are bound by ribosomes, even though they lack canonical features of translation, this raises fascinating questions similar to those raised by pervasive transcription, which occurs even in regions of the genome that do not produce stable RNA products (Birney et al., 2”
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. (2012, background): “Large-scale genomic studies have identified a significant number of transcripts that do not code for proteins (Kapranov et al. 2002, 2007; Bertone 2004; Carninci et al. 2005; ENCODE Project Con- sortium et al. 2007; Ponjavic et al. 2007; Fejes-Toth et al. 2009; Guttman et al. 2009, 2010; Cabili et…”