The Eukaryotic Genome as an RNA Machine

By Paulo P. Amaral, Marcel E. Dinger, Tim R. Mercer, John S. Mattick. Science, 2008

630 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/227377d6b2578c15e826c8337a63eb2b91a79607

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In Molecular Biology

Citations in the corpus

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation (2010, background): “Mammalian genomes harbor fewer protein-coding genes than initially anticipated, and gene numbers do not proportionally increase with increased genome complexity (for review, see Amaral et al., 2008; Mattick, 2009).”
Cancer epigenetics: from mechanism to therapy. (2012, background): “Noncoding RNAs The high-throughput genomic platforms have established that virtually the entire genome is transcribed; however, only 2% of this is subsequently translated (Amaral et al., 2008).”
Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. (2008, background): “Kcnq1ot1 Is a Regulatory Noncoding Antisense RNA To date, very few long ncRNAs, such as Xist, Tsix, Air, and HOTAIR, have been shown to possess regulatory functions (Amaral et al., 2008; Umlauf and Fraser, 2008).”
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs (2014, background): “Concomitant with this increased growth of characterized lncRNAs is an increasing understanding toward biological mechanisms, as well as a growing awareness and recognition of the importance of lncRNAs in virtually every cellular and regulatory process (4).”
Long noncoding RNAs and the genetics of cancer (2013, background): “…which exhibit exquisite cell-specific and developmental dynamic expression patterns (Dinger et al, 2008; Mercer et al, 2008, 2010; Pang et al, 2009; Cabili et al, 2011; Khaitan et al, 2011), capable of transacting a wide repertoire of regulatory functions (Amaral et al, 2008; Mercer et al, 2009).”
The many pathways of RNA degradation. (2009, background): “Recent analyses have demonstrated that yeast and human cells transcribe almost their entire genomes, implying the existence of a huge mass of hidden, or cryptic, ncRNAs, which are believed to be generally transcribed by RNA polymerase II (reviewed in Amaral et al., 2008).”
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs (2012, background): “In summary, it is now clear that the human and other mammalian genomes produce thousands of lncRNAs (33).”
Fast Computation and Applications of Genome Mappability (2012, background): “The long non-coding RNAs (lncRNAs) [23,24] also seem to be less unique than protein-coding sequences; interestingly, they contain a significant proportion of nucleotide mapping more than 6 - 7 times in the genome, probably reflecting their tendency to be enriched in repetitive elements such as…”
Non‐coding RNAs: regulators of disease (2010, background): “Overall, there are at least tens of thousands of lncRNAs that show signatures of selection — many of which, like small RNAs, are tissue and developmental stage-specific [97,104–108].”
Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities (2008, background): “[15,16]), the functions of the vast majority remain unknown and”