Non–coding RNA genes and the modern RNA world

By Sean R. Eddy. Nature reviews genetics, 2001

1,434 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/664803cda3f5f42a351690855e0821a0e46cea7f

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Citations in the corpus

Gene map of the extended human MHC (2004, background): “Compared with protein-coding genes, non-coding RNA genes (except for tRNA genes) are much more difficult to predict, and at the moment they still lack experimental verificatio”
Comparing the human and chimpanzee genomes: Searching for needles in a haystack (2005, background): “The wealth of new information being generated about noncoding RNA sequences also makes them an intriguing candidates for potential differences (Eddy 2001; Dykxhoorn et al. 2003; Mello and Conte 2004; Kim 2005; Tang 2005).”
The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. (2006, background): “Several reviews have emphasized that the role of ncRNAs in different cellular processes has been largely underestimated (Kelley and Kuroda 2000; Eddy 2001, 2002; Erdmann et al. 2001; Akhtar 2003).”
Rfam: an RNA family database (2003, background): “The number of known RNA genes is expanding rapidly due to the deluge of genomic data, but also aided by recent systematic efforts to detect RNA genes (reviewed in (1-3)).”
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007, background): “Several comparative approaches to RNA gene identification have been developed 6,7,65 that recognize their characteristic properties: compensatory double substitutions of paired nucleotides (for example, A .”
Ribosome profiling provides evidence that large non-coding RNAs do not encode proteins (2013, background): “…including the telomerase RNA, RNase P, small nuclear RNAs, small nucleolar RNAs, vault RNA, microRNAs (miRNAs), and other RNAs that have been clearly demonstrated to function as RNA molecules (Bartel, 2004; Eddy, 2001; Shippen-Lentz and Blackburn, 1990; Stark et al., 1978) (Figures 2 and S2).”
ncRNA- and Pc2 Methylation-Dependent Gene Relocation between Nuclear Structures Mediates Gene Activation Programs (2011, positive): “N IH -PA Author M anuscript N IH -PA Author M anuscript N IH -PA Author M anuscript The notion that ncRNAs can have numerous molecular functions is rapidly evolving (Eddy, 2001; Ponting et al., 2009).”
What is a gene, post-ENCODE? History and updated definition. (2007, background): “, snoRNAs), and protein synthesis (tRNAs and rRNA) (Eddy 2001; Mattick and Makunin 2006).”
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features (2017, background): “Recent studies have well demonstrated that non-coding RNAs (ncRNAs) are pervasively transcribed from plant to animal genomes (1–4).”
The First 50 Plant Genomes (2013, background): “Further complicating annotation is that there are many expressed non-coding RNAs that are functionally important (Eddy, 2001), but not considered genes in a traditional sense.”