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Journal ArticleDOI

Non-coding RNA genes and the modern RNA world.

Sean R. Eddy
- 01 Dec 2001 - 
- Vol. 2, Iss: 12, pp 919-929
TLDR
Non-coding RNAs seem to be particularly abundant in roles that require highly specific nucleic acid recognition without complex catalysis, such as in directing post-transcriptional regulation of gene expression or in guiding RNA modifications.
Abstract
Non-coding RNA (ncRNA) genes produce functional RNA molecules rather than encoding proteins. However, almost all means of gene identification assume that genes encode proteins, so even in the era of complete genome sequences, ncRNA genes have been effectively invisible. Recently, several different systematic screens have identified a surprisingly large number of new ncRNA genes. Non-coding RNAs seem to be particularly abundant in roles that require highly specific nucleic acid recognition without complex catalysis, such as in directing post-transcriptional regulation of gene expression or in guiding RNA modifications.

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Citations
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Journal ArticleDOI

The solution structural ensembles of RNA kink-turn motifs and their protein complexes.

TL;DR: This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA/protein complexes in solution and uncovers the behavior of an important RNA/ protein motif.
Journal ArticleDOI

Gene duplication and other evolutionary strategies: from the RNA world to the future

TL;DR: It is concluded that the major basic Neo-Darwinian principles that include amplification, variation and selection already governed evolution in the RNA and RNP worlds.
Journal ArticleDOI

Dynalign II: common secondary structure prediction for RNA homologs with domain insertions.

TL;DR: A novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures is introduced, implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs.
Journal ArticleDOI

The principle of recursive genome function.

A. Pellionisz
- 20 Jun 2008 - 
TL;DR: The principle of recursive genome function (PRGF) is put forward, effectively reversing two axioms of genomics as the authors used to know it, prior to the Encyclopedia of DNA Elements Project (ENCODE).
Journal ArticleDOI

Computational discovery of folded RNA domains in genomes and in vitro selected libraries.

TL;DR: The application of the program RNABOB is described, which performs structure-based searches by allowing the user to define a desired motif's sequence, paired and spacer elements and then scans a sequence file for regions capable of assuming the prescribed fold.
References
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Journal ArticleDOI

Initial sequencing and analysis of the human genome.

Eric S. Lander, +248 more
- 15 Feb 2001 - 
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI

The sequence of the human genome.

J. Craig Venter, +272 more
- 16 Feb 2001 - 
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Journal ArticleDOI

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14

TL;DR: Two small lin-4 transcripts of approximately 22 and 61 nt were identified in C. elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin- 4 regulates lin- 14 translation via an antisense RNA-RNA interaction.
Journal ArticleDOI

The Complete Genome Sequence of Escherichia coli K-12

TL;DR: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident.
Journal ArticleDOI

Genetic regulatory mechanisms in the synthesis of proteins.

TL;DR: The synthesis of enzymes in bacteria follows a double genetic control, which appears to operate directly at the level of the synthesis by the gene of a shortlived intermediate, or messenger, which becomes associated with the ribosomes where protein synthesis takes place.
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Initial sequencing and analysis of the human genome.

Eric S. Lander, +248 more
- 15 Feb 2001 -