• Corpus ID: 16576645

Conservation and losses of avian non-coding RNA loci

@article{Gardner2014ConservationAL,
  title={Conservation and losses of avian non-coding RNA loci},
  author={Paul P. Gardner and Mario Fasold and Sarah W. Burge and Maria Ninova and Jana Hertel and Stephanie Kehr and Tammy E. Steeves and Sam Griffiths-Jones and Peter F. Stadler},
  journal={arXiv: Genomics},
  year={2014}
}
Here we present the results of a large-scale bioinformatic annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We show that a number of lncRNA-associated loci are conserved between birds and mammals, including several intriguing… 

Figures and Tables from this paper

References

SHOWING 1-10 OF 78 REFERENCES

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

TLDR
The biological relevance of lncRNAs would be highly questionable if they were limited to closely related phyla, but their preservation across diverse amniotes, their apparent conservation in exon structure, and similarities in their pattern of brain expression during embryonic and early postnatal stages together indicate that these are functional RNA molecules.

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

TLDR
The findings show that nearly half of intergenic lncRNA loci have been gained or lost since the last common ancestor of mouse and rat, and they predict that such rapid transcriptional turnover contributes to the evolution of tissue- and lineage-specific gene expression.

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.

TLDR
It is found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that l incRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes.

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

TLDR
It is demonstrated that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFκB, Sox2, Oct4 (also known as Pou5f1) and Nanog, defining a unique collection of functional linc RNAs that are highly conserved and implicated in diverse biological processes.

Evolution of vault RNAs.

TLDR
A systematic and comprehensive analysis of this rapidly evolving class of ncRNAs in deuterostomes is reported, providing a comprehensive collection of computationally predicted vtRNA genes.

Evolution of coding and non-coding genes in HOX clusters of a marsupial

TLDR
It is confirmed that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago and a new potentially functional microRNA as well as conserved miRNAs are identified.

Retroposed SNOfall--a mammalian-wide comparison of platypus snoRNAs.

TLDR
It is shown that the platypus genome contains more than 200 small nucleolar (sno) RNAs among hundreds of other diverse npcRNAs, and a snoRNA-derived retroposon (termed snoRTE) that facilitates a very effective dispersal of an H/ACA sno RNA via RTE-mediated retroposition is revealed.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

TLDR
A draft genome sequence of the red jungle fowl, Gallus gallus, provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes.

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

TLDR
The Genomic tRNA Database (GtRNAdb), currently including over 74 000 tRNA genes predicted from 740 species, is created, currently including information by isotype and genetic locus, easily downloadable primary sequences, graphical secondary structures and multiple sequence alignments.
...