The evolution of lncRNA repertoires and expression patterns in tetrapods

@article{Necsulea2014TheEO,
  title={The evolution of lncRNA repertoires and expression patterns in tetrapods},
  author={Anamaria Necsulea and Magali Soumillon and Maria Warnefors and Ang{\'e}lica Liechti and Tasman Daish and Ulrich Zeller and Julie C. Baker and Frank Gr{\"u}tzner and Henrik Kaessmann},
  journal={Nature},
  year={2014},
  volume={505},
  pages={635-640}
}
Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including… 
Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity
TLDR
It is proposed that these noncoding RNAs in the demosponge Amphimedon queenslandica are an ancient feature of the metazoan genome, consistent with lncRNAs regulating the development of animals, regardless of their level of morphological complexity.
Evolutionary clues in lncRNAs
TLDR
A rapid evolutionary turnover is observable throughout the heterogeneous group of lncRNAs, which highlights the importance of structure on functionality of lNCRNAs as opposed to the poor impact of primary sequence changes.
Developmental dynamics of lncRNAs across mammalian organs and species
TLDR
The expression patterns of lncRNAs across developmental time points in seven major organs, from early organogenesis to adulthood, in seven species, are analyzed and many with dynamic expression patterns across time that show signatures of enrichment for functionality are found.
Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa
TLDR
It is proposed that the high degree of similarity in the structure, organization, and dynamic expression of pig lncRNAs compared with human and mouse lnc RNAs play an important role in organ physiology and development in mammals.
Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs
TLDR
Slncky is presented, a lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-sequencing data and further uses evolutionary constraint to prioritize lnc RNAs that are likely to be functionally important, and develops a sensitive alignment pipeline for aligning lnc RNA loci and proposes new evolutionary metrics relevant for analyzing sequence and transcript evolution.
Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants
TLDR
Comprehensive integration of large-scale lnc RNA data and construction of a phylogenetic tree with orthologous lncRNA families from 25 flowering plants was used to provide an oversight of the evolutionary history of plant lncRNAs including origin, conservation, and Orthologous relationships.
Conservation analysis of long non-coding RNAs in plants
TLDR
An analysis of lncRNAs in five monocot and five dicot species showed that plant lncRNA genes were generally shorter and had fewer exons than protein-coding genes, and those which can form precursors or targets of miRNAs have a conservative identity in different species.
Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs
TLDR
Slnckv is presented, a computational lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-Sequencing data and further prioritizes lnc RNAs by characterizing selective constraint as a proxy for function, and develops a sensitive alignment pipeline for aligning lnc RNA loci and proposes new evolutionary metrics relevant for both sequence and transcript evolution.
Evolutionary annotation of conserved long non-coding RNAs in major mammalian species
TLDR
This work builds comprehensive lncRNA catalogs covering the major mammalian species and demonstrates that lnc RNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts.
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications.
TLDR
The molecular mechanisms promoting the birth and rapid evolution of lncRNA genes are explored, with an emphasis on the influence of bidirectional transcription and transposable elements, two pervasive features of vertebrate genomes that reveal a remarkably dynamic and malleable noncoding transcriptome.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 56 REFERENCES
Long noncoding RNAs in C. elegans.
TLDR
A glimpse into the lncRNA content of a nonvertebrate animal is provided and a resource for future studies of lncRNAs function is provided.
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
TLDR
The most complete human lncRNA annotation to date is presented, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts, and expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes.
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.
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.
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness
TLDR
These analyses reveal lincRNA and macroRNA exon sequences to be subject to the same relatively low degree of sequence constraint, and indicate that each of the two ncRNA catalogues unevenly and lightly samples the true, much larger, nc RNA repertoire of the mouse.
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.
Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome
TLDR
It is predicted that the genomes of not only vertebrates, such as mammals, but also an invertebrate (fruit fly) harbor large numbers of lincRNA loci, including lincRNAs with potential functional analogues in mammals.
Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution
TLDR
This study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that linc RNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation.
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.
Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
TLDR
Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence, is presented and the power of ab initio reconstruction is demonstrated to render a comprehensive picture of mammalian transcriptomes.
...
1
2
3
4
5
...