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| Title |
The distribution and evolution of Arabidopsis thaliana cis natural antisense transcripts
|
|---|---|
| Published in |
BMC Genomics, June 2015
|
| DOI | 10.1186/s12864-015-1587-0 |
| Pubmed ID | |
| Authors |
Johnathan Bouchard, Carlos Oliver, Paul M Harrison |
| Abstract |
Natural antisense transcripts (NATs) are regulatory RNAs that contain sequence complementary to other RNAs, these other RNAs usually being messenger RNAs. In eukaryotic genomes, cis-NATs overlap the gene they complement. Here, our goal is to analyze the distribution and evolutionary conservation of cis-NATs for a variety of available data sets for Arabidopsis thaliana, to gain insights into cis-NAT functional mechanisms and their significance. Cis-NATs derived from traditional sequencing are largely validated by other data sets, although different cis-NAT data sets have different prevalent cis-NAT topologies with respect to overlapping protein-coding genes. A. thaliana cis-NATs have substantial conservation (28-35% in the three substantive data sets analyzed) of expression in A. lyrata. We examined evolutionary sequence conservation at cis-NAT loci in Arabidopsis thaliana across nine sequenced Brassicaceae species (picked for optimal discernment of purifying selection), focussing on the parts of their sequences not overlapping protein-coding transcripts (dubbed 'NOLPs'). We found significant NOLP sequence conservation for 28-34% NATs across different cis-NAT sets. This NAT NOLP sequence conservation versus A. lyrata is generally significantly correlated with conservation of expression. We discover a significant enrichment of transcription factor binding sites (as evidenced by CHIP-seq data) in NOLPs compared to randomly sampled near-gene NOLP-like DNA , that is linked to significant sequence conservation. Conversely, there is no such evidence for a general significant link between NOLPs and formation of small interfering RNAs (siRNAs), with the substantial majority of unique siRNAs arising from the overlapping portions of the cis-NATs. In aggregate, our results suggest that many cis-NAT NOLPs function in the regulation of conserved promoter/regulatory elements that they 'over-hang'. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 19 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 6 | 32% |
| Student > Ph. D. Student | 3 | 16% |
| Professor | 2 | 11% |
| Other | 2 | 11% |
| Student > Doctoral Student | 1 | 5% |
| Other | 4 | 21% |
| Unknown | 1 | 5% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 8 | 42% |
| Biochemistry, Genetics and Molecular Biology | 8 | 42% |
| Environmental Science | 1 | 5% |
| Unknown | 2 | 11% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 18 May 2016.
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#18,414,796
of 22,811,321 outputs
Outputs from BMC Genomics
#8,179
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Outputs of similar age
#192,180
of 266,419 outputs
Outputs of similar age from BMC Genomics
#195
of 230 outputs
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