Prediction of trans-antisense transcripts in Arabidopsis thaliana
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作者:
Wang, Huan
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机构:Chinese Acad Sci, State Key Lab Plant Genom, Inst Genet & Dev Biol, Beijing 100101, Peoples R China
Wang, Huan
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机构:
Chua, Nam-Hai
Wang, Xiu-Jie
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Chinese Acad Sci, State Key Lab Plant Genom, Inst Genet & Dev Biol, Beijing 100101, Peoples R ChinaChinese Acad Sci, State Key Lab Plant Genom, Inst Genet & Dev Biol, Beijing 100101, Peoples R China
Wang, Xiu-Jie
[1
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机构:
[1] Chinese Acad Sci, State Key Lab Plant Genom, Inst Genet & Dev Biol, Beijing 100101, Peoples R China
[2] Grad Univ, Chinese Acad Sci, Beijing 100101, Peoples R China
[3] Rockefeller Univ, Plant Mol Biol Lab, New York, NY 10021 USA
Background: Natural antisense transcripts (NATs) are coding or non-coding RNAs with sequence complementarity to other transcripts (sense transcripts). These RNAs could potentially regulate the expression of their sense partner(s) at either the transcriptional or post-transcriptional level. Experimental and computational methods have demonstrated the widespread occurrence of NATs in eukaryotes. However, most previous studies only focused on cis-NATs with little attention being paid to NATs that originate in trans. Results: We have performed a genome-wide screen of trans-NATs in Arabidopsis thaliana and identified 1,320 putative trans-NAT pairs. An RNA annealing program predicted that most trans-NATs could form extended double-stranded RNA duplexes with their sense partners. Among trans-NATs with available expression data, more than 85% were found in the same tissue as their sense partners; of these, 67% were found in the same cell as their sense partners at comparable expression levels. For about 60% of Arabidopsis trans-NATs, orthologs of at least one transcript of the pair also had trans-NAT partners in either Populus trichocarpa or Oryza sativa. The observation that 430 transcripts had both putative cis- and trans-NATs implicates multiple regulations by antisense transcripts. The potential roles of trans-NATs in inducing post-transcriptional gene silencing and in regulating alternative splicing were also examined. Conclusion: The Arabidopsis transcriptome contains a fairly large number of trans-NATs, whose possible functions include silencing of the corresponding sense transcripts or altering their splicing patterns. The interlaced relationships observed in some cis- and trans-NAT pairs suggest that antisense transcripts could be involved in complex regulatory networks in eukaryotes.
机构:
Univ N Carolina, Lineberger Comprehens Canc Ctr, Dept Cell & Dev Biol, Chapel Hill, NC 27599 USAUniv N Carolina, Lineberger Comprehens Canc Ctr, Dept Cell & Dev Biol, Chapel Hill, NC 27599 USA
机构:
Univ N Carolina, Lineberger Comprehens Canc Ctr, Dept Cell & Dev Biol, Chapel Hill, NC 27599 USAUniv N Carolina, Lineberger Comprehens Canc Ctr, Dept Cell & Dev Biol, Chapel Hill, NC 27599 USA