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Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max).

Zheng H, Qiyan J, Zhiyong N, Hui Z - BMC Genomics (2013)

Bottom Line: We identified a total of 86 microRNA (miRNA) targets that had antisense transcripts in soybean.We globally identified nat-siRNAs, and the targets of nat-siRNAs in soybean.It is likely that the cis-NATs, trans-NATs, nat-siRNAs, miRNAs, and miRNA targets form complex regulatory networks.

View Article: PubMed Central - HTML - PubMed

Affiliation: The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

ABSTRACT

Background: Natural antisense transcripts (NATs) are a class of RNAs that contain a sequence complementary to other transcripts. NATs occur widely in eukaryotes and play critical roles in post-transcriptional regulation. Soybean NAT sequences are predicted in the PlantNATsDB, but detailed analyses of these NATs remain to be performed.

Results: A total of 26,216 NATs, including 994 cis-NATs and 25,222 trans-NATs, were predicted in soybean. Each sense transcript had 1-177 antisense transcripts. We identified 21 trans-NATs using RT-PCR amplification. Additionally, we identified 179 cis-NATs and 6,629 trans-NATs that gave rise to small RNAs; these were enriched in the NAT overlapping region. The most abundant small RNAs were 21, 22, and 24 nt in length. The generation of small RNAs was biased to one stand of the NATs, and the degradation of NATs was biased. High-throughput sequencing of the degradome allowed for the global identification of NAT small interfering RNAs (nat-siRNAs) targets. 446 target genes for 165 of these nat-siRNAs were identified. The nat-siRNA target could be one transcript of a given NAT, or from other gene transcripts. We identified five NAT transcripts containing a hairpin structure that is characteristic of pre-miRNA. We identified a total of 86 microRNA (miRNA) targets that had antisense transcripts in soybean.

Conclusions: We globally identified nat-siRNAs, and the targets of nat-siRNAs in soybean. It is likely that the cis-NATs, trans-NATs, nat-siRNAs, miRNAs, and miRNA targets form complex regulatory networks.

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Distribution of antisense transcripts in soybean. For the 26,216 NATs, the antisense transcripts were sorted according to gene serial number and the number of repeats counted for every transcript. Transcripts had a range of 1–177 antisense transcripts in soybean.
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Figure 1: Distribution of antisense transcripts in soybean. For the 26,216 NATs, the antisense transcripts were sorted according to gene serial number and the number of repeats counted for every transcript. Transcripts had a range of 1–177 antisense transcripts in soybean.

Mentions: We analyzed 66,213 soybean transcripts downloaded from the Phytozome database (http://www.phytozome.net/index.php) [26]. Over 13% (8,634) of the transcripts had at least one antisense transcript in soybean. Among these transcripts, over 50% (4,788) had only one antisense transcript, while the others had from 2 to 177 antisense transcripts (Figure 1). A total of 26,216 NATs were identified in soybean. The NATs were categorized into cis-NATs and trans-NATs according to the transcript origin from the genomic loci. Mapping of the NAT transcripts to the soybean genome identified 994 cis-NATs and 25,222 trans-NATs (Additional files 1 and 2).


Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max).

Zheng H, Qiyan J, Zhiyong N, Hui Z - BMC Genomics (2013)

Distribution of antisense transcripts in soybean. For the 26,216 NATs, the antisense transcripts were sorted according to gene serial number and the number of repeats counted for every transcript. Transcripts had a range of 1–177 antisense transcripts in soybean.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3643859&req=5

Figure 1: Distribution of antisense transcripts in soybean. For the 26,216 NATs, the antisense transcripts were sorted according to gene serial number and the number of repeats counted for every transcript. Transcripts had a range of 1–177 antisense transcripts in soybean.
Mentions: We analyzed 66,213 soybean transcripts downloaded from the Phytozome database (http://www.phytozome.net/index.php) [26]. Over 13% (8,634) of the transcripts had at least one antisense transcript in soybean. Among these transcripts, over 50% (4,788) had only one antisense transcript, while the others had from 2 to 177 antisense transcripts (Figure 1). A total of 26,216 NATs were identified in soybean. The NATs were categorized into cis-NATs and trans-NATs according to the transcript origin from the genomic loci. Mapping of the NAT transcripts to the soybean genome identified 994 cis-NATs and 25,222 trans-NATs (Additional files 1 and 2).

Bottom Line: We identified a total of 86 microRNA (miRNA) targets that had antisense transcripts in soybean.We globally identified nat-siRNAs, and the targets of nat-siRNAs in soybean.It is likely that the cis-NATs, trans-NATs, nat-siRNAs, miRNAs, and miRNA targets form complex regulatory networks.

View Article: PubMed Central - HTML - PubMed

Affiliation: The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

ABSTRACT

Background: Natural antisense transcripts (NATs) are a class of RNAs that contain a sequence complementary to other transcripts. NATs occur widely in eukaryotes and play critical roles in post-transcriptional regulation. Soybean NAT sequences are predicted in the PlantNATsDB, but detailed analyses of these NATs remain to be performed.

Results: A total of 26,216 NATs, including 994 cis-NATs and 25,222 trans-NATs, were predicted in soybean. Each sense transcript had 1-177 antisense transcripts. We identified 21 trans-NATs using RT-PCR amplification. Additionally, we identified 179 cis-NATs and 6,629 trans-NATs that gave rise to small RNAs; these were enriched in the NAT overlapping region. The most abundant small RNAs were 21, 22, and 24 nt in length. The generation of small RNAs was biased to one stand of the NATs, and the degradation of NATs was biased. High-throughput sequencing of the degradome allowed for the global identification of NAT small interfering RNAs (nat-siRNAs) targets. 446 target genes for 165 of these nat-siRNAs were identified. The nat-siRNA target could be one transcript of a given NAT, or from other gene transcripts. We identified five NAT transcripts containing a hairpin structure that is characteristic of pre-miRNA. We identified a total of 86 microRNA (miRNA) targets that had antisense transcripts in soybean.

Conclusions: We globally identified nat-siRNAs, and the targets of nat-siRNAs in soybean. It is likely that the cis-NATs, trans-NATs, nat-siRNAs, miRNAs, and miRNA targets form complex regulatory networks.

Show MeSH