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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 transcripts in the NATs. All 8,634 NAT transcripts were categorized as cis- or trans-NATs. Of these, 768 transcripts formed only cis-NATs, 1,200 transcripts formed both cis- and trans-NATs, and the other 6,666 transcripts were trans-NAT transcripts.
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Figure 3: Distribution of transcripts in the NATs. All 8,634 NAT transcripts were categorized as cis- or trans-NATs. Of these, 768 transcripts formed only cis-NATs, 1,200 transcripts formed both cis- and trans-NATs, and the other 6,666 transcripts were trans-NAT transcripts.

Mentions: For the trans-NATs, one transcript commonly had many antisense transcripts [15,24]. The number of antisense transcripts ranged from 1 to 177 in soybean, possibly a consequence of the homologous genes in the gene families frequently having the same antisense transcript [24]. The soybean genome has gone through at least two rounds of polyploidy and subsequent diploidization events. Segmental duplications and chromosome-level homology are common in the soybean genome [33-36], and approximately 75% of genes have multiple copies [37]. Some transcripts can form both cis-NATs and trans-NATs [15]. Of the 8,634 transcripts in soybean, 1,200 transcripts were involved in both cis- and trans-NATs (Figure‚ÄČ3). These genes may be regulated by cis- and/or trans-NATs.


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 transcripts in the NATs. All 8,634 NAT transcripts were categorized as cis- or trans-NATs. Of these, 768 transcripts formed only cis-NATs, 1,200 transcripts formed both cis- and trans-NATs, and the other 6,666 transcripts were trans-NAT transcripts.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Distribution of transcripts in the NATs. All 8,634 NAT transcripts were categorized as cis- or trans-NATs. Of these, 768 transcripts formed only cis-NATs, 1,200 transcripts formed both cis- and trans-NATs, and the other 6,666 transcripts were trans-NAT transcripts.
Mentions: For the trans-NATs, one transcript commonly had many antisense transcripts [15,24]. The number of antisense transcripts ranged from 1 to 177 in soybean, possibly a consequence of the homologous genes in the gene families frequently having the same antisense transcript [24]. The soybean genome has gone through at least two rounds of polyploidy and subsequent diploidization events. Segmental duplications and chromosome-level homology are common in the soybean genome [33-36], and approximately 75% of genes have multiple copies [37]. Some transcripts can form both cis-NATs and trans-NATs [15]. Of the 8,634 transcripts in soybean, 1,200 transcripts were involved in both cis- and trans-NATs (Figure‚ÄČ3). These genes may be regulated by cis- and/or trans-NATs.

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
Related in: MedlinePlus