Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice

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Abstract Background Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand.Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms.Genome-wide in silico analysis china glaze fairytale bliss has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRNAs), which participate in important biogenesis mechanisms for transcriptional and post-transcriptional regulation in rice.

However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs.Results We applied high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq) to deeply sequence mRNA for assessing sense and antisense transcripts that were derived under salt, drought and cold stresses, and normal conditions, in the model plant rice (Oryza sativa).Combined with RAP-DB genome annotation (the Rice Annotation Project Database build-5 data set), 76,013 transcripts corresponding to 45,844 unique gene loci were assembled, in which 4873 gene loci were newly identified.

Of 3819 putative rice cis-NATs, 2292 were detected as expressed and giving rise to small RNAs from their overlapping regions through integrated analysis of ssRNA-seq data rei?llinen pizzalapio and small RNA data.Among them, 503 cis-NATs seemed to be associated with specific conditions.The deep sequence data from isolated epidermal cells of rice seedlings further showed that 54.

0% of cis-NATs were expressed simultaneously in a population of homogenous cells.Nearly 9.7% of rice transcripts were involved in one-to-one or many-to-many cis-NATs formation.

Furthermore, only 17.4-34.7% of 223 many-to-many cis-NAT groups were all expressed and generated nat-siRNAs, indicating that only some cis-NAT groups may be involved in complex regulatory networks.

Conclusions Our study profiles an abundance of cis-NATs and nat-siRNAs in rice.These data are valuable for gaining insight into the complex function of the rice transcriptome.