Co-transcriptional and post-transcriptional features of transcriptome in soybean shoot apex and leaf

Transcription is the first step of central dogma, in which the genetic information stored in DNA is copied into RNA. Other than mature RNA sequencing (RNA-seq), high throughput nascent RNA assays have been established and applied to provide details of transcription. We present here the first profiling of nascent RNA from trifoliate leaf and shoot apex of soybean. In combination of nascent RNA (chromatin bond RNA, CB RNA) and RNA-seq, we found that introns are largely spliced co-transcriptionally. Although alternative splicing (AS) is mainly determined at nascent RNA biogenesis, differential AS between tissues at mature RNA does not correlate well with co-transcriptional differential AS. Overall, RNA abundance is moderately correlated between nascent RNA and mature RNA in one tissue, but their fold changes between tissues is highly correlated at nascent RNA and mature RNA level. Thousands of novel transcripts (mainly noncoding RNA) were detected by CB RNA-seq, including two natural antisense RNA overlapped with two important genes controlling soybean reproductive development, FT2a and Dt1a. Taken together, we demonstrated the adoption of CB RNA-seq in soybean, which may shed light on gene expression regulation on important agronomic traits in leguminous crops.