Cotranscriptional and Posttranscriptional Features of the Transcriptome in Soybean Shoot Apex and Leaf.

Jiafu Zhu,Baohui Liu,Han Zhao,Fanjiang Kong,Min Liu,Zhicheng Dong

doi:10.3389/fpls.2021.649634

Jiafu Zhu, Baohui Liu + Show 4 more

Open Access

https://doi.org/10.3389/fpls.2021.649634

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Abstract

Transcription is the first step of central dogma, in which the genetic information stored in DNA is copied into RNA. In addition to mature RNA sequencing (RNA-seq), high-throughput nascent RNA assays have been established and applied to provide detailed transcriptional information. Here, we present the profiling of nascent RNA from trifoliate leaves and shoot apices of soybean. In combination with nascent RNA (chromatin-bound RNA, CB RNA) and RNA-seq, we found that introns were largely spliced cotranscriptionally. Although alternative splicing (AS) was mainly determined at nascent RNA biogenesis, differential AS between the leaf and shoot apex at the mature RNA level did not correlate well with cotranscriptional differential AS. Overall, RNA abundance was moderately correlated between nascent RNA and mature RNA within each tissue, but the fold changes between the leaf and shoot apex were highly correlated. Thousands of novel transcripts (mainly non-coding RNA) were detected by CB RNA-seq, including the overlap of natural antisense RNA with two important genes controlling soybean reproductive development, FT2a and Dt1. Taken together, we demonstrated the adoption of CB RNA-seq in soybean, which may shed light on gene expression regulation of important agronomic traits in leguminous crops.

Highlights

Transcription, the first step of gene expression, is accomplished by the multisubunit protein complex RNA polymerase
The spatial and temporal expression of genes in the shoot apex largely determines the architecture of crop plants, including the numbers of branches, flowers, and nodes, which affect the yield per plant
MRNA of Dt1 was detected in the shoot apex at 15 days after emergence under a long-day condition (Liu et al, 2010); we set to investigate the transcriptome of the shoot apex from 10- to 15-day-old plants (Figure 1A, see section “Materials and Methods”)

Summary

Introduction

Transcription, the first step of gene expression, is accomplished by the multisubunit protein complex RNA polymerase. Messenger RNA precursors (pre-mRNAs) are subjected to multiple processing steps, including 5 capping, splicing of introns, 3 cleavage and polyadenylation, and editing (Bentley, 2014). These steps are known as posttranscriptional processing. High-throughput sequencing of nascent RNA revealed genomewide cotranscriptional splicing (Khodor et al, 2011; Nojima et al, 2015; Drexler et al, 2020).

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Conclusion