Zhu Jiafu, Zhao Han, Kong Fanjiang, Liu Baohui, Liu Min, Dong Zhicheng
Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China.
Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
Front Plant Sci. 2021 Apr 9;12:649634. doi: 10.3389/fpls.2021.649634. eCollection 2021.
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, and . 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.
转录是中心法则的第一步，其中储存在DNA中的遗传信息被复制到RNA中。除了成熟RNA测序（RNA-seq）外，高通量新生RNA分析方法也已建立并应用于提供详细的转录信息。在此，我们展示了大豆三出复叶和茎尖新生RNA的分析。结合新生RNA（染色质结合RNA，CB RNA）和RNA-seq，我们发现内含子大多在转录同时被剪接。虽然可变剪接（AS）主要在新生RNA生物合成时被确定，但在成熟RNA水平上，叶片和茎尖之间的差异AS与转录同时的差异AS相关性不佳。总体而言，每个组织内新生RNA和成熟RNA之间的RNA丰度呈中度相关，但叶片和茎尖之间的倍数变化高度相关。通过CB RNA-seq检测到数千种新转录本（主要是非编码RNA），包括天然反义RNA与两个控制大豆生殖发育的重要基因的重叠，以及。综上所述，我们证明了CB RNA-seq在大豆中的应用，这可能为豆科作物重要农艺性状的基因表达调控提供线索。
