Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies
Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies
复制标题
使用下一代测序技术解码植物转录组和表观转录组的共/转录后复杂性
DOI：
10.1042/bst20190492
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发表时间：
2020
影响因子：
3.9
通讯作者：
Lianfeng Gu
中科院分区：
文献类型：
--
作者：
Anireddy S.N. Reddy;Jie Huang;Naeem H. Syed;Asa Ben-Hur;Suomeng Dong;Lianfeng Gu
下一代测序（NGS）技术- Illumina RNA-seq，Pacific Biosciences同种型测序（PacBio Iso-seq）和Oxford Nanopore直接RNA测序（DRS）-揭示了植物转录组的复杂性及其在共/转录后水平的调控。使用短的以及全长的和单分子的DRS读数对成熟mRNA、来自核连续测定的转录物和新生的染色质结合的mRNA进行的全局分析揭示了不同形式的RNA聚合酶II在转录过程中的潜在作用，以及共转录前mRNA剪接和多聚腺苷酸化的程度。这些工具还允许绘制含帽RNA中的全转录组起始位点、poly（A）位点选择、poly（A）尾长和RNA碱基修饰。从最近的研究中出现的主题是，在共/转录后水平的基因表达的重编程响应于发展的线索和压力可能发挥了至关重要的作用，在引发适当的反应，最佳的生长和植物在不利条件下的生存。虽然发育线索和不同的压力调节共/转录后剪接的机制在很大程度上是未知的，最近的一些研究表明，外部线索的目标spliceosomal和剪接调节蛋白来调节选择性剪接。在这篇综述中，我们提供了一个概述的动态和复杂性的植物转录组，剪接调控机制的见解，并讨论了关键的差距，共/转录后研究，需要使用不同的基因组和生物化学方法来解决。
Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.