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Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation

Anireddy S N Reddy1, Jie Huang2, Naeem H Syed3

  • 1Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, U.S.A.

Biochemical Society Transactions
|November 16, 2020
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing reveals complex plant transcriptome regulation. Advanced RNA sequencing methods uncover co-/post-transcriptional control crucial for plant development and stress response.

Keywords:
abiotic stressesbiotic stressesco-transcriptional processingepitranscriptomegene regulationnanopore direct RNA sequencing

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Area of Science:

  • Plant molecular biology
  • Transcriptomics
  • Gene regulation

Background:

  • Next-generation sequencing (NGS) technologies like Illumina RNA-seq, PacBio Iso-seq, and Oxford Nanopore direct RNA sequencing (DRS) have illuminated plant transcriptome complexity.
  • Understanding co-/post-transcriptional regulation is vital for plant adaptation to developmental cues and environmental stresses.

Purpose of the Study:

  • To review recent discoveries in plant transcriptome dynamics and co-/post-transcriptional regulation.
  • To provide mechanistic insights into RNA processing and splicing.
  • To identify critical research gaps in plant RNA biology.

Main Methods:

  • Global analysis of mature mRNAs, nuclear run-on transcripts, and nascent chromatin-bound mRNAs.
  • Utilizing short and full-length/single-molecule direct RNA sequencing reads.
  • Mapping transcriptome-wide start sites, poly(A) site choice, poly(A) tail length, and RNA base modifications.

Main Results:

  • Uncovered roles of RNA polymerase II in transcription, co-transcriptional splicing, and polyadenylation.
  • Detailed mapping of regulatory RNA features including transcription start sites and polyadenylation.
  • Emerging evidence suggests co-/post-transcriptional reprogramming is key for plant responses to stress and development.

Conclusions:

  • Co-/post-transcriptional regulation significantly impacts plant gene expression, growth, and survival.
  • While external cues are known to influence splicing, the precise mechanisms remain largely unelucidated.
  • Further genomic and biochemical research is needed to fully understand plant RNA processing and regulation.