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Alternative RNA Splicing02:18

Alternative RNA Splicing

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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
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Alternative splicing impacts the rice stripe virus response transcriptome.

Shanshan Li1, Wenbin Guo2, Chen Wang1

  • 1College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.

Virology
|September 5, 2023
PubMed
Summary

This study reveals how alternative splicing (AS) in rice plants changes after Rice stripe virus (RSV) infection. Key findings highlight AS gene enrichment in basal metabolism and RNA splicing pathways, crucial for plant defense.

Keywords:
Alternative splicing (AS)Differential transcript usage (DTU)Differentially alternative spliced (DAS)Differentially expressed genes (DEGs)Genome-wideRice stripe virus (RSV)Transcriptome

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Area of Science:

  • Molecular Biology
  • Plant Pathology
  • Genomics

Background:

  • Alternative splicing (AS) is a critical post-transcriptional modification in eukaryotes.
  • AS events in plants responding to viral infections remain largely unexplored.
  • Understanding AS is vital for plant defense mechanisms against pathogens.

Purpose of the Study:

  • To investigate genome-wide alternative splicing changes in rice upon Rice stripe virus (RSV) infection.
  • To identify specific pathways affected by differential gene expression and alternative splicing.
  • To provide a foundational understanding of AS dynamics in rice-virus interactions.

Main Methods:

  • Genome-wide transcriptome analysis of rice plants infected with Rice stripe virus (RSV).
  • Identification and analysis of differentially expressed (DE) genes and differentially alternative spliced (DAS) genes.
  • KEGG pathway analysis and heatmap clustering to interpret gene functions and transcript usage.

Main Results:

  • DE genes were significantly enriched in plant-pathogen interaction pathways.
  • DAS genes were predominantly enriched in basal metabolism and RNA splicing pathways.
  • Differential transcript usage (DTU) clusters showed strong enrichment in mRNA splicing and calcium binding.

Conclusions:

  • Rice plants exhibit significant gene-wide alternative splicing alterations following RSV infection.
  • These AS changes are linked to fundamental cellular processes including metabolism, RNA splicing, and defense responses.
  • The study provides crucial insights into the molecular mechanisms underlying plant-virus interactions.