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Alternative RNA Splicing02:18

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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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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
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Alternative splicing dynamically regulates common carp embryogenesis under thermal stress.

Shuimu Hu1, Guopeng Tian1, Yulin Bai1

  • 1State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.

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|October 2, 2024
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Summary

Thermal stress significantly impacts alternative splicing (AS) during common carp (Cyprinus carpio) embryogenesis. This study reveals widespread AS changes and identifies key genes involved in thermal adaptation in polyploid fish.

Keywords:
Alternative splicingCyprinus carpioEmbryogenesisThermal stress

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Area of Science:

  • Aquatic biology
  • Genomics
  • Developmental biology

Background:

  • Thermal stress is a critical environmental factor impacting fish development and survival.
  • Common carp (Cyprinus carpio) are vulnerable to heat stress during embryonic and larval stages.
  • The role of alternative splicing in common carp embryogenesis under thermal stress is not well understood.

Purpose of the Study:

  • To comprehensively profile alternative splicing (AS) during common carp embryogenesis under varying temperatures.
  • To identify stage-specific and temperature-specific AS genes and events.
  • To elucidate the regulatory mechanisms of thermal stress on AS in common carp.

Main Methods:

  • RNA sequencing (RNA-seq) across eight developmental stages and four temperatures.
  • Identification of stage-specific AS (SAS) genes and temperature-specific differentially expressed genes (TDEGs).
  • Analysis of temperature-specific differentially AS (TDAS) genes, protein-protein interaction (PPI) networks, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.

Main Results:

  • A total of 5,835 SAS genes, 21,368 TDEGs, and 2,652 TDAS genes were identified.
  • Early developmental stages (morula, gastrula) showed heightened sensitivity to thermal stress, with significant increases in AS.
  • TDAS genes were primarily involved in intracellular transport, protein modification, localization, and biosynthetic processes; subgenome B showed higher AS activity.
  • Key TDAS genes (e.g., taf2, hnrnpa1, drg2) and regulatory roles of lncRNAs in thermal stress response were identified.

Conclusions:

  • Thermal stress influences alternative splicing regulation in common carp embryogenesis at multiple levels.
  • This study fills knowledge gaps regarding AS in common carp embryogenesis and thermal stress response.
  • Findings contribute to understanding environmental adaptation mechanisms in polyploid fish during development.