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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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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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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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Using the E1A Minigene Tool to Study mRNA Splicing Changes
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Splicing conservation signals in plant long noncoding RNAs.

Jose Antonio Corona-Gomez1, Irving Jair Garcia-Lopez1, Peter F Stadler2,3,4,5,6,7

  • 1Unidad de Genómica Avanzada, Langebio, Cinvestav, 36821 Irapuato, Guanajuato, Mexico.

RNA (New York, N.Y.)
|April 4, 2020
PubMed
Summary

This study reveals that splicing conservation in plant long noncoding RNAs (lncRNAs) indicates evolutionary deep conservation. This finding provides a new method for identifying functional lncRNAs in plants.

Keywords:
conservationevolutionevolutionary plasticitylncRNAlong noncoding RNAsmultiple sequence alignmentssplice sites

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Long noncoding RNAs (lncRNAs) regulate gene expression and chromatin states in eukaryotes.
  • Plant lncRNAs are crucial for development but few are functionally characterized.
  • High sequence divergence in plant lncRNAs hinders conservation studies.

Purpose of the Study:

  • To characterize splicing conservation of lncRNAs in Brassicaceae.
  • To identify evolutionarily conserved lncRNAs in plants.
  • To establish a computational workflow for identifying functional plant lncRNAs.

Main Methods:

  • Generated whole-genome alignment of 16 Brassica species.
  • Identified synthenic lncRNA orthologs.
  • Measured splice site conservation using a scoring system trained on transcriptomes.

Main Results:

  • 17.9% of intergenic lncRNAs showed splicing conservation in at least one exon.
  • This estimate is higher than previously reported for lncRNA conservation in plants.
  • Splicing conservation suggests stabilizing selection, similar to vertebrates.

Conclusions:

  • Provided conclusive evidence for deeply conserved lncRNAs in plants.
  • Demonstrated splicing conservation as a marker for functional lncRNAs.
  • Described a generally applicable computational workflow for identifying functional plant lncRNAs.