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RNA Splicing01:32

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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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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Evaluation of Exon Inclusion Induced by Splice Switching Antisense Oligonucleotides in SMA Patient Fibroblasts
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Short cryptic exons mediate recursive splicing in Drosophila.

Brian Joseph1,2, Shu Kondo3, Eric C Lai4

  • 1Department of Developmental Biology, Sloan-Kettering Institute, New York, NY, USA.

Nature Structural & Molecular Biology
|April 11, 2018
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Summary
This summary is machine-generated.

Researchers investigated recursive splicing in Drosophila, revealing that unannotated cryptic splice donor sites are essential for recognizing intronic ratchet points (RPs). This mechanism, involving cryptic RP exons, is conserved and unified across species.

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Area of Science:

  • Molecular Biology
  • Genetics
  • RNA Splicing

Background:

  • Long introns in Drosophila are processed via an unusual recursive splicing strategy.
  • Ratchet points (RPs), adjacent splice sites, were hypothesized as 'zero-nucleotide exons' for intron removal.

Purpose of the Study:

  • To elucidate the mechanism of recursive splicing in Drosophila.
  • To investigate the role of intronic ratchet points (RPs) in intron processing.

Main Methods:

  • CRISPR-Cas9 gene editing to disrupt intronic RPs in Drosophila melanogaster.
  • Functional minigene assays to validate splice site recognition.
  • Bioinformatic analysis of splice donor site enrichment.

Main Results:

  • Disruption of RPs caused loss-of-function phenotypes.
  • Selective disruption of RP splice donors led to constitutive retention of unannotated exons.
  • Cryptic splice donor sites are critical for recognizing intronic RPs, defining them as cryptic RP exons.
  • Conserved splice donors are enriched downstream of RPs, suggesting a general mechanism.

Conclusions:

  • Recursive splicing in Drosophila involves the recognition of cryptic RP exons.
  • This mechanism is conserved and broadly applicable, unifying Drosophila and mammalian splicing.
  • Unannotated cryptic splice sites play a crucial role in complex intron processing.