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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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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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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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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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Spliceman2: a computational web server that predicts defects in pre-mRNA splicing.

Kamil Jan Cygan1,2, Clayton Hendrick Sanford3, William Guy Fairbrother1,2,4

  • 1Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02903, USA.

Bioinformatics (Oxford, England)
|September 16, 2017
PubMed
Summary
This summary is machine-generated.

Spliceman2 is an improved tool that predicts how mutations affect pre-messenger RNA (mRNA) splicing. It now handles larger datasets and visualizes variant effects, aiding in understanding genetic disease.

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Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Splicing is crucial for eukaryotic gene expression, removing introns and joining exons.
  • Splicing elements are mutation hotspots, leading to various genetic diseases.
  • Previous tool Spliceman (2012) predicted mutation effects on splicing based on positional dependence.

Purpose of the Study:

  • To present an improved version of the Spliceman tool, Spliceman2.
  • To enhance the prediction of splicing mutation likelihood and impact.
  • To provide better tools for scientists and physicians to understand single nucleotide variations' effects on splicing.

Main Methods:

  • Incorporation of industry-standard input options, including Variant Call Format (VCF) files for larger datasets.
  • Development of visualization features to display variant locations within exons and introns.
  • Integration with RNAcompete motif libraries for predicting disruption/creation of trans-acting factor binding sites.

Main Results:

  • Spliceman2 accepts larger input files than its predecessor.
  • The tool visualizes variant locations and predicted splicing effects.
  • Integration with RNAcompete provides insights into disrupted/created trans-acting factor binding sites.

Conclusions:

  • Spliceman2 offers enhanced capabilities for predicting splicing mutation likelihood.
  • New features facilitate a deeper understanding of how sequence variants impact pre-mRNA splicing.
  • The tool aids scientists and physicians in interpreting the functional consequences of genetic variations on splicing.