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Related Concept Videos

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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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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A Reporter Based Cellular Assay for Monitoring Splicing Efficiency
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Cotranscriptional splicing efficiencies differ within genes and between cell types.

Karan Bedi1,2,3, Brian R Magnuson2,3, Ishwarya Narayanan1,3

  • 1Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA.

RNA (New York, N.Y.)
|May 12, 2021
PubMed
Summary
This summary is machine-generated.

Co-transcriptional splicing, where RNA polymerase II (RNAPII) processes pre-mRNA during transcription, is less efficient than previously thought in human cells. RNA-binding proteins (RBPs) appear to regulate this complex process in a cell-type and intron-specific manner.

Keywords:
RNA-binding proteinscell linescotranscriptionalspliceosomesplicing

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Pre-messenger RNA (mRNA) splicing by the spliceosome removes introns and ligates exons.
  • Splicing can occur concurrently with transcription, facilitated by interactions between spliceosome components and elongating RNA polymerase II (RNAPII).
  • The regulation and efficiency of co-transcriptional splicing in human cells remain poorly understood.

Purpose of the Study:

  • To investigate the efficiency of co-transcriptional splicing across numerous introns in human cells.
  • To explore cell-type specific variations in splicing efficiency.
  • To identify factors, including RNA-binding proteins (RBPs), that correlate with splicing efficiency.

Main Methods:

  • Utilized Bru-seq and BruChase-seq techniques to analyze co-transcriptional splicing efficiencies.
  • Examined over 17,000 introns across six distinct human cell lines.
  • Correlated RBP binding signals with observed splicing efficiencies.

Main Results:

  • Less than half of all analyzed introns were spliced co-transcriptionally.
  • Splicing efficiencies varied significantly between cell lines and within genes, indicating cell-type specific regulation.
  • Co-transcriptional splicing efficiency did not correlate with gene length, intron position, splice site strength, or GC content.
  • Binding signals of RBPs, including spliceosomal components (SF3B4, U2AF1, U2AF2) and others (BUD13, PUM1, SND1), correlated with splicing efficiency.

Conclusions:

  • Co-transcriptional splicing is not universally efficient in human cells and exhibits cell-type and intron-specific regulation.
  • RNA-binding proteins play a crucial role in determining splicing outcomes.
  • Nascent RNA splicing patterns contribute to the complexity of gene expression regulation.