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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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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.

Yan Song1, Olga B Botvinnik2, Michael T Lovci3

  • 1Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.

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|July 5, 2017
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Summary

Alternative splicing (AS) creates diverse cell isoforms. A new computational framework, Expedition, reveals that up to 20% of AS exons are bimodal, offering new insights into cell states.

Keywords:
RNA processingalternative splicingbimodalitydifferentiationmodalityneuronpost-transcriptionsingle cellstem cells

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Area of Science:

  • Molecular Biology
  • Genomics
  • Computational Biology

Background:

  • Alternative splicing (AS) generates significant protein diversity from a limited number of genes.
  • Understanding the biological and evolutionary significance of AS variation at the single-cell level remains challenging.

Purpose of the Study:

  • To develop a computational framework (Expedition) for detecting and analyzing alternative splicing patterns in single cells.
  • To investigate the prevalence and characteristics of AS variation during cellular differentiation.

Main Methods:

  • Expedition framework: outrigger (splice graph transversal), anchor (Bayesian modality assignment), bonvoyage (non-negative matrix factorization visualization).
  • Application to single pluripotent stem cells during neuronal differentiation.

Main Results:

  • Identified that up to 20% of alternative splicing (AS) exons exhibit bimodality in single cells.
  • Bimodal exons are associated with conserved intronic sequences, distinct cis-regulatory motifs, and cell-type-specific splicing.
  • Observed high dynamism of bimodal exons during cellular transitions, preserving reading frames.

Conclusions:

  • Expedition provides a novel approach to characterize AS complexity in single cells.
  • Bimodal AS reveals intricate cell states not apparent through conventional gene expression analysis.
  • Systematic single-cell AS analysis redefines the understanding of AS complexity in cell biology and evolution.