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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Programmable mutually exclusive alternative splicing for generating RNA and protein diversity.

Melina Mathur1, Cameron M Kim1, Sarah A Munro1,2,3,4

  • 1Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.

Nature Communications
|June 19, 2019
PubMed
Summary

Scientists developed a new synthetic biology platform to control alternative splicing, generating multiple proteins from a single gene. This advances programmable protein design and expands coding capacity in engineered systems.

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Area of Science:

  • Synthetic biology
  • Molecular biology
  • Genomics

Background:

  • Alternative splicing is crucial for proteomic diversity but underutilized in engineered systems.
  • Current synthetic approaches primarily control single protein expression via alternative splicing.

Purpose of the Study:

  • To create a modular platform for regulating multiple programmable exons undergoing mutually exclusive alternative splicing.
  • To generate functionally distinct proteins from a single genetic construct.

Main Methods:

  • Developed an intron framework to enforce mutual exclusivity of two internal exons.
  • Designed graded consensus sequence elements to control isoform ratios.
  • Applied the framework to program DNA-binding domains of transcription factors.

Main Results:

  • Successfully generated multiple, functionally distinct proteins through programmable mutually exclusive alternative splicing.
  • Demonstrated graded control over isoform ratios using engineered sequence elements.
  • Showcased differential control of downstream gene activation by programmed transcription factors.

Conclusions:

  • The developed splicing platform enables the generation of diverse protein isoforms.
  • This approach advances the programming of modular proteins in synthetic biology.
  • The platform has the potential to significantly increase the coding capacity of engineered biological systems.