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Characterization of cis-acting elements that control oscillating alternative splicing.

Gesine Goldammer1, Alexander Neumann1, Miriam Strauch1

  • 1a Laboratory of RNA Biochemistry , Freie Universität Berlin, Institute of Chemistry and Biochemistry , Berlin , Germany.

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|September 12, 2018
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Summary

Daily rhythms in alternative splicing (AS) are controlled by specific RNA elements. This study identifies cis-regulatory sequences and SR proteins that govern body-temperature driven rhythmic AS in the mouse U2af26 gene.

Keywords:
Alternative splicingSR proteinsbody temperature cyclecircadian clockiCLIPminigenephosphorylationsplicing network

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Area of Science:

  • Molecular Biology
  • Genetics
  • RNA Biology

Background:

  • Alternative splicing (AS) is crucial for adapting gene expression to environmental changes.
  • Daily oscillations in AS are observed, but the underlying cis-regulatory sequences remain poorly understood.
  • Understanding these regulatory elements is key to deciphering temporal gene expression control.

Purpose of the Study:

  • To identify and characterize cis-regulatory RNA elements controlling body-temperature driven rhythmic AS.
  • To elucidate the role of specific RNA-binding proteins, particularly SR proteins, in this process.
  • To define the sequence requirements for generating daily rhythms in AS.

Main Methods:

  • Utilized the mouse U2af26 gene as a model system.
  • Employed minigene assays to study cis-regulatory element function.
  • Integrated RNA-sequencing (RNA-Seq), siRNA screening, and individual-nucleotide resolution cross-linking and immunoprecipitation (iCLIP).

Main Results:

  • Identified a network of cis-regulatory sequences essential for rhythmic AS of U2af26.
  • Demonstrated that two enhancer elements are necessary for oscillating AS.
  • Pinpointed a single nucleotide enhancer element in exon 6 crucial for SRSF2 binding and SRSF7 cooperation.
  • Revealed a global role for SR proteins in temperature-dependent rhythmic AS, with sequence element position dictating splicing direction.

Conclusions:

  • Defined specific cis-acting RNA elements and SR proteins that regulate daily rhythms in alternative splicing.
  • Established a link between body temperature, SR protein phosphorylation, and rhythmic AS.
  • Provided insights into the sequence-specific interactions governing temporal gene regulation through AS.