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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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The human branchpoint-interacting stem loop sequence and structure regulates U2 snRNA expression, branchpoint

Meredith B Stevers1, Sol Katzman2, Melissa S Jurica1,3

  • 1Molecular, Cell & Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.

Biorxiv : the Preprint Server for Biology
|September 5, 2025
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Summary
This summary is machine-generated.

The branchpoint interacting stem loop (BSL) in U2 snRNA impacts spliceosome assembly. Altering BSL structure affects splicing and gene expression, potentially activating cancer pathways.

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Gene Expression

Background:

  • Spliceosome assembly initiates with U2 small nuclear ribonucleoprotein (snRNP) engaging introns, forming a branch helix.
  • Branch helix formation is mutually exclusive with the branchpoint interacting stem loop (BSL) in U2 snRNA.
  • The role of BSL structure in human intron splicing remains unclear due to flexible branchpoint sequences.

Purpose of the Study:

  • To investigate the influence of BSL structure on U2 snRNP biogenesis and splicing efficiency in human introns.
  • To examine the effects of perturbing BSL base-pairing on splicing and gene expression.
  • To analyze transcriptome-wide changes upon expression of U2 snRNA with altered BSL sequences.

Main Methods:

  • Utilized an orthogonal U2 snRNA and splicing reporter system to study BSL perturbations.
  • Assessed the impact of altered BSL base-pairing on U2 snRNA expression and reporter splicing.
  • Performed transcriptome-wide analysis to identify gene expression changes.

Main Results:

  • Changes in BSL base-pairing differentially affected U2 snRNA expression and splicing efficiency.
  • High complementarity between branchpoint sequences and U2 snRNA enhanced splicing with wild-type and stabilized BSL.
  • Altering BSL or branchpoint recognition sequences led to similar splicing and gene expression changes, including upregulation of oncogenic pathways.

Conclusions:

  • BSL structure influences U2 snRNP biogenesis, with introns driving BSL stem unwinding after initial base pairing.
  • Altered U2 snRNA variants are tolerated by cells, but their presence triggers a response involving upregulation of cancer-associated genes.
  • These findings highlight the intricate regulation of splicing by U2 snRNA structure and its implications for cellular response and disease pathways.