# Regulation and impact of alternative splicing in biology and disease

> **NIH NIH R35** · UNIVERSITY OF CALIFORNIA-IRVINE · 2023 · $392,500

## Abstract

Pre-mRNA splicing is a fundamental process required for the expression of most metazoan genes. Defects in
splicing lead to human genetic disease, and splicing mutations in a number of genes involved in growth control
have been implicated in multiple types of cancer. Insights into the basic mechanisms of pre-mRNA splicing
and splice site recognition are therefore fundamental to understanding regulated gene expression and human
disease. The control of alternative splicing is a highly combinatorial process, where many inputs dictate the
splicing outcome for each exon. A critical feature of these regulatory mechanisms is the specific interaction of
trans-acting splicing factors with cis-acting RNA elements. We use a highly integrated approach to investigate
the molecular mechanisms that regulate pre-mRNA splicing. This includes knockout and knock-in tissue
culture models, reconstitution assays using radioligands, transcriptomics, bioinformatics, kinetics, structure-
function and biochemical techniques. In the next five years, we aim to address several outstanding challenges
in the field, pursuing the following novel research directions. (1) Our demonstration that splicing regulatory
proteins display highly position-dependent activities that negatively or positively influence splice site choice
changed the way we think about the classical splicing activators (SR proteins) and the classical splicing
repressors (hnRNPs). It is now appreciated that the context-dependent activation or repression of U1 snRNP
serves as a gateway to allow the abundant U1 snRNP to fulfill its splicing function and its role to protect the
pre-mRNA from premature degradation. However, it is not understood how splicing regulators achieve
activation or repression of U1snRNP at the 5’ splice site. We aim to dissect the mechanisms of splicing
repression by embracing multi-system approaches and by understanding the role of U1 snRNP conformers in
mediating spliceosomal assembly. (2) Intron retention is an important alternative splicing pathway that has
eluded extensive study. Thus, its regulation is not well-understood. The existence of inefficiently spliced
introns within coding exons (exitrons) further highlights the biological importance of understanding when
introns are removed efficiently and when they are not. We will decipher the rules of efficient intron removal
and investigate the impact of cis-acting elements in this process using synthetic biology approaches. The
argument is that the depth of the sequence variation tested in massively parallel reporter assays is far greater
than the testing landscape that the human genome offers. Here, we will take advantage of our expertise in
experimental molecular biology and bioinformatics. (3) It has become widely appreciated that gene expression
events are highly integrated, with evidence suggesting that most pre-mRNA processing occurs co-
transcriptionally. Defects in any one of these steps has been linked to disease. However, most ...

## Key facts

- **NIH application ID:** 10680397
- **Project number:** 5R35GM145254-02
- **Recipient organization:** UNIVERSITY OF CALIFORNIA-IRVINE
- **Principal Investigator:** Klemens J Hertel
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $392,500
- **Award type:** 5
- **Project period:** 2022-08-09 → 2027-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10680397

## Citation

> US National Institutes of Health, RePORTER application 10680397, Regulation and impact of alternative splicing in biology and disease (5R35GM145254-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10680397. Licensed CC0.

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