# Pre-mRNA intronic structures in trans factor binding and alternative splicing

> **NIH NIH R35** · CLEMSON UNIVERSITY · 2022 · $368,463

## Abstract

Project Summary
Splicing is the process of removing intronic regions from a precursor messenger RNA (mRNA) and combining
exons into a mature transcript. Alternative splicing results in differential intron removal, producing multiple
alternatively spliced isoforms arising from a common precursor mRNA. The dysregulation of splicing is estimated
to underlie at least 15% of human diseases, and is likely to contribute to many more. Splice reactions are
performed by the spliceosome, an RNA protein complex that is assembled onto precursor mRNA in stages. The
final activity of the spliceosome is influenced by a combination of trans-acting spliceosome factors and cis
elements within the precursor mRNA. However, factors involved in cis element function, like sequence motifs
and RNA structure folds, are not fully understood, and a majority of such elements remain unidentified. This is
particularly true for branchpoint selection, an essential early stage of spliceosome assembly within the intron
around the catalytic adenosine. Although the branchpoint is loosely recognized as a highly degenerate sequence
motif, it influences downstream splice site selection. My first goal is to elucidate the impact of RNA structure
on branchpoint selection by focusing on RNA structure-mediated binding by the spliceosome
associated SF3B complex. To do so, I will develop RNA secondary structure models for SF3B-dependent
precursor RNAs to identify enriched structural motifs. My work will entail the first large-scale derivation of intronic
secondary structures, including branchpoint regions, which will aid in better understanding of how RNA structures
around cis regulatory elements influence splicing. My second goal is to develop a system to identify cis
splicing regulatory elements and rapidly test their functional significance. To identify regulatory elements,
I will identify cis features on mRNAs, including protein binding sites, conservation and RNA secondary structure,
and use machine learning to discover novel signatures of functionally relevant cis regulatory regions. The
functional impact of such sites on alternative splicing will be experimentally tested through use of antisense
oligonucleotide (ASO) that can block or inhibit the regulatory region. I will set up a positive feedback loop where
I can predict cis splice regulatory elements and immediately test their impact on splicing with ASOs, incorporating
the test results back into the model to improve predictions. This system will lead to accurate prediction of cis
regulatory splicing elements within any gene of interest. Accurate identification of cis elements will improve our
ability to understand co-regulation of alternative splicing. The long-term vision of my research is to demystify
the splicing code by clarifying the role of RNA structure in splicing and developing a powerful system to identify
functional cis regulatory splicing elements and test their activity.

## Key facts

- **NIH application ID:** 10453785
- **Project number:** 5R35GM142851-02
- **Recipient organization:** CLEMSON UNIVERSITY
- **Principal Investigator:** Lela Lynn Lackey
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $368,463
- **Award type:** 5
- **Project period:** 2021-08-01 → 2026-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10453785

## Citation

> US National Institutes of Health, RePORTER application 10453785, Pre-mRNA intronic structures in trans factor binding and alternative splicing (5R35GM142851-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10453785. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*