# Molecular Mechanisms Coupling Transcription and Splicing

> **NIH NIH F32** · YALE UNIVERSITY · 2021 · $17,141

## Abstract

PROJECT SUMMARY
Precursor messenger RNA (pre-mRNA) processing is an essential aspect of gene expression that occurs
concurrently with transcription by RNA polymerase II. One essential step in pre-mRNA processing is the removal
of non-coding introns and ligation of coding exons together (pre-mRNA splicing) by the spliceosome. The
spliceosome assembles on the nascent RNA during transcription, and splicing is completed soon after the intron
has been transcribed. Thus, the splicing and transcription machineries are spatially and temporally coupled –
working in concert to ensure timely and accurate expression of cellular mRNAs. Mutations or perturbations of
either process change gene output and are frequently associated with human disease. Remarkably, the
mechanisms coordinating splicing with transcription are poorly understood. The proposed work combines
established techniques and novel approaches to elucidate how the two cellular processes regulate one another.
The Neugebauer lab recently developed single-molecule intron tracking (SMIT) and other RNAseq-based
approaches to measure the in vivo kinetics of splicing relative to transcription. Specific Aim 1 investigates the
contribution of intron sequence and other RNA features to the splicing reaction and determines how co-
transcriptional splicing can influence gene output. Specific Aim 2 combines SMIT and other RNAseq-based
approaches with Pol II mutant backgrounds to reveal the impact of the C-terminal domain and post-translational
modifications of RNA polymerase II on splicing. In particular, this aim asks how the CTD contributes to the
efficient splicing of multiple introns in a single transcript. These experiments will generate new mechanistic
insights into how RNA polymerase interacts with the spliceosome to promote efficient RNA splicing. Specific
Aim 3 investigates the influence of the splicing machinery on transcriptional dynamics and polymerase pausing
using potent splicing inhibitors and genetic tools that cause the spliceosome to remain associated with the
nascent transcript. These approaches and aims will provide an entry point for developing expertise in
transcription, bioinformatics, RNA-seq based methods and other computational approaches. In addition, the
proposed work will generate unprecedented molecular insight into the cross-talk between essential processes
in gene expression and provide fundamental knowledge that will be vital in future studies on how splicing and
transcription are altered in disease.

## Key facts

- **NIH application ID:** 10369291
- **Project number:** 3F32GM134572-01A1S1
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** Tucker Joe Carrocci
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $17,141
- **Award type:** 3
- **Project period:** 2020-04-01 → 2021-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10369291

## Citation

> US National Institutes of Health, RePORTER application 10369291, Molecular Mechanisms Coupling Transcription and Splicing (3F32GM134572-01A1S1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10369291. Licensed CC0.

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