# New Paradigms for the molecular basis of RNA polymerase I transcription

> **NIH NIH R01** · UPSTATE MEDICAL UNIVERSITY · 2024 · $122,450

## Abstract

Project Summary
Eukaryotic RNA polymerase I (Pol I) transcribes ribosomal RNA, a key component of ribosomes. Pol I transcription
accounts for the majority of the total RNA in cells, and its upregulation in human cells is a hallmark of cancer while
its downregulation is a hallmark of several developmental disorders. Pol I transcription is understudied compared
to transcription by Pol II and even Pol Ill. Our preliminary work suggests fundamental differences between Pol I
and Pols II and 111 that are the basis for this proposal. Our broad long-term objectives are to determine the molecular
mechanism of Pol I transcription and how its dysregulation leads to cancer and developmental disorders. There
are major gaps in our understanding of (1} the structural organization and architecture of Pol I transcription
complexes; (2) the mechanism for how Pol I initiation factors interact with rDNA, which encodes ribosomal RNA;
and (3) the molecular function of several key Pol I transcription factors in the activation process. The first rationale
for this work is that determining the mechanism and regulation of Pol I transcription will form the molecular basis
for understanding how Pol I defects lead to human disease. Our central hypothesis is that Pol I factors use a
unique mechanism to carry out transcription and their structure and function is different from the mechanisms
governing Pol II and Ill transcription. The second rationale is that understanding the Pol I transcription mechanism
at the most basic and fundamental levels will translate to a better understanding of the connection between Pol I
and cancer, leading to new cancer therapeutic strategies. Our proposed research will use a conceptually and
technically innovative cross-organismal and interdisciplinary approach that employs a combination of bioinformatic,
computational, molecular, biochemical, genetic, genomic, proteomic, and structural methods in the yeast and
human cells. Guided by strong preliminary studies, we will test two specific aims: (1) Determine the unique
"coactivator" role of TAT A-binding protein (TSP) in Pol I transcription, and (2) Determine the mechanism of Pol I
transcription activation. To accomplish these aims, we will use well-established and complementary approaches
to identify and map novel Pol I interactions in their native context. We will complement these studies with structural
modeling in combination with molecular, genetic, and biochemical functional assays to identify Pol I factor functions
conserved from yeast to humans. The proposed research is significant because it will lead to a detailed description
of the Pol I transcription mechanism and will provide a conceptual framework for understanding the link between
Pol I and human disease. Ultimately, this work will illuminate new avenues for diagnosis, potential interventions,
and the development of therapies targeting these novel protein-protein and protein-DNA interactions.

## Key facts

- **NIH application ID:** 11035882
- **Project number:** 3R01GM141033-04S1
- **Recipient organization:** UPSTATE MEDICAL UNIVERSITY
- **Principal Investigator:** Bruce Alan Knutson
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $122,450
- **Award type:** 3
- **Project period:** 2021-03-05 → 2026-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11035882

## Citation

> US National Institutes of Health, RePORTER application 11035882, New Paradigms for the molecular basis of RNA polymerase I transcription (3R01GM141033-04S1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/11035882. Licensed CC0.

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