# A Chemical Footprinting Approach towards Poly-ADP-Ribosylation-regulated Biomolecular Condensation

> **NIH NIH R01** · COLUMBIA UNIVERSITY HEALTH SCIENCES · 2022 · $322,321

## Abstract

Project Summary
Poly-ADP-ribosylation (PARylation) is a protein posttranslational modification (PTM) that is catalyzed by a
family of enzymes called Poly-ADP-ribose polymerases (PARPs). Among the various PARP enzymes, PARP1
is a nuclear protein that is critically involved in cell stress responses. The PARylation level in a quiescent cell is
usually very low. In response to genotoxic stress, PARP1 binds to nicked DNA and is rapidly activated,
resulting in the synthesis of a large number of PARylated proteins and initiation of the DNA damage repair
(DDR) mechanisms. Indeed, four PARP1 inhibitors have recently been approved by the FDA to treat BRCA-
mutated ovarian and/or breast cancers. Besides the role in regulating DDR in the context of human
malignancies, recent evidence suggests that PARylation serves as a death signal in neurons. Importantly,
genetic deletion or pharmacological inhibition of PARP1 offers profound protection against brain dysfunction in
the animal models of many neurological disorders (e.g., Parkinson’s disease, amyotrophic lateral sclerosis,
traumatic brain injury and cerebellar ataxia). PARP1 is directly activated by a variety of neurotoxic stimulants,
and aberrant PARylation promotes the formation of biomolecular condensates. Despite the established role of
PARylation in the regulation of phase-transition, the structural aspects of this process are elusive. To address
this, we will leverage our published work and the extensive experience of my lab. These preliminary data are
largely focused on two different programs. First, PARylation is a notorious PTM for mass spectrometrists,
because of its labile and heterogenous nature. We recently were able to overcome these challenges, and
develope a large-scale mass spectrometric approach towards comprehensive characterization of the Asp- and
Glu-PARylated proteome. Using this approach, we have defined the global PARylated proteome under various
genotoxic conditions. Second, biomolecular condensates are a class of membrane-less organelles, whose
structural dynamics are less amenable to traditional biophysical tools. To address this, we previously
developed a mass spectrometry-based chemical “footprinting” method for the structural analysis of these
protein fibrils. Based on these results, we will develop a novel, tunable footprinting approach for the
characterization of the structural dynamics of biomolecular condensates (Aim 1). Then we will use tunable
footprinting to study how PARylation regulates phase-transition in vitro (Aim 2) and in intact nuclei (Aim 3). The
information garnered from these studies will provide a fundamental understanding of this critical biological
process, paving the way for targeting PARP1 for the treatment of neurological disorders.

## Key facts

- **NIH application ID:** 10610165
- **Project number:** 7R01NS122533-02
- **Recipient organization:** COLUMBIA UNIVERSITY HEALTH SCIENCES
- **Principal Investigator:** Yonghao Yu
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $322,321
- **Award type:** 7
- **Project period:** 2022-09-01 → 2026-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10610165

## Citation

> US National Institutes of Health, RePORTER application 10610165, A Chemical Footprinting Approach towards Poly-ADP-Ribosylation-regulated Biomolecular Condensation (7R01NS122533-02). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10610165. Licensed CC0.

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