# Nanopore based profiling of epigenetic state

> **NIH NIH R01** · JOHNS HOPKINS UNIVERSITY · 2022 · $634,009

## Abstract

Project Summary:
Though a reference human genome and even excellent characterization of the epigenome (ENCODE, Epigenetics
Roadmap, 4D Nucleome Project) has been generated, we still lack a clear understanding of how the different
facets of the epigenome collaborate to control gene expression. With the advent of affordable DNA-sequencing
technologies, methods have been developed for examining nuclear organization, protein-DNA interaction,
chromatin accessibility, and methylation state. But these methods generally interrogate only one aspect of the
epigenome at a time and reads are typically too short to provide critical correlative information. We propose the
development of a novel epigenetic characterization methodology, in this round of funding focusing on protein-
DNA interaction through leveraging the long reads and modified bases detectable with a nanopore sequencing
platform. We will enhance the signal from subtle modifications being used to profile protein-DNA interactions.
We are developing a method to insert sequence tags (nanoTUBI) near the sites of protein-DNA binding. And we
will implement these methods focusing on long read sequencing, gaining insights into long correlative
measurements and heretofore unexplored repetitive areas, phasing the entire epigenome. These tools and
analysis pipelines will grant new insights into mechanisms of gene regulation, as well as their implications for
human disease.

## Key facts

- **NIH application ID:** 10460357
- **Project number:** 5R01HG009190-06
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** Winston George Timp
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $634,009
- **Award type:** 5
- **Project period:** 2021-08-01 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10460357

## Citation

> US National Institutes of Health, RePORTER application 10460357, Nanopore based profiling of epigenetic state (5R01HG009190-06). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10460357. Licensed CC0.

---

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