# Experimental and bioinformatics platform for epigenome analysis using nanopore sequencing

> **NIH NIH R01** · OHIO STATE UNIVERSITY · 2022 · $417,483

## Abstract

PROJECT SUMMARY / ABSTRACT
The epigenetic status of genomes including nucleosome occupancy, chromatin accessibility and DNA methylation,
is highly relevant to the regulation of DNA-template biological processes from transcription to DNA replication and
repair. Most existing techniques for characterizing epigenome utilize Next Generation Sequencing (NGS)
following the biochemical reactions that capture the signals (e.g., bisulfite conversion, cross-linking and
chromatin immunoprecipitation/ChIP). The development of these techniques has dramatically accelerated the
research of different epigenetics events and has led to many important biological findings. As the new
technique nanopore sequencing has been optimized to convey robust sequencing data of single DNA
molecules with long read length, it brings in new discernible information that is useful for addressing certain
challenging but important epigenetics problems. We develop an experimental protocol MeSMLR-seq and a
series of bioinformatics methods to define the multiple types of epigenetic events, including nucleosome
occupancy, chromatin accessibility and DNA methylation, at the rarely explored genome regions and biological
context by leveraging the unique information of nanopore sequencing. Utilizing these experimental and
bioinformatics methods, we aim to interrogate the following problems during the epigenetic reprogramming of
early embryonic development and primordial germ cell development: in Aim 1, we will study the epigenetic
regulation of transposable element expression and transposition. Aim 2 will construct the allele-specific
epigenome and identify the genome loci with significant epigenome difference between alleles. Aim 3 will
identify significant difference of the epigenomes between DNA strands and investigate their regulatory roles
and dynamics during epigenetic reprogramming. These studies are anticipated to provide the first experimental
and bioinformatics platform for improve our understanding of epigenome with complex biomedical context in a
comprehensive manner.

## Key facts

- **NIH application ID:** 10495371
- **Project number:** 5R01GM136886-02
- **Recipient organization:** OHIO STATE UNIVERSITY
- **Principal Investigator:** Kin Fai Au
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $417,483
- **Award type:** 5
- **Project period:** 2021-09-27 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10495371

## Citation

> US National Institutes of Health, RePORTER application 10495371, Experimental and bioinformatics platform for epigenome analysis using nanopore sequencing (5R01GM136886-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10495371. Licensed CC0.

---

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