# Locus-specific Imaging of Dynamic Histone Methylations during Reprogramming

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2020 · $585,407

## Abstract

Locus-specific Imaging of Dynamic Histone Methylations during Reprogramming
Reprogramming fibroblasts into induced pluripotent stem cells (iPSCs) represents a revolutionary advancement
in the understanding of how specific gene regulations can guide the life of a cell. Epigenetic modifications
including chromatin remodeling are early events during the reprogramming process. Histone methylation at
different residues can recruit differential sets of chromatin remodeling complexes to regulate chromatin
structures and silence/activate gene expressions accordingly. These histone methylations and their
combinations at different genomic loci can serve as codes to determine the overall gene expression profile and
phenotypic outcomes. However, it is still not understood how histone methylations at specific loci are dynamically
regulated during the reprogramming processes in which cells undergo a highly heterogeneous modulation at
single cell levels. In this proposal, we will harness the power of directed evolution and high-throughput screening
method to systematically develop specific/sensitive FRET (fluorescence resonance energy transfer) biosensors
for the monitoring of crucial histone methylations in single cells. We will further develop biosensors with distinct
and orthogonal FRET pairs that can simultaneously monitor two different histone methylations in a single live
cell for the production of high-resolution images of multiplex epigenetic landscapes. These multiplex histone
methylations obtained from individual cells during reprogramming will then be analyzed and integrated together
to construct the dynamic histone methylation landscapes. These epigenetic modulations will also be visualized
at specific loci to assign the corresponding genomic addresses on the evolving landscape of histone
methylations. Established fluorescence markers of cell fate will further be applied to determine how histone
methylation codes are coordinated for the regulation of reprogramming. As such, the success of the project
should have transformative impact in the field of epigenetics and genetics at single cell levels, particularly related
to stem cell reprogramming. Three specific aims are accordingly proposed: Aim 1. Develop high-throughput
screening methods for the engineering of FRET biosensors to monitor various histone methylations; Aim 2.
Engineer FRET biosensors with distinct colors to monitor the evolving multiplex landscape of histone
methylations during reprogramming; Aim 3. Unravel the evolving histone methylation landscapes at specific loci
during reprogramming. While the focus of this proposal is to develop tools targeting histone methylations at
specific loci and reprogramming outcomes, the strategies and approaches can be extended to monitor, in
principle, any epigenetic modification in single cells, including but not limited to histone acetylation and
phosphorylation. The developed biosensors for single cell imaging of epigenetic landscape evolution shoul...

## Key facts

- **NIH application ID:** 9922921
- **Project number:** 5R01GM125379-04
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** SHU CHIEN
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $585,407
- **Award type:** 5
- **Project period:** 2017-08-03 → 2021-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9922921

## Citation

> US National Institutes of Health, RePORTER application 9922921, Locus-specific Imaging of Dynamic Histone Methylations during Reprogramming (5R01GM125379-04). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/9922921. Licensed CC0.

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