# Epigenetic Profiling of Single Cells by In Situ Labeling for Studying Hematopoiesis

> **NIH NIH F31** · UNIVERSITY OF WASHINGTON · 2021 · $44,693

## Abstract

Epigenetic Profiling of Single Cells by In Situ Labeling for Studying Hematopoiesis
 Proper regulation of genome activity and architecture is critical for development, growth, and function of
a multicellular organism.1,2 Much of the regulation is believed to involve “epigenetic” modifications on DNA-
associated histone proteins,3–5 known as histone marks, which guide the compaction of nucleosomes into
higher order chromatin states that in turn regulate the expression of transcription factors that govern cell
differentiation and commitment.6,7 Because of limitations in assays used to measure these epigenetic states in
single cells, the roles of these histone marks in controlling chromatin structure and gene expression remain
poorly understood and vigorously debated. Thus, new methods are required for epigenetic profiling of cells. In
Aim 1, I propose to develop a new assay to interrogate the epigenetic state of single mammalian cells with the
capability to quantify the abundance of histone marks that inhabit multiple (≤20) distinct genomic loci in situ. In
Aim 2, I propose to apply this epigenetic profile assay to study hematopoietic stem cell (HSC) differentiation in
order to demonstrate the value of the developed epigenetic profiling method. Hematopoiesis is the formation of
blood cells including cells of the immune system which are critical for all animals including humans. In this
process, HSCs relinquish pluripotency to commit to unique fates and form blood cells by asynchronously
expressing a variety of transcription factors.3,18 Dysregulation at the epigenetic level of hematopoiesis is known
to cause blood diseases such as acute myeloid leukemia.19 Because of this, methods capable of detecting the
differentiated and epigenetic state of mammalian cells are important for the study of developing HSCs and the
progression of leukemic diseases. Using these epigenetic profiles together with transcriptomic (mRNA) profiles
that are already established,3 I will determine unique identities for each cell according to their epigenetic marks
and differentiated state. I will also identify which epigenetic marks and loci are important for cell fate decision
making. The ability to probe epigenetic states by measuring histone marks at many distinct genomic loci (e.g.,
for transcription factors and their enhancers, etc.) at the single-cell level will be broadly enabling to researchers
across a wide range of disciplines. In addition, the method will provide crucial information on the epigenetic
modifications present in HSCs.
Hypothesis: The epigenetic profile of a cell will reflect its differentiated state and will reveal strong
associations between histone marks and expression levels.
Aim 1: Develop a multiplexed assay to quantify the levels of five different histone marks present at
multiple (≤20) genomic loci.
Aim 2: Apply epigenetic profiling assay to the study of hematopoietic stem cell (HSC) differentiation.

## Key facts

- **NIH application ID:** 10242007
- **Project number:** 5F31HL142132-04
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** Marcus Woodworth
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $44,693
- **Award type:** 5
- **Project period:** 2018-09-16 → 2022-09-15

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10242007

## Citation

> US National Institutes of Health, RePORTER application 10242007, Epigenetic Profiling of Single Cells by In Situ Labeling for Studying Hematopoiesis (5F31HL142132-04). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10242007. Licensed CC0.

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