# Epigenetic Control of Hematopoietic Gene Expression

> **NIH NIH R01** · CHILDREN'S HOSP OF PHILADELPHIA · 2022 · $496,041

## Abstract

Abstract
Numerous fundamental principles of gene regulation and epigenetics have been unraveled using erythroid
cells as a model system. This application will exploit our expertise in erythroid development and chromatin
architecture to dissect the diverse activities of CTCF, a central multi-functional transcription factor.
CTCF can activate or repress transcription, slow elongation by RNA polymerase 2, form long range
chromosomal contacts, block enhancer activity, and form chromatin domain boundaries. CTCF bound sites
(CBS) can be tissue-specific or tissue-invariant. A leading question in the field is how does CTCF exert these
distinct activities. Other key open questions are how lineage-dependent functions and chromatin binding by
CTCF are specified. Utilizing an auxin-inducible CTCF degradation system in an erythroid cell line we found
that, unexpectedly, CBS are turned over with highly variable kinetics. This leads to the hypothesis that location-
specific differences in susceptibility to degradation may be a reflection of CTCF chromatin residence time that
is locally specified by chromatin context. We further hypothesize that such differences in residence times are
critical features of distinct CTCF mechanisms of action. In Specific Aim 1 we will first determine erythroid- and
maturation stage-specific CBS genome wide, globally assess auxin-modulated CBS dynamics in both
immature and mature erythroid cells, and examine consequences of acute CTCF depletion on gene
expression. The determinants of CBS specificity and dynamics will be dissected via genome editing and
targeted proteomics (ChIP-SICAP). In Specific Aim 2, we will test the hypothesis that CBS dynamics are a
function of chromatin residence time. This will be measured by single molecule tracking (SMT) of CTCF, to be
carried out in collaboration with Dr. Melike Lakadamyali at UPenn. These studies will include perturbative
manipulations of CTCF.
By combining acute CTCF degradation with PRO-seq we discovered that many genes with CBS near the start
site exhibit increased transcription in the anti-sense direction upon CTCF loss. This suggests a novel role of
CTCF in governing transcription directionality. In Specific Aim 3 we will determine the mechanism by which
CTCF regulates transcription directionality, exploring chromatin looping versus functioning as an elongation
barrier as possible alternative mechanisms. Single molecule RNA FISH will be employed to study the
dynamics and mechanisms of transcription directionality.
These studies address longstanding questions as to how CTCF accomplishes its diverse functions, including
new ones discovered here, and are expected to have broad ramifications for the fields of gene regulation and
nuclear architecture.

## Key facts

- **NIH application ID:** 10393003
- **Project number:** 5R01DK058044-21
- **Recipient organization:** CHILDREN'S HOSP OF PHILADELPHIA
- **Principal Investigator:** Gerd A Blobel
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $496,041
- **Award type:** 5
- **Project period:** 2002-03-01 → 2024-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10393003

## Citation

> US National Institutes of Health, RePORTER application 10393003, Epigenetic Control of Hematopoietic Gene Expression (5R01DK058044-21). Retrieved via AI Analytics 2026-06-10 from https://api.ai-analytics.org/grant/nih/10393003. Licensed CC0.

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