# Understanding CTCF boundaries controlling Hox gene expression

> **NIH NIH R01** · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · 2021 · $467,966

## Abstract

Understanding CTCF boundaries controlling Hox gene expression
Summary
Spatial and temporal control of gene expression is crucial for the development of multicellular
organisms. Although changes in looping interactions between enhancers and transcription start
sites is an acknowledged mode of gene regulation, the contribution of larger 3D genomic
reorganizations to gene expression and normal development is largely obscure. We propose
experiments to clarify how the CTCF transcription factor controls chromatin structure at the Hox
clusters to ensure proper Hox gene expression and thus, body patterning.
During embryonic development, precise expression of Hox genes instructs cells to recognize
their relative position in body axes. Hox genes are organized in four clusters with individual
genes in these clusters expressed in patterns that are spatially and temporally collinear with
their physical chromosomal organization. Collinear Hox gene expression along the spinal cord
controls motor neuron (MN) subtypes and thus their connectivity. During MN differentiation, the
Hox clusters undergo a chromatin and 3-D reorganization from a single repressed state to two
domains harboring either transcribed or repressed genes. The two chromatin states are
insulated by CTCF binding at the boundary, maintaining stable Hox chromatin states inherited
though development to ensure proper MN connectivity. Of relevance, we recently demonstrated
that the CTCF boundary is essential to normal body patterning during embryonic development
in vivo. To understand how CTCF maintains insulated chromatin and 3-D boundaries at Hox
clusters we propose: 1) To understand how disrupting the CTCF-mediated chromatin boundary
affects subtype identity of spinal MNs; 2) To determine the molecular basis of establishing a
CTCF-dependent boundary; 3) An advanced proteomics study to identify factors required by
chromatin associated CTCF for its insulator activity, emphasizing those whose interaction is
RNA-dependent.

## Key facts

- **NIH application ID:** 10116495
- **Project number:** 5R01NS100897-04
- **Recipient organization:** NEW YORK UNIVERSITY SCHOOL OF MEDICINE
- **Principal Investigator:** Esteban Orlando Mazzoni
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $467,966
- **Award type:** 5
- **Project period:** 2018-03-15 → 2023-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10116495

## Citation

> US National Institutes of Health, RePORTER application 10116495, Understanding CTCF boundaries controlling Hox gene expression (5R01NS100897-04). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10116495. Licensed CC0.

---

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