# Regulation and function of developmentally programmed 3 CpG island methylation

> **NIH NIH R21** · BAYLOR COLLEGE OF MEDICINE · 2020 · $215,700

## Abstract

PROJECT SUMMARY
Establishment and maintenance of epigenetic states that govern and stabilize cell fate upon differentiation are
crucial for the development of multicellular organisms. DNA methylation, which is mitotically heritable, is an
important component of mammalian epigenetic gene regulation. Over the past decade, the Human Epigenome
Projects have comprehensively profiled tissue- and cell-type-specific DNA methylation and identified dynamic
methylation differences. The timing of developmentally programmed DNA methylation and associated
mechanisms of transcriptional regulation during early cell-lineage specification, however, remain poorly
understood. This proposal builds upon our recent discovery that, in addition to canonical transcriptional
repression by DNA methylation at promoter CpG islands (CGIs), transcriptional activation of a group of
developmental genes is related to gene body CGI methylation during human embryonic stem cell (hESC)
differentiation. One particular gene of interest is Hypermethylated in cancer 1 (HIC1) gene, which is a tumor
suppressor and a candidate gene for a developmental disorder Miller-Dieker syndrome. We found that CGI
methylation at the 3' end of HIC1 (3' CGI methylation) is highly conserved in human and mouse, and may
specify mesenchymal Hic1-expressing during fetal development. More importantly, our preliminary studies
suggest that 3' CGI methylation regulates Hic1 transcription via a CCCTC-binding factor (CTCF)-dependent
mechanism. Based on these findings, the proposed research uses mouse models to investigate whether and
how the 3' CGI methylation controls the temporal and spatial expression of Hic1 in developing embryos.
Specifically, we will: 1  Investigate the mechanism by which 3' CGI methylation regulates Hic1 gene
activation. Using Hic1-citrine (a yellow fluorescent protein) reporter mice, we will perform chromatin
immunoprecipitation followed by quantitative PCR (ChIP-qPCR) to systemically map CTCF-bindings at the
Hic1 locus in tissues known to express Hic1 in mouse embryos. 2  Investigate the function of Hic1 3' CGI
methylation during mouse development. Using a novel mouse model to enable CRISPR-based targeted DNA
demethylation, we will determine whether Hic1 3' CGI demethylation affects transcriptional regulation of Hic1
from embryonic development into birth, and whether defective epigenetic regulation leads to developmental
defects. Altogether, this exploratory project will establish a combination of novel technologies for in vivo studies
to dissect epigenetic transcriptional regulation. The successful completion of these studies will yield important
insights into the function role of DNA methylation for mammalian development.

## Key facts

- **NIH application ID:** 9884427
- **Project number:** 1R21HD101035-01
- **Recipient organization:** BAYLOR COLLEGE OF MEDICINE
- **Principal Investigator:** Miaohsueh Chen
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $215,700
- **Award type:** 1
- **Project period:** 2019-12-01 → 2021-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9884427

## Citation

> US National Institutes of Health, RePORTER application 9884427, Regulation and function of developmentally programmed 3 CpG island methylation (1R21HD101035-01). Retrieved via AI Analytics 2026-06-11 from https://api.ai-analytics.org/grant/nih/9884427. Licensed CC0.

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