Date of Award

2021

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Neuroscience

First Advisor

Marisa S. Bartolomei

Abstract

DNA is organized into spatially distinct units by architectural protein CTCF to enrich for intradomain enhancer-promoter contacts, but developmental and tissue specific regulation of architecture in vivo is poorly defined. By profiling neonatal mouse tissues at the imprinted Grb10-Ddc locus, putative tissue- and allele-specific chromatin was revealed, which we interrogated by deletions in vivo. We uncovered a new tissue-specific intronic insulator at Grb10 that is distinct from the classic differentially methylated imprinting control region, acquiring its own allele-specific DNA methylation during development, ultimately regulating gene expression of the entire cluster in heart and muscle. Termed CTCF-Binding Region 2.3 (CBR2.3), this insulator assembles a paternal-specific contact domain with Ddc located 150 kb away, restricting a newly validated cardiac enhancer to the paternal Ddc promoter. Paternal deletion of CBR2.3 in mice reconfigures the chromatin topology to mimic the maternal chromosome, resulting in Grb10-Ddc misexpression and cardiac phenotypes. This in vivo validation of a robust allelic and tissue-specific insulator offers mechanistic insight into how genes utilize different layers of spatial organization to achieve variation in gene expression in development.

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Additional Files

Supp.Table 3.xlsx (5567 kB)
Supp.Table 4.xlsx (17 kB)

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