Tissue-specific Grb10/Ddc insulator drives allelic architecture for cardiac development

Area of Science:

• Genetics
• Epigenetics
• Molecular Biology

Background:

• Imprinted gene expression relies on DNA methylation at imprinting control regions (ICRs).
• Secondary differentially methylated regions (DMRs) reinforce but do not control imprinting across entire gene clusters.
• The precise mechanisms governing tissue-specific imprinting of unlinked genes remain incompletely understood.

Purpose of the Study:

• To investigate the regulatory elements controlling tissue-specific imprinting of the Grb10 and Ddc genes.
• To identify and characterize novel DMRs involved in the imprinting of these genes.
• To elucidate the function of identified regulatory elements in gene expression and chromatin architecture.

Main Methods:

• Utilized polymorphic mice to map regulatory regions.
• Identified an intronic secondary DMR (CBR2.3) with paternal-specific CTCF binding at the Grb10 gene.
• Performed deletion of paternal CBR2.3 to assess its impact on chromatin looping and gene expression.

Main Results:

• Discovered an unconventional intronic secondary DMR (CBR2.3) at Grb10 that interacts with Ddc.
• Deletion of paternal CBR2.3 disrupted chromatin looping and led to ectopic enhancer-promoter contacts.
• Observed altered Grb10-Ddc expression patterns with developmental defects in heart and muscle tissues.

Conclusions:

• Uncovered a novel intronic secondary DMR functioning as an insulator for the Grb10-Ddc imprinting domain.
• This DMR is essential for tissue-specific, monoallelic expression of multiple genes, a role previously attributed exclusively to ICRs.
• Redefined the Grb10-Ddc imprinting domain, revealing a new layer of epigenetic regulation.