Tissue- and expression level-specific chromatin looping at maize b1 epialleles.

Area of Science:

• Plant genetics
• Epigenetics
• Molecular biology

Background:

• The maize b1 gene exhibits paramutation, a heritable change in gene expression.
• Two epialleles, B-I and B', show distinct tissue-specific regulation and expression levels.
• A distant hepta-repeat element is crucial for paramutation and high b1 expression.

Purpose of the Study:

• To investigate the role of chromatin looping in the transcriptional regulation of maize b1 epialleles.
• To determine how the hepta-repeat interacts with the b1 gene's transcription start site (TSS).
• To identify other regulatory elements involved in epiallele-specific expression.

Main Methods:

• Chromosome conformation capture (3C) to analyze physical interactions between DNA regions.
• Formaldehyde-assisted isolation of regulatory elements (FAIRE) to identify active regulatory regions.

Main Results:

• The hepta-repeat physically interacts with the b1 gene's TSS in a tissue- and expression-dependent manner.
• Multiple repeats are necessary for stabilizing this chromatin interaction.
• High b1 expression involves a complex multiloop structure with multiple interacting DNA regions.
• FAIRE identified additional potentially regulatory interacting regions.

Conclusions:

• Chromatin looping, mediated by specific DNA interactions, is essential for regulating maize b1 epiallele expression and paramutation.
• The formation of a multiloop structure involving the hepta-repeat and other elements drives high b1 expression.
• These findings reveal a novel mechanism of epigenetic gene regulation in plants.