Modular insulators: genome wide search for composite CTCF/thyroid hormone receptor binding sites

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• The CTCF protein is crucial for transcriptional regulation, including enhancer blocking.
• Previous work identified composite CTCF and thyroid hormone receptor (TR) binding sites in specific genes.
• Thyroid hormone can relieve enhancer blocking mediated by CTCF.

Purpose of the Study:

• To investigate the prevalence of composite CTCF and TR binding sites across the genome.
• To determine the functional role of these sites in regulating enhancer blocking.
• To elucidate the mechanism by which thyroid hormone influences enhancer blocking at these sites.

Main Methods:

• Genome-wide analysis to identify CTCF and TR binding site co-occurrence.
• Functional assays using episomal constructs to study enhancer blocking.
• Investigation of poly(ADP-ribose) modification and histone deacetylation.
• Analysis of TR binding dependency for CTCF function.

Main Results:

• Approximately 18% of CTCF regions contain TR binding motifs, suggesting a common genomic feature.
• Episomal constructs confirmed CTCF-mediated enhancer blocking is dependent on poly(ADP-ribose) modification and histone deacetylation.
• Thyroid hormone-sensitive enhancer blocking was observed in a novel composite element.
• Basal enhancer blocking by CTCF requires unliganded TR binding.

Conclusions:

• Composite CTCF/TR binding sites are a significant feature of the genome and play a role in regulating enhancer blocking.
• Thyroid hormone signaling modulates enhancer blocking through these composite sites.
• CTCF's enhancer blocking activity is intrinsically linked to TR binding, highlighting a novel regulatory mechanism.