Examination of the Chromatin Structure of Xlr3b Using the Chromosome Conformation Capture Assay

Imprinted genes contain epigenetic modifications that influence expression patterns based on parent-of-origin. Recent studies have shown that imprinted genes contribute to numerous human diseases and disorders. Xlr3b, an imprinted gene on the X chromosome, has been implicated in social and behavioral deficits characteristic of disorders such as Turner syndrome and autism. The imprinting mechanism of this gene is still unknown, and this study analyzed the native chromatin structure of Xlr3b through the chromosome conformation capture assay to determine if there are any long-range interactions that regulate the expression of this gene. Brain tissue from a mouse model of Turner syndrome (39, Xm) was used in this protocol, and the samples were analyzed through PCR amplification with primers designed to capture interacting fragments. No long-range interactions were found with the maternal copy of Xlr3b, indicating that the expression is not promoted by a distant enhancer. However, it remains a possibility that the imprinting mechanism of Xlr3b is regulated by insulating interactions within the paternal chromosome