Quantifying Chromatin Accessibility of Individual Gene Family Members by Combining Ligation-Mediated PCR with Real-Time PCR

It's All in the Family The importance of epigenetic changes in disease states has become increasingly recognized; therefore studies exploring the role of chromatin in regulating gene expression have never been more relevant. However, restriction enzyme cleavage of intact nuclei, which is the classical method for determining chromatin accessibility, was designed to measure the accessibility of only single copy genes. Espinoza and Feeney have recently developed an assay to measure the chromatin accessibility of each individual gene within a highly homologous gene family. Their technique relies on a combination of ligation-mediated PCR and real-time PCR to yield data that is both sensitive and qualitative. In a proof-of-principle experiment, they checked the relative accessibility of the three members of the immunoglobulin VHS107 family. Their starting material was 106 freshly isolated mouse pro-B cells, in which this gene family is actively undergoing rearrangement. The results they obtained—that the V1 gen...