High-resolution analysis of c-fos chromatin accessibility using a novel DNase I-PCR assay

Abstract

In our previous study, c-fos chromatin accessibility was assayed using DNase I digestion and Southern blot analysis. This low-resolution mapping of c-fos chromatin accessibility demonstrated that serum stimulation of the c-fos enhancer induces a reversible increase in c-fos DNase I sensitivity and suggested that a 5' to 3' gradient of DNase I sensitivity may form downstream from the c-fos enhancer. To confirm the existence of a 5' to 3' gradient of accessibility, we have recently developed a high-resolution polymerase chain reaction (PCR) assay for DNase I sensitivity. Using this novel DNase I assay, we have reliably detected position- and time-dependent gradients of chromatin accessibility around the c-fos enhancer. These data confirm our earlier results and further support the hypothesis that the changes in c-fos chromatin accessibility originate near the 5' enhancer. As a technique for future examinations of gene structure, our data demonstrate the value of the DNase I-PCR assay for rapidly preparing comprehensive and high-resolution maps of chromatin accessibility for any sequenced genomic region.