Coordinated transcription of the mammalian basement membrane gene family: Chromatin structure and DNA sequence analysis

We have taken a novel approach in an attempt to better understand the mechanism(s) of the coordinated regulation of the mammalian basement membrane gene family. Our approach incorporates both experimental and computational methods. Using methods in experimental molecular biology, we looked at the in vivo chromatin organization in the 5' regions of the mouse entactin and laminin gamma1 genes. We discovered that the chromatin structures of these genes are well defined in a manner that reflects the transcriptional states of these genes. We have identified the specific regions on these genes where chromatin structure facilitates the interactions of DNA sequences to potential transcriptional factors. Using a computational algorithm that we have developed for this study, we analyzed all known mouse and human basement membrane gene 5' sequences with a collection of >4,600 known and putative transcription factor binding sites. We discovered that 10 of the >4,600 potential transcription factor binding sites, as well as 35 additional novel sequence motifs are conserved among the 11 known basement membrane gene sequences. We performed a novel alignment analysis of the positioning of these potential sites with the in vivo chromatin organization in the cells that express these genes and discovered that these sites are specifically aligned with the regions of chromatin that are accessible to potential transcription factors. Our results suggest that these sites could be functional in vivo. The convergence of the results from two fundamentally unique analyses provides strong support for the proposal that the 10 potential transcription factor binding sites could represent key components of a novel coordinated transcriptional regulatory mechanism.