Global Survey of Chromatin Accessibility Using DNA Microarrays

Abstract

An increasing number of studies indicate a central role for chromatin remodeling in the regulation of gene expression. Current methods for high-resolution studies of the relationship between chromatin accessibility and transcription are low throughput, making a genome-wide study impractical. To enable the simultaneous measurement of the global chromatin accessibility state at the resolution of single genes, we developed the Chromatin Array technique, in which chromatin is separated by its condensation state using either the solubility differences of mono-and oligonucleosomes in specific buffers or controlled DNase I digestion and selection of the large refractory (condensed) DNA fragments. By probing with a comparative genomic hybridization style microarray, we can determine the condensation state of thousands of individual loci and correlate this with transcriptional activity. Applying this technique to the breast tumor model cell line, MCF7, we found that when the condensation is homogeneous in the population of cells, expression is inversely proportional to the level of accessibility and the two methods of accessibility-based target selection correlate well. Using functional annotation and comparative genomic hybridization data, we have begun to decipher the possible biological implications of the relationship between chromatin accessibility and expression.

Distinct modes of DNA accessibility in plant chromatin

“…DNA inaccessibility is thought to restrict recognition of DNA templates by regulatory proteins and thus to hinder transcription while accessible chromatin structures may facilitate transcription 15,26 . It is also possible that increased DNA accessibility is a consequence of transcriptional activity.…”

Measuring Arabidopsis Chromatin Accessibility Using DNase I-Polymerase Chain Reaction and DNase I-Chip Assays

“…As an example, the chromatin sensitivity was analyzed for two silent transposable element (TE) genes (Ta2 and Cinful-like) and two active genes (GAPDHa and ACTIN7 [ACT7]) in Arabidopsis. We and others have shown that transcription is generally associated with accessible chromatin (Weil et al, 2004;Boyle et al, 2008;Bell et al, 2010;Shu et al, 2012;Zhang et al, 2012). Thus, we predict that the two TE genes should be much less sensitive to DNase I than the two active genes and, therefore, can be used as insensitive and sensitive controls in future assays.…”

“…Therefore, analysis methods based on PCR have been developed (Pfeifer and Riggs, 1991;Feng and Villeponteau, 1992;McArthur et al, 2001;Dorschner et al, 2004;Martins et al, 2007). In recent years, DNase I assays were coupled to high-throughput genome-wide profiling strategies such as genome tiling arrays and next-generation sequencing (Crawford et al, 2004(Crawford et al, , 2006Sabo et al, 2004Sabo et al, , 2006Weil et al, 2004). While much has been learned about the accessibility of chromatin in animal and yeast systems, our knowledge of chromatin accessibility in plants is limited.…”

“…Its applicability has been manifested by detecting regulatory elements, such as promoters, enhancers, and insulators, as DNase I-hypersensitive sites (Wang and Simpson, 2001;Crawford et al, 2004Crawford et al, , 2006Dorschner et al, 2004;Sabo et al, 2006;Boyle et al, 2008;Naughton et al, 2010;Pique-Regi et al, 2011). DNase I sensitivity can also be used as a measure for the general accessibility of chromatin (Weil et al, 2004).…”

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

“…Numerous studies of nucleosomal positioning have been carried out for individual genomic regions, indicating that positioning can be both flexible and constrained (e.g., Lu et al 1994;Kornberg and Lorch 1999;Sekinger et al 2005). Recently, these studies have been extended genomewide through the analysis of populations of nucleosomes using high-density microarrays (for the yeast Sacchromyces cerevisiae) (Yuan et al 2005) and using the Chromatin Array technique (for human cell lines) (Weil et al 2004). These studies have shed considerable light on DNA sequence and other factors influencing nucleosome occupancy; certainly the results serve as a strong argument for pursuing a genome-wide analysis of nucleosome positioning and dynamics at an increasingly detailed level (Satchwell et al 1986;Dong et al 1990;Lu et al 1994;Travers and Muyldermans 1996;Flaus and Richmond 1998;Crawford et al 2006).…”