Chromatin Configuration Determines Cell Responses to Hormone Stimuli

Transcription factor access is highly cell-specific.    Sometimes the receptor and ligand direct the action, but most often access is preprogrammed by different combinations of cell-specific factors (grey ??) and remodeling systems (green??).

Transcription factor access is highly cell-specific. Sometimes the receptor and ligand direct the action, but most often access is preprogrammed by different combinations of cell-specific factors (grey ??) and remodeling systems (green??).

Ever since selective gene expression was established as the central driver of cell behavior, researchers have been working to understand the forces that control gene transcription. Aberrant gene expression can cause or promote many diseases, including cancer, and alterations in gene expression are the goal of many therapeutic agents. Recent work has focused on the potential role of chromatin structure as a contributor to gene regulation. Chromatin can exist in a tightly packed/inaccessible or loose/accessible configuration depending on the interactions between DNA and its associated proteins. Patterns of chromatin structure can differ between cell types and can also change within cells in response to certain signals. Cancer researchers are particularly interested in the role of chromatin in gene regulation because many of the genomic regions found to be associated with cancer risk are in open chromatin structures.

Researchers in the CCR Laboratory of Receptor Biology and Gene Expression are studying the cellular actions of nuclear receptors to gain insight into how gene expression is regulated. When bound and activated by hormones called glucocorticoids, the glucocorticoid receptor binds to certain regions of DNA and regulates expression of numerous target genes. Glucocorticoids cause different patterns of gene expression in different tissues, although the reasons for this are not well understood. Staff scientist Sam John, Ph.D., in Gordon Hager’s laboratory, worked with other CCR researchers and John Stamatoyannopoulos, M.D., at the University of Washington to look at how chromatin structure affects which DNA regions glucocorticoid receptor can bind. The results were published in a recent issue of Nature Genetics.

The primary goal of the research was to determine the global relationship between the pre-existing chromatin structure and the pattern of glucocorticoid receptor binding. Cultured cells from two different tissues—the mammary gland and the pituitary, were treated with glucocorticoids and binding distributions were characterized. The researchers identified accessible regions of DNA across the genome using a technique called digital DNAse I profiling, an approach that uses a scissor-like enzyme capable of cutting DNA in regions where it is loosely packed. In both cell types, less than three percent of the genome was found to be accessible. However, patterns of chromatin accessibility differed significantly: less than one third of the accessible sites were the same in both mammary and pituitary cells.

A technique called ChIP-seq was then used to identify the specific regions of DNA to which the activated glucocorticoid receptor bound after the cells were treated with glucocorticoids. These experiments revealed that the vast majority of the DNA sites—more than 70 percent in mammary cells and 95 percent in pituitary cells—were within the tiny percentage of the genome that was accessible prior to hormone treatment.

These results provide a major new paradigm: pre-existing patterns of chromatin accessibility play a dominant role in determining where regulatory factors like glucocorticoid receptor bind upon activation, and likely contribute significantly to tissue-specific differences in gene activation in response to external signals and drugs. Chromatin accessibility was found to be even more important than the sequences of the DNA regions to which the glucocorticoid receptor bound. These findings define a previously unknown framework for understanding the interactions between DNA and the proteins that regulate gene expression and provide insight into how hormones can exert different effects in different tissues.

Summary Posted: 02/2011

Reference

Nat Genet. 2011 Jan 23. Reviewed by Donna Kerrigan PubMed Link