The Human Epigenome and Cell-Type-Specific Gene Expression

Differences in gene expression is what causes diversity between cells despite the fact that almost all human cells have the same genome and it represents the process through which a protein or other molecule encoded by a gene is produced. Along with promoters and insulators, enhancers are a regulatory element of this process, scattered across the genome and acting to assemble proteins that regulate the transcription of individual genes and constitute what is called the epigenome, a second “dimension” to the genome that determines fundamental biological processes.

A recent research identified and mapped 55,000 enhancers by analyzing more than 14 million DNA probes corresponding to the entire human genome by using a type of genome-wide analysis called ChIP-chip analysis to locate promoters, enhancers, insulators and other regulatory DNA sequences for each gene, using this approach to identify these elements in multiple cell types and investigate their roles in gene expression. ChIP-chip is used to localize protein binding sites that may help identify functional elements of the genome.

About the study and its importance, principal investigator Bing Ren, PhD, associate professor of Cellular and Molecular Medicine at the University of California, San Diego School of Medicine and head of the Laboratory of Gene Regulation at the Ludwig Institute for Cancer Research stated:

“Expanding the knowledge of enhancers is critical for understanding the mechanisms that control gene expression. As only two percent of the genome encodes proteins, there is so much left to discover about what was once considered non-coding ‘junk DNA’ and how that other 98 percent contributes to human disease.
Our studies show that enhancers play much more prominent role than previously appreciated in cell-type-specific gene expression, helping to explain what causes cells to differentiate into liver or brain or skin cells, or why these cells might become cancerous.
In our analyses, we were surprised to find that the chromatin signatures at promoter sites were similar across all cells. However, we found that enhancers are marked with highly cell-type specific modification patterns. These patterns suggested that enhancers are of primary importance in the differentiation of specific cell types.”