3. New views of the genome's regulatory landscape
The ENCODE Project continues to illuminate the complex process of gene regulation and chromatin, the combination of DNA and protein that packages DNA in the nucleus. The scale of new data from The ENCODE Project is allowing more accurate characterization than ever of the factors that regulate gene expression. In this issue, Cheng and colleagues have applied a statistical model to the large-scale ENCODE gene expression and transcription factor binding datasets to assess the accuracy of gene expression prediction. Among a number of insights into the predictability of gene expression, their work suggests that gene expression differences in different cell lines are directly reflected in quantitative differences in transcription factor binding levels, challenging the classic "on" or "off" transcription factor binding model.
In addition to studies investigating the myriad transcription factors in the cell, researchers in The ENCODE Consortium are also investigating the function of specific factors genome-wide. Wang et al. present a genome-wide analysis in diverse cell types of the binding pattern of CTCF, a well-known insulator that can suppress the effect of regulatory enhancers on its target gene when bound, playing a role in a number of fundamental genomic processes. The team found that the binding pattern of CTCF is surprisingly plastic yet reproducible, and is significantly different between normal and immortal cells, a finding that could have important implications in cancer.
ENCODE studies are spurring the development of new methods to integrate large genome-wide datasets of different types and to overcome the limitations of current techniques. For example, to investigate the relationship between nucleosome remodeling, histone modifications, and transcription factor binding that governs gene regulation, Kundaje and colleagues have develo
|Contact: Peggy Calicchia|
Cold Spring Harbor Laboratory