In Nature this week, a team led by investigators at the Ludwig Institute for Cancer Research at the University of California, San Diego, discusses the 3D organization of the human and mouse genomes in both embryonic stem cells and terminally differentiated cell types. In its study, the team analyzed more than 1.7-billion read pairs of Hi-C data corresponding to pluripotent and differentiated cells, identifying "large, megabase-sized local chromatin interaction domains," which it has dubbed "'topological domains,' as a pervasive structural feature of the genome organization." In addition, the researchers report having found that "the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs, and short interspersed element retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome," they write.
An international team led by researchers at the University of North Carolina at Chapel Hill reports its application of a competition ChIP approach to measure Rap1 transcription-factor binding dynamics across the Saccharomyces cerevisiae genome. "Long Rap1 residence was coupled to transcriptional activation, whereas fast binding turnover, which we refer to as 'treadmilling', was linked to low transcriptional output," the authors report having found. "We propose that transcription factor binding turnover is a major point of regulation in determining the functional consequences of transcription factor binding, and is mediated mainly by control of competition between transcription factors and nucleosomes," they add.
Elsewhere in Nature this week, researchers at the John Innes Centre in Norwich, UK, and their colleagues report a "direct mechanism by which increasing temperature causes the bHLH transcription factor Phytochrome Interacting Factor4 to activate FT [Flowering Locus T]" in Arapidopsis thaliana. The team says its study adds to researchers' molecular understanding of how temperature affects flowering, which it adds, "will be important for mitigating the effects of climate change."
The well known saying goes
The well known saying goes like "New things are well forgotten old ones". These topological domains are used to be termed chromatin loops. Interestingly "the insulator binding protein CTCF" was found frequently at the boundaries at the base of these loops. This protein is also found bound to promoters of important genes anchoring them to the base of the loop and protecting from methylation. CTCF inactivating mutations may lead to gene inactivation and remodeling the chromatin.
Michael Lerman, Ph.D., M.D.