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This Week in Genome Research: Dec 10, 2014

An Australian-led team takes a look at alternative functions for an RNA polymerase I transcription factor called upstream binding transcription factor 1 (UBTF). Through chromatin immunoprecipitation sequencing on mouse and human cell lines, the researchers identified thousands of binding sites for the UBTF1/2 isoforms in the mammalian genomes, including enrichment in and around genes transcribed by polymerase II. Their follow-up experiments suggest that UBTF1 and UBTF2 help to coordinate expression by Pol I and Pol II enzymes, augmenting overall genome stability.

The plant-specific RNA polymerase IV enzyme contributes to control over the small interfering RNA production system in Arabidopsis plants, according to a study by researchers in the US and China. With the help of RNA sequencing and double-stranded RNA sequencing on Arabidopsis lines deficient in siRNA precursor processing, the team tracked down tens of thousands of Pol IV-dependent siRNA sites in the genome, while subsequent experiments revealed features of these sites and their effects on RNA-directed DNA methylation in mutant plants.

Finally, researchers with the Fred Hutchinson Cancer Research Center explore nucleosome structural patterns across the budding yeast genome using a combination of micrococcal nuclease sequencing, chromatin immunoprecipitation sequencing, and other approaches. Their results suggest that histone and DNA interactions have asymmetrical features at a small subset of yeast nucleosomes. The team's subsequent experiments indicate that this asymmetry involves a stable intermediate structure comprised of nucleosomes interacting with components of a chromatin remodeling complex called RSC.