In a Nucleic Acids Research paper published online in advance this week, researchers show that different DNA methyltransferase domains "are responsible for targeting DNA methylation to specific regions of the genome," which may be associated with histone modifications. First, the team created HEK 293T cells transfected with 13 DNMTs. They then assessed methylation changes induced be each DNMT. "We found that DNMTs have specific and overlapping target sites and their DNA methylation target profiles are a reflection of the DNMT domains," the authors write.
Investigators in Germany describe their investigations of the "mechanism by which nucleosomes are positioned at the promoters of active and silent rRNA genes" in Nucleic Acids Research this week. The researchers suggest that the "repressed state is the default chromatin organization of the rDNA and gene activation requires ATP-dependent chromatin remodeling activities that move the promoter-bound nucleosome about 22 bp upstream," where subsequent ATP-dependent chromatin remodeling suppresses RNA Pol I transcription initiation in vitro. "Once initiated, RNA Polymerase I is capable of elongating through reconstituted chromatin without apparent displacement of the nucleosomes," the authors write.
The University of Pennsylvania's Hakon Hakonarson and his colleagues describe ANNOVAR, a tool that can "annotate single nucleotide variants and insertions/deletions," and is capable of "examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1,000 Genomes Project and dbSNP," the authors write. ANNOVAR can be run on a desktop computer, the team reports, and takes only four minutes to perform gene-based annotation and 15 to perform variants reduction on 4.7 million variants, "making it practical to handle hundreds of human genomes in a day."
Also in Nucleic Acids Research this week, German researchers describe the "transcriptional properties of human NANOG1 and NANOG2 in acute leukemic cells." Because NANOG1 belongs to a gene family that includes several pseudogenes and tandem duplication, it had previously been unclear which NANOG family members were transcribed in leukemia cells. The team developed a novel PCR method to distinguish between NANOG1, NANOG2, and pseudogenes; they found that "human hematopoietic stem cells and different leukemic cells transcribe NANOG2," and suggest that the "transcriptional activation of NANOG2 represents a 'gain-of-stem cell function' in acute leukemia."