In Genome Research this week, researchers at the University of California, San Diego, report that allele-specific methylation is prevalent in the human genome and is contributed by CpG-SNPs. Using bisultfite sequencing, the team performed a chromosome-wide survey of ASM in 16 human pluripotent and adult cell lines; they observed such methylation on 23-37 percent heterozygous SNPs. "Furthermore, we found that a significant fraction (38-88 percent) of ASM regions are dependent on the presence of heterozygous SNPs in CpG dinucleotides that disrupt their methylation potential," the authors write, adding that their study "suggests a potential role for CpG-SNP in connecting variation with the epigenome."
In another paper published online in advance this week, investigators in Switzerland report their analysis of the RNA polymerase III transcriptome. By localizing Pol III and some of its transcription factors genome-wide, the team describes a "minimal Pol III transcriptome in dividing IMR90hTert fibroblasts," consisting of nearly 500 actively transcribed genes, "including a few dozen candidate novel genes," of which the team validated nine.
Researchers in Germany communicate their transcriptomic and proteomic analyses of Pristionchus pacificus, a nematode model organism. The P. pacificus proteome, the authors write, contains a high proportion of pioneer proteins — "small proteins with no known homologs in other species." Furthermore, the median predicted protein size in the species is "unusually low," at 240 amino acids. The authors write that their study is "the first comparison of related nematode models at the proteome level."
An international research team describes their method to "sequence, assemble, and analyze complete mitochondrial genomes from large numbers of samples," using Orcinus orca — killer whales — as a case study. Using high-throughput sequencing, the team analyzed the mitochondrial genome variation within 139 samples; their subsequent phylogenetic analysis "indicated that each of the known ecotypes represents a strongly supported clade with divergence times ranging from approximately 150,000 to 700,000 years ago," the authors write. The team suggests that "phylogeographic mitogenomics will become an important tool for improved statistical phylogeography and more precise estimates of divergence times."