In Genome Biology this week, researchers at Harvard and MIT "describe computational methods for [the] analysis of repetitive elements from short-read sequencing data," as used to examine histone modifications in human and mouse cells. Daniel Day and colleagues show that they were able to obtain accurate enrichment estimates "for individual repeat types and small sets of repeat instances" and that "there are distinct combinatorial patterns of chromatin marks associated with major annotated repeat families."
Investigators at Uppsala University in Sweden and their international colleagues explore the molecular evolution of genes in the zebra finch and chicken genomes. The team performed "whole-genome comparative analysis of gene sequence evolution" in the two birds and found "clear differences in the substitution rate at four-fold degenerate sites," and "positively selected and/or rapidly evolving genes" in the avian lineages. The researchers suggest that their report paves the way for functional genetic studies of avian genes.
A research team led by investigators at University Hospital Regensburg in Germany reports that "active DNA demethylation in human post-mitotic cells correlates with activating histone modifications, but not transcription levels" in a recent Genome Biology paper. "Using a global, comparative CpG methylation profiling approach we identified many novel examples of active DNA demethylation and characterised accompanying transcriptional and epigenetic events at these sites during monocytic differentiation," the authors write, adding that active DNA demethylation, they found, "is not restricted to proximal promoters and that the time-course of demethylation varies for individual CpGs."
Richard Gibbs at Baylor College of Medicine in Houston and his colleagues report their method for whole-exome capture in solution that requires "as little as 3Gbp of raw sequence data," and "allows the discovery of greater than 95 percent of all expected heterozygous single-base variants," they write. Gibbs et al. suggest that their approach is an "effective tool for identifying rare coding alleles in large-scale genomic studies."