In a paper published online in advance in Genome Research this week, investigators at Sweden's Karolinska Institutet, along with their colleagues at Illumina, present an approach to generate single-cell RNA-seq expression profiles that can be "clustered to form a two-dimensional cell map," upon which expression data can be projected. "The resulting cell map integrates three levels of organization: the whole population of cells, the functionally distinct subpopulations it contains, and the single cells themselves — all without need for known markers to classify cell types," the authors write.
Researchers at the University of Kentucky and the Benaroya Research Institute at Virginia Mason in Seattle this week "demonstrate the value of data from diverse, amphibian genomes in studies of vertebrate genome evolution," they write. The team used comparative mapping techniques to study how genes are organized in Ambystoma mexicanum, or Mexican axolotl, as the species "presents relatively few chromosomes and a gigantic genome." The authors report an "extensive conservation of synteny between Ambystoma, chicken, and human, and a positive correlation between the length of conserved segments and genome size," they write, adding their postulation that "the maintenance of gene order relationships between chromosomal segments that have greatly expanded and contracted in salamander and chicken genomes, respectively, suggests selection to maintain synteny relationships and/or extremely low rates of chromosomal rearrangement."
The Wellcome Trust Centre for Cell Biology's Aimée Deaton et al. this week report their discovery of "cell type-specific DNA methylation at intragenic CpG islands in the immune system" of mouse. Using MAP-seq on murine hematopoietic cells, "we found that large differences in gene expression were accompanied by surprisingly few DNA methylation changes," the authors write, adding their finding that "elevated intragenic CGI methylation correlated with silencing of the associated gene."
In another Genome Research advance online publication, the University of Chicago's Francesca Luca and colleagues present "a reduced representation approach to population genetic analyses," based on a protocol for preparing resequencing targets, which they've applied to 19 individuals from 18 human populations "to test the serial founder model of human dispersal and to estimate the time of the Out of Africa migration." The team says its study represents "the first attempt to provide a timeframe for the colonization of Australia based on large-scale resequencing data," and adds that its reduced representation approach is applicable to any species for which a draft or complete reference genome sequence is available.