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This Week in Genome Research: May 2, 2012

In Genome Research this week, an international team of researchers reports on its reconstruction of ancient mitochondrial DNA links between Europe and Africa. The team analyzed 69 mitochondrial genomes belonging to various sublineages of macro-haplogroup L from a wide range of European populations. Used phylogeographic analyses, they show that about 65 percent of the European L lineages arrived in Europe relatively recently, including during the Arab conquest of the Iberian Peninsula or during the period of the slave trade. "However," the authors write, "the remaining 35 percent of L mtDNAs form European-specific subclades, revealing that there was gene flow from sub-Saharan Africa toward Europe as early as 11,000 yr ago."

Also in Genome Research this week, researchers in the US and Japan examine the impact of human postmeiotic sex chromatin on the evolution of sex chromosomes. In their study, the researchers show that chromosome inactivation is highly conserved between humans and mice and that it has an impact on the way sex chromosomes evolve. In human sex chromosomes, in particular, "inactivation established during meiosis is maintained into spermatids with the silent compartment postmeiotic sex chromatin," they write. "Human PMSC is illuminated with epigenetic modifications such as trimethylated lysine 9 of histone H3 and heterochromatin proteins CBX1 and CBX3, which implicate a conserved mechanism underlying the maintenance of sex chromosome inactivation in mammals."

Researchers in Australia and Chile perform a genome-wide analysis of the stability of long non-coding RNA in Genome Research this week. The team used a custom non-coding RNA array to determine the half-lives of about 800 lncRNAs and about 1,200 mRNAs in the mouse Neuro-2a cell line, and found that only a small number of lncRNAs are unstable. "LncRNA half-lives vary over a wide range, comparable to, although on average less than, that of mRNAs, suggestive of complex metabolism and widespread functionality," the team says. "Analysis of lncRNA features revealed that intergenic and cis-antisense RNAs are more stable than those derived from introns, as are spliced lncRNAs compared to unspliced (single exon) transcripts." The team also created an online interactive resource to allow users to easily navigate lncRNA and mRNA stability profiles.

Finally in Genome Research this week, researchers in the US and Belgium present a DNA hypermethylation module for the progenitor cell signature of cancer. The team used a genome-wide analysis to show that about 75 percent of hypermethylated genes are marked by PcG in both embryonic stem cells and adult stem or progenitor cells. "A large number of these genes are key developmental regulators, and a subset, which we call the 'DNA hypermethylation module,' comprises a portion of the PcG target genes that are down-regulated in cancer," the authors write. "When DNA [is] hypermethylated in tumors, we find that these genes are further repressed. We also show that the methylation status of these genes can cluster important subtypes of colon and breast cancers."

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.