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This Week in Genome Research: Feb 5, 2014

An international team led by investigators at BGI-Shenzhen and the University of Copenhagen used bisulfite- and transcriptome sequencing to explore the epigenetics of environment-influenced sex determination in the recently sequenced half-smooth tongue sole, Cynoglossus semilaevis — a flatfish in which sex is determined by both genetic and environmental factors. The researchers assessed five pooled gonad samples for the study, representing male, female, pseudo-male, and crossed C. semilaevis. In the process, they detected methylation shifts that dial down expression from the female "W" chromosome and bump up the representation of male "Z" chromosome genes during environmentally-induced sex reversal, for example. Those included epigenetic shifts passed on to pseudo-male fish in the next generation.

A French-led team looks at microRNA levels — and their expression effects — in dendritic cells from individuals infected with Mycobacterium tuberculosis. By comparing miRNA and expression levels in infected and uninfected cells from 65 individuals with European ancestry, the researchers identified 91 miRNAs that were muted in infected cells and another 64 that were found at elevated levels. Among them were at least two miRNAs associated with expression quantitative trait loci involved in infection response. The analysis also uncovered infection-related changes in the way that miRNAs interact with target messenger RNAs in the genome.

A pre-cancerous condition called myelodysplastic syndrome, which often progresses to acute myeloid leukemia, involves hyper-methylation at hundreds of genes, according to another Genome Research study. Researchers from the US and Japan did DNA methylation profiling in spleen and bone marrow samples from mice carrying mutations associated with MDS and AML — a search that unearthed hundreds of hyper-methylated genes in each of the MDS mouse models, along with a rise in methylation patterns associated with age. Roughly two-thirds of the corresponding genes showed higher-than-usual methylation in samples from humans with MDS, too. "Our data show consistency in patterns of aberrant DNA methylation in human and mouse MDS," study authors write, "and suggest that, epigenetically, MDS displays an accelerated aging phenotype."