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This Week in Nucleic Acids Research: Dec 23, 2015

A Whitehead Institute for Biomedical Research-led team introduces a web-based tool for doing head-to-head comparisons of gene expression profiles in different tissue or cell types. The "Metabolic Gene Rapid Visualizer," or MERAV, is meant to serve as a tool for assessing genome-wide expression and metabolic patterns within various cell types, including cancer. The database currently contains thousands of gene expression sets generated representing normal tissue, primary tumor samples, and cancer cell lines, the researchers explain. "We created the MERAV database and analysis tools in order to harness aggregate array data for deeper insights into gene expression across the entire human genome and across normal cell lines, primary tumors, and cancer cell lines," they write.

Researchers from the US and Germany describe DNA methylation differences that can distinguish between two different subtypes of neurons in the prefrontal cortex of the human brain. Using genotyping arrays, RNA sequencing, and/or methylation arrays, the team scrutinized SNP, expression, and methylation patterns in so-called GABAergic interneurons and glutamatergic projection neurons from autopsy samples for nine individuals between the ages of 19 years and 46 years old. The analysis uncovered methylation differences outside of cytosine and guanine-rich regions that appear to track more closely with neuronal subtypes than gene expression patterns.

A team from Cleveland Clinic and Case Western Reserve University has uncovered an epigenetics-related role for the KLLN gene in maintaining the stability of the genome. The researchers used chromatin immunoprecipitation in combination with sequencing to characterize binding patterns for the protein product of KLLN, a gene previously found to be hypermethylated in the germline of some individuals with a cancer predisposition condition called Cowden syndrome. Their results suggest that KLLN interacts with a histone mark called H3K9me3 in ways that influence everything from the formation of pericentric heterochromatin and gene expression to broader genome stability.