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Genome Biology Examines Cell-Type Specific Schizophrenia Epigenetics, Mustard Variation, and More

Researchers from the Georgia Institute of Technology, UT Southwestern Medical Center, and elsewhere compare methylation and gene expression profiles from neuronal and oligodendrocyte cells from post-mortem brain samples from individuals with or without schizophrenia. The team did whole-genome bisulfite sequencing and RNA sequencing on fluorescence-activated nuclei-sorted brain cells from dozens of frozen brain bank samples, representing dorsolateral prefrontal cortex tissue in individuals with schizophrenia and unaffected controls. Along with distinct epigenetic features found in neuron and oligodendrocyte cell types, the authors saw more modest methylation differences in these brain cells in schizophrenia cases and controls, particularly at cell type-specific epigenetic sites.  

A team from China, the US, and Taiwan retrace genomic variation and selection in the mustard plant Boechera stricta, an Arabidopsis thaliana relative, using with whole-genome sequencing on hundreds of accessions. The researchers focused on 517 B. stricta accessions selected from across the plant's western US range, identifying four genetically distinct clusters of the plant that split from one another between 30,000 years and 180,000 years ago. Within the B. stricta genomes, meanwhile, they uncovered a handful of particularly diverse parts of the genome that appeared to have undergone balancing selection on ancestral sequences related to disease resistance. From these and other findings, the authors suggest that "elevated genetic diversity due to balancing selection … may increase population differentiation by sorting balanced polymorphisms during divergence processes."

Finally, a University of Southern California-led team describes a long-read sequencing protocol for taking a look at copy number patterns when starting with short DNA molecules. The approach — known as "sampling molecules using re-ligated fragments," or SMURF-seq — includes a random ligation step to fuse short pieces of DNA into long molecules, the investigators explain. When they used SMURF-seq, in combination with Oxford Nanopore MinION long-read platform, to assess copy number variants in a normal diploid genome and in rearranged cancer genomes, the authors found that the approach compared favorably with other CNV profiling approaches. "We used SMURF-seq with the low-cost MinION sequencer to obtain data similar to that expected from typical short-read sequencing," they report, "and generated high-quality CNV profiles from this output."