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This Week in Nucleic Acids Research: Aug 1, 2018

Spanish researchers describe chromatin accessibility profiles in the Plasmodium falciparum malaria parasite across four stages of development. The team turned to ATAC-seq to assay actively transcribed regions of the P. falciparum genome, related histone modifications, and new regulatory regions. The analysis suggests chromatin accessibility in the malaria parasite genome typically lines up with transcriptional dynamics over the course of development, for example. And, the authors say, the results point to "genome-wide regulatory regions likely to play an essential function in the developmental transitions and in [clonally variant gene] expression in P. falciparum."

A Van Andel Research Institute Center for Epigenetics team introduces SeSAMe software for masking artificial epigenetic alterations that occur when hybridization fails at sequence deletion sites with methylation profiling arrays. To address these artifacts, the researchers established a SeSAMe software package that hinges on the "P-value with out-of-band array hybridization," or pOOBAH. "Our method effectively masks deleted and hyperpolymorphic regions," they write, "reducing or eliminating spurious reports of epigenetic silencing at oft-deleted tumor suppressor genes such as CDKN2A and RB1 in cases with somatic deletions."

Researchers from Canada, Ireland, the US, and the UK map out transcriptional start sites and regulatory patterns in the pathogenic bacterial species Acinetobacter baumannii. Using differential RNA sequencing, the team profiled transcription start sites in pooled cultures of the A. baumannii strain ATCC 17978 that were grown under 16 distinct conditions in the lab and sampled over time. The analysis revealed more than 3,700 transcription start sites, along with 110 small RNAs that appeared to largely conserved across A. baumannii, but missing in other species from the genus. The authors also used their data to dig into regulation of a chloramphenicol antibiotic resistance contributor called craA, demonstrating that promoters for the drug efflux pump could be dialed down under low-nutrient growth conditions.