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This Week in Nucleic Acids Research: Jan 16, 2019

The 3' ends of microRNAs undergo more alternative processing than previously appreciated, according to a new Nucleic Acids Research study. Researchers from Seoul National University updated a small RNA sequencing approach so that its ligation bias during library preparation is minimized, an approach they called accurate quantification by sequencing, or AQ-seq. This approach enabled them to uncover improperly annotated 5' end usage and strand preference within public databases as well as find a number of miRNAs originating from of 3p strands are highly uridylated. The researchers added that this approach could be extended to improve other ligation-based sequencing methods.

Also in Nucleic Acids Research, investigators from the Max Planck Institute for Biophysical Chemistry present a workflow dubbed Quantification of Rare Amino acid Substitutions, or QRAS, that relies on the combination of the chromatographic enrichment of peptides containing amino acid substitutions with targeted mass spectrometry. Applying this approach, the researchers found that most missense errors are too rare to be detected by other methods, but that there are some error hotspots for certain mismatches. They add that QRAS is "is a reliable tool to analyze very rare proteogenomic events."

Finally, researchers from the University of Virginia examined CNV breakpoints within the Plasmodium falciparum genome, which often confer resistance to malaria treatments and are often found in long A/T tracks. They identified breakpoints in 35 parasite clones and predicted that stable hairpins would form near these sites. They suggested that the A/T track in conjunction with the hairpins leads to double-strand breaks, which when repaired non-faithfully lead to CNV formation.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.