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This Week in Nucleic Acids Research: Dec 19, 2018

German researchers present an updated genome annotation for Aspergillus niger, a fungal species that's often tapped to produce large quantities of specific organic acids, enzymes, or other proteins. The team considered more than 150 published, array-based transcriptome datasets, putting together gene co-expression networks representing 9,579 A. niger genes. Along with gene ontology analyses informed with experimental data from other Aspergillus species, the co-expression clues helped to tease out biological roles for almost 9,300 of the A. niger genes, including genes coding for four secondary metabolite-related transcription factors assessed in more detail.

A Johns Hopkins University and University of California, Irvine, team describes a high-throughput sequencing strategy for profiling RNA structure. The approach — known as "Light Activated Structural Examination of RNA by high-throughput sequencing," or LASER-Seq — uses deep sequencing and light-activated chemical probes, the researchers say. They note that LASER-Seq compares favorably with other RNA analysis methods, and say the LASER step in the process "can be used to rapidly survey for ligand binding sites in an unbiased fashion."

Finally, researchers from the University of Colorado School of Medicine report on a transcriptome resampling-based method for delving more deeply into gene expression patterns in pooled single-cell RNA sequence libraries. "[W]e developed a strategy to physically recover the DNA molecules comprising transcriptome subsets, enabling deeper interrogation of the isolated molecules by another round of DNA sequencing," they write. When the team applied this approach to scRNA-seq libraries from blood platelet-producing megakaryocyte cells, for example, it saw a jump in both sequencing depth and in the number of gene transcripts detected in each cell. 

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.