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This Week in Nucleic Acids Research: Apr 13, 2016

Researchers from the US and the UK introduce a variant caller for finding single nucleotide changes, multiple nucleotide variants, small insertions and deletions, or complex structural variant from DNA sequences, RNA sequences, or both. The team notes that the approach, known as VarDict, is designed to scale with sequence depth to pick up lower frequency variants in tumor samples or in circulating DNA. When they applied VarDict to simulated and real tumor data, for example, the study's authors found that the method compared favorably with existing variant callers.

An Italian team presents findings from a study of RNA interactions in human colorectal cancer samples in another Nucleic Acids Research study. Using array-based gene expression and microRNA profiles on 14 matched colorectal tumor and normal samples, the researchers put together a network of interactions between messenger RNAs and miRNAs that revealed what they called miRNA 'micro-societies' interacting with cancer-related genes and regulatory sequences. When the authors took a closer look at these RNA interacting modules, meanwhile, they saw an upstream regulatory role for miR-145, which appears to be a "potent upstream regulator of a complex RNA-RNA crosstalk."

Finally, Huazhong Agricultural University researchers explore epigenetic patterns across cotton fiber development as a means of better understanding the more general role that DNA methylation plays in single-cell differentiation. Using a combination of small RNA sequencing, transcriptome sequencing, bisulfite sequencing, and sequencing methods aimed at assessing chromatin patterns, the team tracked DNA methylation, chromatin dynamics, and regulatory features in cotton fiber. Along with a general increase in DNA methylation, for example, they saw hints of the methylation shifts that appeared to influence differentiation-related processes such as lipid production as well as reactive oxygen species distribution in the specific parts of the fiber over time.

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.