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This Week in Nucleic Acids Research: Nov 25, 2015

Researchers from the University of California, Los Angeles, bring together individual transcriptome and genome sequence data as a means of uncovering previously unappreciated variation in transcript splicing patterns. Using data for 75 individuals, the team mapped each person's RNA sequence data onto his or her personal genome sequences, uncovering more than 500 splice site junctions that were specific to individuals. The set included 437 previously unknown splice junctions and 94 sites in the genome that have been linked to particular traits or diseases through prior genome-wide association studies. "Collectively," the study's authors say, "our work demonstrates that the personal genome approach to RNA-seq read alignment enables the discovery of a large but previously unknown catalog of splicing variations in human populations."

A team from the National Human Genome Research Institute and Pennsylvania State University report on a repository for systems biology-based data generated on human and mouse blood cells. The online database — known as the hematopoietic Systems Biology Repository, or SBR-Blood — is designed to let users search for a range of array and/or sequencing-based information on a specific cell type or within a given hematopoietic cell lineage, the researchers note. This information is paired with tools for analyzing expression profiles, DNA methylation patterns, transcription factor distributions, histone modification patterns, and more in the blood cells, they say. "Our goal in designing SBR-Blood is to provide users with the ability to make informed and appropriate analytical decisions and to focus on the important biological questions relevant to hematopoiesis without having to install and master different sets of bioinformatics tools," they add.

French researchers report on apparent relationships between repetitive elements and three-dimensional structure stability in human, mouse, and Drosophila genomes. With the help of data from Hi-C experiments, the team considered inter-chromosomal contact frequencies in these genomes in the context of various repetitive sequence elements. Indeed, results of the analysis pointed to frequent co-localization between inter-chromosomal contacts and specific repetitive element groups, including the SINE family elements. "Taken together," authors of the analysis argue, "these results support a contribution of specific repetitive elements in maintaining and/or reshaping genome architecture over evolutionary times."

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.