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This Week in PNAS: Jun 2, 2015

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from the US and Switzerland present findings from a spatiotemporal study of long, non-coding RNA expression in developing and adult mouse brains. Using RNA sequencing, the team looked at the transcriptional patterns in mice at two weeks of embryonic development and in adult mice seven and 14 weeks old, both in wild type mice and in 13 mouse models, each missing a different lncRNA. In the absence of at least four of the lncRNAs, for example, the study's authors saw changes in the expression of nearby protein-coding genes. Together, they say, the results "provide a resource to facilitate future examination of the specific functional relevance of these genes in neural development, brain function, and disease."

A team from Denmark and the US look at the role that extrachromosomal, circular DNAs play in yeast genetic variation. The researchers relied on an approach called Circle-Seq to characterize nearly 1,800 different eccDNAs — ranging in size from 1,000 to 38,000 bases — in the budding yeast Saccharomyces cerevisiae. Their results suggest that these extrachromosomal sequences can stem from parts of the yeast genome with repeat rich- or poor-parts of the genome, though the genes most commonly found in the eccDNAs included tandemly repeated genes and transposon remnants. Based on the nature and extent of the sequences found in eccDNAs, meanwhile, the authors argue that "eccDNAs may be precursors to the copy number variation in eukaryotic genomes." 

Finally, Japanese researchers report on the song-learning effects of altering activity of transcription factor called cAMP response element-binding protein, which is believed to help regulate neural activity-dependent gene expression during post-natal learning and experiences. To do this, the team turned to viral vector-mediated genomic DNA modification to develop a transgenic zebra finch line with diminished or elevated activity by the CREB transcription factor. In songbirds with altered CREB activity, the investigators saw a dip in song-learning abilities, though the birds' intrinsic ability to sing and hear was not affected.

The Scan

ChatGPT Does As Well As Humans Answering Genetics Questions, Study Finds

Researchers in the European Journal of Human Genetics had ChatGPT answer genetics-related questions, finding it was about 68 percent accurate, but sometimes gave different answers to the same question.

Sequencing Analysis Examines Gene Regulatory Networks of Honeybee Soldier, Forager Brains

Researchers in Nature Ecology & Evolution find gene regulatory network differences between soldiers and foragers, suggesting bees can take on either role.

Analysis of Ashkenazi Jewish Cohort Uncovers New Genetic Loci Linked to Alzheimer's Disease

The study in Alzheimer's & Dementia highlighted known genes, but also novel ones with biological ties to Alzheimer's disease.

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.