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Archive - Aug 19, 2015

First Genome-Wide Annotation of Long, Primary miRNA Transcripts Suggests Complex Regulatory Mechanisms

MicroRNAs are short, noncoding RNAs that play critical roles in regulating gene expression in normal physiology and disease. Despite having tightly controlled expression levels, little is known about how miRNAs themselves are regulated because their genes are poorly defined. In a study published online on August 19, 2015 in Genome Research, researchers devised a strategy for genome-wide annotation of primary miRNA transcripts, providing extensive new annotations in human and mouse, and shedding light on mechanisms of regulation of microRNA gene expression. The article is titled “Genome-Wide Annotation of MicroRNA Primary Transcript Structures Reveals Novel Regulatory Mechanisms.” Although mature miRNAs are only ~22 nucleotides, their transcripts are up to hundreds of kilobases long. Primary miRNA transcripts, or pri-miRNAs, are quickly processed into mature miRNAs from hairpin structures located in the exons or introns of pri-miRNA transcripts. Because processing occurs very quickly, standard methods such as RT-PCR or RNA sequencing detect full-length pri-miRNAs with poor sensitivity. Many miRNA genes, therefore, lack annotated features such as a promoter or splice sites, hindering progress in understanding their transcriptional and post-transcriptional regulation. To overcome this, researchers from the University of Texas Southwestern Medical Center and Johns Hopkins University stabilized pri-miRNAs by expressing a dominant negative form of DROSHA, the RNase III enzyme responsible for pri-miRNA cleavage, in a variety of human and mouse cell lines. By deeply sequencing nuclear RNAs and applying the computational tool StringTie to assemble transcripts, the researchers were able to annotate 69% of human miRNAs and 75% of mouse miRNAs.

Wild Honey Bees Evolve Rapidly to Overcome New Disease; Dopamine Receptor Gene (Aversion Learning & Grooming) and Numerous Developmental Genes Altered; Bees Are Also Smaller and Wings Are Different

An international research team has some good news for the struggling honeybee, and the millions of people who depend on them to pollinate crops and other plants. These valuable pollinators have faced widespread colony losses over the past decade, largely due to the spread of a predatory mite called Varroa destructor. But the bees might not be in as dire a state as it seems, according to research recently published in Nature Communications. Researchers found a population of wild bees from around Ithaca, New York, which is as strong today as ever, despite the mites invading the region in the mid-1990s. “They took a hit, but they recovered,” said Dr. Alexander Mikheyev, a professor at the Okinawa Institute of Science and Technology Graduate University (OIST) in Japan and lead paper author. The research was published online on August 9, 2015 in an open-access article in Nature Communications. The article is titled “Museum Samples Reveal Rapid Evolution by Wild Honey Bees Exposed to a Novel Parasite.” “The population appears to have developed genetic resistance.” Dr. Mikheyev and his collaborators at OIST and Cornell University studied the population genetics of the wild colony by comparing the DNA of specimens collected in 1977 with bees collected from the same forest in 2010. To conduct the study, they developed a new DNA analysis tool that works especially well for degraded DNA stored in museum samples. Such a study is extremely rare, especially with bees. Few people collect them, and even fewer collect in a way that is good enough for a population level study. Luckily, Cornell Professor Tom Seeley worked in this area during his Ph.D., and deposited his samples in the Cornell University Insect Collection.