Sex-biased mouse liver lincRNAs: validation and impact of mouse knockout models that perturb hepatic growth signaling

Sexual dimorphism has a broad impact on human health and disease, including autoimmune diseases, cardiovascular diseases, and liver diseases, specifically hepatocellular carcinoma. Pituitary growth hormone (GH) secretion has a major impact on sex differences in the liver. Previous studies show that signal transducer and activator transcription factor 5b (STAT5b) impacts male-biased gene expression. Somatostatin (SST) inhibits the release of GH, and this in turn impacts STAT5b activity and GH regulation feedback. Long intergenic noncoding RNAs (lincRNAs), which do not encode proteins, have various roles in diverse biological processes including cell differentiation, chromatin remodeling, and gene regulation. In the present study, we discovered lincRNAs in mouse liver using RNA-seq datasets, and identified male and female-biased lincRNAs. Moreover, we validated the sex-specificity of lincRNAs by performing real time PCR (qPCR) and analyzing UCSC genome browser screen shots by comparing male and female expression patterns. We validated the sex-specificities of 22 lincRNAs. Moreover, we investigated whether pituitary GH secretion impacts the regulation of these sex-biased lincRNAs in the same manner as seen in sex-biased protein coding RefSeq genes. qPCR experiments investigated the impact of GH secretion by using SST and STAT5b knockout mouse models, and hypophysectomized, and intermittent (pulsatile) GH-treated mice. Our results show that pituitary GH secretion impacts the regulation of sex-biased lincRNAs. The last part of this thesis investigates the molecular and functional role of sexbiased lincRNAs by using The Database for Annotation, Visualization, and Integrated Discovery (DAVID)

eGenomics: Cataloguing Our Complete Genome Collection III

This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS) specification (v1.1), consensus on a variety of features to be added to the Genome Catalogue (GCat), agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates) and working towards a single, global list of all public genomes and metagenomes

Report of the 13th Genomic Standards Consortium Meeting, Shenzhen, China, March 4–7, 2012

This report details the outcome of the 13th Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5–7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundatio