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      Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy

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          Abstract

          In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans.

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          Cutadapt removes adapter sequences from high-throughput sequencing reads

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            STRING v10: protein–protein interaction networks, integrated over the tree of life

            The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness. The STRING database (http://string-db.org) aims to provide a critical assessment and integration of protein–protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10.0 of STRING covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein–protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks.
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              TopHat: discovering splice junctions with RNA-Seq

              Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or ‘reads’, can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites. Results: We mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20 000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development. Availability: TopHat is free, open-source software available from http://tophat.cbcb.umd.edu Contact: cole@cs.umd.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press
                2160-1836
                January 2021
                28 November 2020
                : 11
                : 1
                : jkaa014
                Affiliations
                Department of Biological Sciences, North Carolina State University , Raleigh, NC 27695-7614, USA
                The Department of Entomology and Plant Pathology, North Carolina State University , Raleigh, NC 27695-7613, USA
                The Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University , Greenwood, SC 29646, USA
                The Comparative Medicine Institute, North Carolina State University , Raleigh, NC 27695, USA
                The Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University , Raleigh NC 27695-7244, USA
                Author notes
                Present address: LifeEDIT Therapeutics Inc., 104 T.W. Alexander Dr., Building 20, Research Triangle Park, NC 27709 USA.
                Present address: BioSkryb, 701 W Main St, Suite 200, Durham, NC 27701 USA.
                Corresponding author: Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University, 851 Main Campus Drive, Partners III Building, Room 231, Raleigh NC 27695-7244, USA. macarbon@ 123456ncsu.edu
                Author information
                http://orcid.org/0000-0002-2312-7245
                http://orcid.org/0000-0002-5086-2480
                Article
                jkaa014
                10.1093/g3journal/jkaa014
                7849908
                d17a75ce-9781-4011-8c24-32d16aa515d4
                © The Author(s) 2020. Published by Oxford University Press on behalf of Genetics Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 14 October 2020
                : 16 November 2020
                : 16 November 2020
                Page count
                Pages: 16
                Categories
                Investigation
                AcademicSubjects/SCI01180

                Genetics
                mybpc3,cmybp-c,drosophila melanogaster,feline hcm,hypertrophic cardiomyopathy
                Genetics
                mybpc3, cmybp-c, drosophila melanogaster, feline hcm, hypertrophic cardiomyopathy

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