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muscle RNA-seq

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https://www.readbyqxmd.com/read/28209124/rna-seq-and-metabolomic-analyses-of-akt1-mediated-muscle-growth-reveals-regulation-of-regenerative-pathways-and-changes-in-the-muscle-secretome
#1
Chia-Ling Wu, Yoshinori Satomi, Kenneth Walsh
BACKGROUND: Skeletal muscle is a major regulator of systemic metabolism as it serves as the major site for glucose disposal and the main reservoir for amino acids. With aging, cachexia, starvation, and myositis, there is a preferential loss of fast glycolytic muscle fibers. We previously reported a mouse model in which a constitutively-active Akt transgene is induced to express in a subset of muscle groups leading to the hypertrophy of type IIb myofibers with an accompanying increase in strength...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28209092/fibroblast-growth-factor-1-fgf-1-promotes-adipogenesis-by-downregulation-of-carboxypeptidase-a4-cpa4-a-negative-regulator-of-adipogenesis-implicated-in-the-modulation-of-local-and-systemic-insulin-sensitivity
#2
Jingjing He, Daniel L Chen, Dorit Samocha-Bonet, Kevin R Gillinder, Johanna L Barclay, Graham W Magor, Andrew C Perkins, Jerry R Greenfield, Gongshe Yang, Jonathan P Whitehead
Fibroblast growth factor-1 (FGF-1) promotes differentiation of human preadipocytes into mature adipocytes via modulation of a BMP and Activin Membrane-Bound Inhibitor (BAMBI)/Peroxisome proliferator-activated receptor (PPARγ)-dependent network. Here, we combined transcriptomic and functional investigations to identify novel downstream effectors aligned with complementary analyses of gene expression in human adipose tissue to explore relationships with insulin sensitivity. RNA-Seq and qRT-PCR analysis revealed significant down-regulation of carboxypeptidase A4 (CPA4) following FGF-1 treatment or induction of differentiation of human preadipocytes in a BAMBI/PPARγ-independent manner...
December 2016: Growth Factors
https://www.readbyqxmd.com/read/28204905/transcriptome-assembly-and-identification-of-genes-and-snps-associated-with-growth-traits-in-largemouth-bass-micropterus-salmoides
#3
Shengjie Li, Hao Liu, Junjie Bai, Xinping Zhu
Growth is one of the most crucial economic traits of all aquaculture species, but the molecular mechanisms involved in growth of largemouth bass (Micropterus salmoides) are poorly understood. The objective of this study was to screen growth-related genes of M. salmoides by RNA sequencing and identify growth-related single-nucleotide polymorphism (SNP) markers through a growth association study. The muscle transcriptomes of fast- and slow-growing largemouth bass were obtained using the RNA-Seq technique. A total of 54,058,178 and 54,742,444 qualified Illumina read pairs were obtained for the fast-growing and slow-growing groups, respectively, giving rise to 4,865,236,020 and 4,926,819,960 total clean bases, respectively...
February 15, 2017: Genetica
https://www.readbyqxmd.com/read/28195222/rna-seq-based-detection-of-differentially-expressed-genes-in-the-skeletal-muscle-of-duroc-pigs-with-distinct-lipid-profiles
#4
T F Cardoso, A Cánovas, O Canela-Xandri, R González-Prendes, M Amills, R Quintanilla
We have used a RNA-seq approach to investigate differential expression in the skeletal muscle of swine (N = 52) with divergent lipid profiles i.e. HIGH (increased intramuscular fat and muscle saturated and monounsaturated fatty acid contents, higher serum lipid concentrations and fatness) and LOW pigs (leaner and with an increased muscle polyunsaturated fatty acid content). The number of mRNAs and non-coding RNAs (ncRNAs) expressed in the porcine gluteus medius muscle were 18,104 and 1,558, respectively...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28193870/disruption-of-quercetin-metabolism-by-fungicide-affects-energy-production-in-honey-bees-apis-mellifera
#5
Wenfu Mao, Mary A Schuler, May R Berenbaum
Cytochrome P450 monooxygenases (P450) in the honey bee, Apis mellifera, detoxify phytochemicals in honey and pollen. The flavonol quercetin is found ubiquitously and abundantly in pollen and frequently at lower concentrations in honey. Worker jelly consumed during the first 3 d of larval development typically contains flavonols at very low levels, however. RNA-Seq analysis of gene expression in neonates reared for three days on diets with and without quercetin revealed that, in addition to up-regulating multiple detoxifying P450 genes, quercetin is a negative transcriptional regulator of mitochondrion-related nuclear genes and genes encoding subunits of complexes I, III, IV, and V in the oxidative phosphorylation pathway...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28188264/immortalized-human-myotonic-dystrophy-muscle-cell-lines-to-assess-therapeutic-compounds
#6
Arandel Ludovic, Polay-Espinosa Micaela, Matloka Magdalena, Bazinet Audrey, De Dea Diniz Damily, Naouar Naïra, Rau Frédérique, Jollet Arnaud, Edom-Vovard Frédérique, Mamchaoui Kamel, Tarnopolsky Mark, Puymirat Jack, Battail Christophe, Boland Anne, Deleuze Jean-Francois, Mouly Vincent, Klein F Arnaud, Furling Denis
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are autosomal dominant neuromuscular diseases caused by microsatellite expansions and belong to the family of RNA dominant disorders. Availability of cellular models in which the DM mutation is expressed within its natural context is essential to facilitate efforts to identify new therapeutic compounds. Here we generated immortalized DM1 and DM2 human muscle cell lines that display nuclear RNA-aggregates of expanded repeats, a hallmark of myotonic dystrophy. Selected clones of DM1 and DM2 immortalized myoblasts behave as parental primary myoblasts with a reduced fusion capacity of immortalized DM1 myoblasts when compared to control and DM2 cells...
February 10, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28163789/a-porcine-gluteus-medius-muscle-genome-wide-transcriptome-analysis-dietary-effects-of-omega-6-and-omega-3-fatty-acids-on-biological-mechanisms
#7
Magdalena Ogłuszka, Agnieszka Szostak, Marinus F W Te Pas, Ewa Poławska, Paweł Urbański, Tadeusz Blicharski, Chandra S Pareek, Edyta Juszczuk-Kubiak, Jenelle R Dunkelberger, Jarosław O Horbańczuk, Mariusz Pierzchała
BACKGROUND: The level of omega-6 and omega-3 polyunsaturated fatty acids can affect many cellular systems and function via nuclear receptors or the bioactive lipid regulation of gene expression. The objective of this study was to investigate changes in the muscle transcriptome and the biological functions regulated by increased consumption of omega-3 and omega-6 fatty acids in the pig gluteus medius muscle. RESULTS: The transcriptome of the gluteus medius muscle was studied for pigs subjected to either a control diet or a diet supplemented with linseed and rapeseed oil to increase polyunsaturated fatty acid content...
2017: Genes & Nutrition
https://www.readbyqxmd.com/read/28158238/de-novo-transcriptome-sequencing-and-analysis-of-male-pseudo-male-and-female-yellow-perch-perca-flavescens
#8
Yan-He Li, Han-Ping Wang, Hong Yao, Paul O'Bryant, Dean Rapp, Liang Guo, Eman A Waly
Transcriptome sequencing could facilitate discovery of sex-biased genes, biological pathways and molecular markers, which could help clarify the molecular mechanism of sex determination and sexual dimorphism, and assist with selective breeding in aquaculture. Yellow perch has unique gonad system and sexual dimorphism and is an alternative model to study mechanism of sex determination, sexual dimorphism and sexual selection. In this study, we performed the de novo assembly of yellow perch gonads and muscle transcriptomes by high throughput Illumina sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28132643/comparative-transcriptomics-of-elasmobranchs-and-teleosts-highlight-important-processes-in-adaptive-immunity-and-regional-endothermy
#9
Nicholas J Marra, Vincent P Richards, Angela Early, Steve M Bogdanowicz, Paulina D Pavinski Bitar, Michael J Stanhope, Mahmood S Shivji
BACKGROUND: Comparative genomic and/or transcriptomic analyses involving elasmobranchs remain limited, with genome level comparisons of the elasmobranch immune system to that of higher vertebrates, non-existent. This paper reports a comparative RNA-seq analysis of heart tissue from seven species, including four elasmobranchs and three teleosts, focusing on immunity, but concomitantly seeking to identify genetic similarities shared by the two lamnid sharks and the single billfish in our study, which could be linked to convergent evolution of regional endothermy...
January 30, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28058586/key-genes-in-stomach-adenocarcinoma-identified-via-network-analysis-of-rna-seq-data
#10
Li Shen, Lizhi Zhao, Jiquan Tang, Zhiwei Wang, Weisong Bai, Feng Zhang, Shouli Wang, Weihua Li
RNA-seq data of stomach adenocarcinoma (STAD) were analyzed to identify critical genes in STAD. Meanwhile, relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated. Gene expression data of STAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. Relationships with correlation coefficient > 0.6 were retained in the gene co-expression network. Functional enrichment analysis was performed for the genes in the network with DAVID and KOBASS 2...
January 5, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28057818/dna-methylation-assessment-from-human-slow-and-fast-twitch-skeletal-muscle-fibers
#11
Gwenaelle Begue, Ulrika Raue, Bozena Jemiolo, Scott W Trappe
A new application of the Reduced Representation Bisulfite Sequencing method was developed using low-DNA input to investigate the epigenetic profile of human slow- and fast-twitch skeletal muscle fibers. Successful library construction was completed with as little as 15 ng of DNA and high quality sequencing data were obtained with 32 ng of DNA. Analysis identified 143,160 differentially methylated CpG-sites across 14,046 genes. In both fiber types, selected genes predominantly expressed in slow or fast fibers were hypomethylated, which was supported by the RNA-Seq analysis...
January 5, 2017: Journal of Applied Physiology
https://www.readbyqxmd.com/read/28045018/targeted-rna-seq-profiling-of-splicing-pattern-in-the-dmd-gene-exons-are-mostly-constitutively-spliced-in-human-skeletal-muscle
#12
Anne-Laure Bougé, Eva Murauer, Emmanuelle Beyne, Julie Miro, Jessica Varilh, Magali Taulan, Michel Koenig, Mireille Claustres, Sylvie Tuffery-Giraud
We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) NB transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28026080/transcriptomic-gene-profiling-of-porcine-muscle-tissue-depending-on-histological-properties
#13
Katarzyna Ropka-Molik, Anna Bereta, Kacper Żukowski, Katarzyna Piórkowska, Artur Gurgul, Grzegorz Żak
In pig, the histological profile of muscle tissue, especially the proportion of individual fiber types, is one of the main factors affecting meat quality properties. In the present research, RNA sequencing (RNA-seq) by using next generation sequencing method was applied to estimate the whole gene expression profile of Longissimus lumborum muscle of pigs (Large White breed) differing in the percentage of two fiber types (slow-twitch (type I) fibers and fast-twitch glycolytic (type IIB) fibers). The RNA-seq approach allowed us to identify 355 differentially expressed genes (DEGs) indicated as significant (false discovery rate-adjusted P < 0...
December 27, 2016: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/28011237/estradiol-regulates-expression-of-mirnas-associated-with-myogenesis-in-rainbow-trout
#14
Prasanthi P Koganti, Jian Wang, Beth Cleveland, Hao Ma, Gregory M Weber, Jianbo Yao
17β-Estradiol (E2) is a steroid hormone that negatively affects muscle growth in rainbow trout, but the mechanism associated with this response is not fully understood. To better characterize the effects of E2 on muscle, we identified differentially regulated microRNAs (miRNAs) and muscle atrophy-related transcripts in juvenile rainbow trout exposed to E2. Small RNA-Seq analysis of E2-treated vs. control muscle identified 36 differentially expressed miRNAs including those known to be involved in myogenesis, cell cycle, apoptosis, and cell death...
December 21, 2016: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28008606/derivation-of-marker-gene-signatures-from-human-skin-and-their-use-in-the-interpretation-trancriptional-changes-associated-with-dermatological-disorders
#15
Barbara Bo-Ju Shih, Ajit Johnson Nirmal, Denis John Headon, Arne Nalpon Akbar, Neil Andrew Mabbott, Tom Charles Freeman
Numerous studies have explored the altered transcriptional landscape associated with skin diseases to understand the nature of these disorders. However, data interpretation represents a significant challenge due to a lack of good maker sets for many of the specialised cell types that make up this tissue, whose composition may fundamentally alter during disease. Here we have sought to derive expression signatures that define the various cell types and structures that make up human skin, and demonstrate how they can be used to aid the interpretation of transcriptomic data derived from this organ...
December 23, 2016: Journal of Pathology
https://www.readbyqxmd.com/read/28005961/comparative-transcriptomic-study-of-muscle-provides-new-insights-into-the-growth-superiority-of-a-novel-grouper-hybrid
#16
Ying Sun, Yu Huang, Guojun Hu, Xinhui Zhang, Zhiqiang Ruan, Xiaomeng Zhao, Chuanyu Guo, Zhujing Tang, Xiaofeng Li, Xinxin You, Haoran Lin, Yong Zhang, Qiong Shi
Grouper (Epinephelus spp.) is a group of fish species with great economic importance in Asian countries. A novel hybrid grouper, generated by us and called the Hulong grouper (Hyb), has better growth performance than its parents, E. fuscoguttatus (Efu, ♀) and E. lanceolatus (Ela, ♂). We previously reported that the GH/IGF (growth hormone/insulin-like growth factor) system in the brain and liver contributed to the superior growth of the Hyb. In this study, using transcriptome sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR), we analyzed RNA expression levels of comprehensive genes in the muscle of the hybrid and its parents...
2016: PloS One
https://www.readbyqxmd.com/read/27996962/an-atlas-of-transcriptional-chromatin-accessibility-and-surface-marker-changes-in-human-mesoderm-development
#17
Pang Wei Koh, Rahul Sinha, Amira A Barkal, Rachel M Morganti, Angela Chen, Irving L Weissman, Lay Teng Ang, Anshul Kundaje, Kyle M Loh
Mesoderm is the developmental precursor to myriad human tissues including bone, heart, and skeletal muscle. Unravelling the molecular events through which these lineages become diversified from one another is integral to developmental biology and understanding changes in cellular fate. To this end, we developed an in vitro system to differentiate human pluripotent stem cells through primitive streak intermediates into paraxial mesoderm and its derivatives (somites, sclerotome, dermomyotome) and separately, into lateral mesoderm and its derivatives (cardiac mesoderm)...
December 20, 2016: Scientific Data
https://www.readbyqxmd.com/read/27939935/catalase-deletion-promotes-prediabetic-phenotype-in-mice
#18
Claire Heit, Stephanie Marshall, Surrendra Singh, Xiaoqing Yu, Georgia Charkoftaki, Hongyu Zhao, David J Orlicky, Kristofer S Fritz, David C Thompson, Vasilis Vasiliou
Hydrogen peroxide is produced endogenously and can be toxic to living organisms by inducing oxidative stress and cell damage. However, it has also been identified as a signal transduction molecule. By metabolizing hydrogen peroxide, catalase protects cells and tissues against oxidative damage and may also influence signal transduction mechanisms. Studies suggest that acatalasemic individuals (i.e., those with very low catalase activity) have a higher risk for the development of diabetes. We now report catalase knockout (Cat(-/-)) mice, when fed a normal (6...
February 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27936208/developmental-stage-muscle-and-genetic-type-modify-muscle-transcriptome-in-pigs-effects-on-gene-expression-and-regulatory-factors-involved-in-growth-and-metabolism
#19
Miriam Ayuso, Almudena Fernández, Yolanda Núñez, Rita Benítez, Beatriz Isabel, Ana I Fernández, Ana I Rey, Antonio González-Bulnes, Juan F Medrano, Ángela Cánovas, Clemente J López-Bote, Cristina Óvilo
Iberian pig production includes purebred (IB) and Duroc-crossbred (IBxDU) pigs, which show important differences in growth, fattening and tissue composition. This experiment was conducted to investigate the effects of genetic type and muscle (Longissimus dorsi (LD) vs Biceps femoris (BF)) on gene expression and transcriptional regulation at two developmental stages. Nine IB and 10 IBxDU piglets were slaughtered at birth, and seven IB and 10 IBxDU at four months of age (growing period). Carcass traits and LD intramuscular fat (IMF) content were measured...
2016: PloS One
https://www.readbyqxmd.com/read/27930992/alteration-of-development-and-gene-expression-induced-by-in-ovo-nanoinjection-of-3-hydroxybenzo-c-phenanthrene-into-japanese-medaka-oryzias-latipes-embryos
#20
Kun Chen, Yuki Tsutsumi, Shuhei Yoshitake, Xuchun Qiu, Hai Xu, Yasuyuki Hashiguchi, Masato Honda, Kosuke Tashiro, Kei Nakayama, Takeshi Hano, Nobuo Suzuki, Kazuichi Hayakawa, Yohei Shimasaki, Yuji Oshima
Benzo[c]phenanthrene (BcP) is a highly toxic polycyclic aromatic hydrocarbon (PAHs) found throughout the environment. In fish, it is metabolized to 3-hydroxybenzo[c]phenanthrene (3-OHBcP). In the present study, we observed the effects of 1nM 3-OHBcP on the development and gene expression of Japanese medaka (Oryzias latipes) embryos. Embryos were nanoinjected with the chemical after fertilization. Survival, developmental stage, and heart rate of the embryos were observed, and gene expression differences were quantified by messenger RNA sequencing (mRNA-Seq)...
January 2017: Aquatic Toxicology
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