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muscle RNA-seq

Scott D Wagner, Tomofumi Kurobe, Bruce G Hammock, Chelsea H Lam, Gary Wu, Natalia Vasylieva, Shirley J Gee, Bruce D Hammock, Swee J Teh
Pesticides in urban runoff are a major source of pollutants in aquatic ecosystems. Fipronil, a phenylpyrazole insecticide, found in structural pest control products, turf grass control, and home pet flea medication, has recently increased in use and is commonly detected in urban runoff. However, little is known about the effects of fipronil on aquatic organisms at early developmental stages. Here, we evaluated toxicity of fipronil to embryos of Japanese Medaka (Oryzias latipes, Qurt strain) using a high-throughput 96-well plate toxicity test...
January 2017: Chemosphere
Yi-Ying Chiou, Yanyan Yang, Naim Rashid, Rui Ye, Christopher P Selby, Aziz Sancar
The mammalian circadian clock is based on a transcription-translation feedback loop (TTFL) consolidated by secondary loops. In the primary TTFL, the circadian locomotor output cycles kaput (CLOCK)-brain and muscle Arnt-like protein-1 (BMAL1) heterodimer acts as the transcriptional activator, and Cryptochrome (CRY) and Period (PER) proteins function as repressors. PER represses by displacing CLOCK-BMAL1 from promoters in a CRY-dependent manner. Interestingly, genes with complex promoters may either be repressed or de-repressed by PER, depending on the particular promoter regulatory elements...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Limin Sun, Man Bai, Lujie Xiang, Guishan Zhang, Wei Ma, Huaizhi Jiang
The Qianhua Mutton Merino (QHMM) is a new sheep (Ovis aries) variety with better meat performance compared with the traditional local variety Small Tail Han (STH) sheep. We aimed to evaluate the transcriptome regulators associated with muscle growth and development between the QHMM and STH. We used RNA-Seq to obtain the transcriptome profiles of the longissimus muscle from the QHMM and STH. The results showed that 960 genes were differentially expressed (405 were up-regulated and 555 were down-regulated). Among these, 463 differently expressed genes (DEGs) were probably associated with muscle growth and development and were involved in biological processes such as skeletal muscle tissue development and muscle cell differentiation; molecular functions such as catalytic activity and oxidoreductase activity; cellular components such as mitochondrion and sarcoplasmic reticulum; and pathways such as metabolic pathways and citrate cycle...
2016: Scientific Reports
Alyssa Charrier, Li Wang, Erin J Stephenson, Siddharth V Ghanta, Chih-Wei Ko, Colleen M Croniger, Dave Bridges, David A Buchner
The peroxisome proliferator-activated receptor (PPAR) family of nuclear receptors are central to the pathophysiology and treatment of metabolic disease through their ability to regulate the expression of genes involved in glucose homeostasis, adipogenesis, and lipid metabolism. However, the mechanism by which PPAR is regulated remains incompletely understood. We generated a transgenic mouse strain (ZFP-TG) that overexpressed Zfp407 primarily in muscle and heart. Transcriptome analysis by RNA-Seq identified 1,300 differentially expressed genes in the muscle of ZFP-TG mice, among which PPAR target genes were significantly enriched...
September 13, 2016: American Journal of Physiology. Endocrinology and Metabolism
Adam G Ciezarek, Luke T Dunning, Catherine S Jones, Leslie R Noble, Emily Humble, Sergio S Stefanni, Vincent Savolainen
Despite 400-450 million years of independent evolution, a strong phenotypic convergence has occurred between two groups of fish: tunas and lamnid sharks. This convergence is characterized by centralization of red muscle, a distinctive swimming style (stiffened body powered through tail movements) and elevated body temperature (endothermy). Furthermore, both groups demonstrate elevated white muscle metabolic capacities. All these traits are unusual in fish and more likely evolved to support their fast-swimming, pelagic, predatory behavior...
October 5, 2016: Genome Biology and Evolution
Xiaomei Sun, Mingxun Li, Yujia Sun, Hanfang Cai, Xianyong Lan, Yongzhen Huang, Yueyu Bai, Xinglei Qi, Hong Chen
Pervasive transcription of the mammalian genome generates numerous long noncoding RNAs (lncRNAs), which are of crucial importance in diverse biological processes. Recent advances in high throughput sequencing technology have helped to accelerate the pace of lncRNAs discovery. However, no study on the overall expression patterns of lncRNAs during muscle development has been conducted. We reported here the first analysis of lncRNAs landscape in bovine embryonic, neonatal and adult skeletal muscle using Ribo-Zero RNA-Seq, a technology which can capture both poly(A)(+) and poly(A)(-) transcripts...
August 30, 2016: Biochimica et Biophysica Acta
Weihua Zeng, Shan Jiang, Xiangduo Kong, Nicole El-Ali, Alexander R Ball, Christopher I-Hsing Ma, Naohiro Hashimoto, Kyoko Yokomori, Ali Mortazavi
Myoblasts are precursor skeletal muscle cells that differentiate into fused, multinucleated myotubes. Current single-cell microfluidic methods are not optimized for capturing very large, multinucleated cells such as myotubes. To circumvent the problem, we performed single-nucleus transcriptome analysis. Using immortalized human myoblasts, we performed RNA-seq analysis of single cells (scRNA-seq) and single nuclei (snRNA-seq) and found them comparable, with a distinct enrichment for long non-coding RNAs (lncRNAs) in snRNA-seq...
August 26, 2016: Nucleic Acids Research
Xiaopeng Ma, Ge Zhan, Monica C Sleumer, Siyu Chen, Weihong Liu, Michael Q Zhang, Xiao Liu
Current approaches to profiling tissue-specific gene expression in C. elegans require delicate manipulation and are difficult under certain conditions, e.g. from dauer or aging worms. We have developed an easy and robust method for tissue-specific RNA-seq by taking advantage of the endogenous trans-splicing process. In this method, transgenic worms are generated in which a spliced leader (SL) RNA gene is fused with a sequence tag and driven by a tissue-specific promoter. Only in the tissue of interest, the tagged SL RNA gene is transcribed and then trans-spliced onto mRNAs...
August 23, 2016: Nucleic Acids Research
Sujatha Jagannathan, Sean Shadle, Rebecca Resnick, Lauren Snider, Rabi N Tawil, Silvère M van der Maarel, Robert K Bradley, Stephen J Tapscott
Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of the double-homeodomain transcription factor DUX4 in skeletal muscle cells. Many different cell culture models have been developed to study the pathophysiology of FSHD, frequently based on endogenous expression of DUX4 in FSHD cells or by mis-expression of DUX4 in control human muscle cells. Although results generated using each model are generally consistent, differences have also been reported, making it unclear which model(s) faithfully recapitulate DUX4 and FSHD biology...
August 15, 2016: Human Molecular Genetics
Bao Yi, Liang Chen, Renna Sa, Ruqing Zhong, Huan Xing, Hongfu Zhang
BACKGROUND: High concentrations of atmospheric ammonia are one of the key environmental stressors affecting broiler production performance, which causes remarkable economic losses as well as potential welfare problems of the broiler industry. Previous reports demonstrated that high levels of ammonia altered body fat distribution and meat quality of broilers. However, the molecular mechanisms and metabolic pathways in breast muscle altered by high concentrations of ambient ammonia exposure on broilers are still unknown...
2016: BMC Genomics
Oliver Rackham, Jakob D Busch, Stanka Matic, Stefan J Siira, Irina Kuznetsova, Ilian Atanassov, Judith A Ermer, Anne-Marie J Shearwood, Tara R Richman, James B Stewart, Arnaud Mourier, Dusanka Milenkovic, Nils-Göran Larsson, Aleksandra Filipovska
The regulation of mitochondrial RNA processing and its importance for ribosome biogenesis and energy metabolism are not clear. We generated conditional knockout mice of the endoribonuclease component of the RNase P complex, MRPP3, and report that it is essential for life and that heart and skeletal-muscle-specific knockout leads to severe cardiomyopathy, indicating that its activity is non-redundant. Transcriptome-wide parallel analyses of RNA ends (PARE) and RNA-seq enabled us to identify that in vivo 5' tRNA cleavage precedes 3' tRNA processing, and this is required for the correct biogenesis of the mitochondrial ribosomal subunits...
August 16, 2016: Cell Reports
Rachel E Foong, Anthony Bosco, Niamh M Troy, Shelley Gorman, Prue H Hart, Anthony Kicic, Graeme R Zosky
Vitamin D deficiency is associated with asthma risk. Vitamin D deficiency may enhance the inflammatory response, and we have previously shown that airway remodeling and airway hyperresponsiveness is increased in vitamin D-deficient mice. In this study, we hypothesize that vitamin D deficiency would exacerbate house dust mite (HDM)-induced inflammation and alterations in lung structure and function. A BALB/c mouse model of vitamin D deficiency was established by dietary manipulation. Responsiveness to methacholine, airway smooth muscle (ASM) mass, mucus cell metaplasia, lung and airway inflammation, and cytokines in bronchoalveolar lavage (BAL) fluid were assessed...
September 1, 2016: American Journal of Physiology. Lung Cellular and Molecular Physiology
M L Hoffman, K N Peck, J L Wegrzyn, S A Reed, S A Zinn, K E Govoni
Poor maternal nutrition during gestation can result in reduced muscle mass and increased adiposity of the muscle tissue in the offspring. This can have long-lasting consequences on offspring health and productivity. However, the mechanisms by which poor maternal nutrition affects postnatal muscle development are poorly understood. We hypothesized that poor maternal nutrition during gestation would alter expression of key pathways and genes involved in growth, development, and maintenance of the muscle of lambs...
July 2016: Journal of Animal Science
Ping Wu, Yulong Li, Jia Cheng, Lin Chen, Ming Zeng, Yuanan Wu, Jianhua Wang, Jianshe Zhang, Wuying Chu
The characterization of the expression and regulation of growth-related genes in the muscles of Chinese perch is of great interest to aquaculturists because of the commercial value of the species. The transcriptome annotation of the skeletal muscles is a crucial step in muscle growth-related gene analysis. In this study, we generated 52 504 230 reads of mRNA sequence data from the fast muscles of the Chinese perch by using Solexa/Illumina RNA-seq. Twenty-one amino acid transporter genes were annotated by searching protein and gene ontology databases, and postprandial changes in their transcript abundance were assayed after administering a single satiating meal to Chinese perch juveniles (body mass, approximately 100 g), following fasting for 1 week...
2016: PloS One
Robert Güth, Alexander Chaidez, Manoj P Samanta, Graciela A Unguez
Skeletal muscle is distinguished from other tissues on the basis of its shape, biochemistry, and physiological function. Based on mammalian studies, fiber size, fiber types, and gene expression profiles are regulated, in part, by the electrical activity exerted by the nervous system. To address whether similar adaptations to changes in electrical activity in skeletal muscle occur in teleosts, we studied these phenotypic properties of ventral muscle in the electric fish Sternopygus macrurus following 2 and 5 days of electrical inactivation by spinal transection...
September 1, 2016: Physiological Genomics
Jennifer Cj Chen, Oliver D King, Yuanfan Zhang, Nicholas P Clayton, Carrie Spencer, Bruce M Wentworth, Charles P Emerson, Kathryn R Wagner
Derepression of DUX4 in skeletal muscle has emerged as a likely cause of pathology in facioscapulohumeral muscular dystrophy (FSHD). Here we report on the use of antisense phosphorodiamidate morpholino oligonucleotides to suppress DUX4 expression and function in FSHD myotubes and xenografts. The most effective was phosphorodiamidate morpholino oligonucleotide FM10, which targets the polyadenylation signal of DUX4. FM10 had no significant cell toxicity, and RNA-seq analyses of FSHD and control myotubes revealed that FM10 down-regulated many transcriptional targets of DUX4, without overt off-target effects...
August 2016: Molecular Therapy: the Journal of the American Society of Gene Therapy
Mrinmoy Ghosh, Hyun-Woo Cho, Jeong-Woong Park, Jae-Young Choi, Young-Hwa Chung, Neelesh Sharma, Amit Kumar Singh, Nam Eun Kim, Raj Kumar Mongre, Do Huynh, Zhang Jiao Jiao, Kyoung Tag Do, Hak-Kyo Lee, Ki-Duk Song, Byung-Wook Cho, DongKee Jeong
The athletic abilities of the horse serve as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. We analyzed differentially expressed genes in triceps brachii muscle tissues collected from Eonjena Taeyang and Jigusang Seryeok Thoroughbred horses and their co-expression networks in a large-scale RNA-sequence dataset comparing expression before and after exercise. High-quality horse transcriptome data were generated, with over 22 million 90-bp pair-end reads...
June 28, 2016: Applied Biochemistry and Biotechnology
Juhui Qiu, Xiaoying Fan, Yixia Wang, Hongbin Jin, Yixiao Song, Yang Han, Shenghong Huang, Yaping Meng, Fuchou Tang, Anming Meng
Hematopoietic stem cells (HSCs) replenish all types of blood cells. It is debating whether HSCs in adults solely originate from the aorta-gonad-mesonephros (AGM) region, more specifically, the dorsal aorta, during embryogenesis. Here, we report that somite hematopoiesis, a previously unwitnessed hematopoiesis, can generate definitive HSCs (dHSCs) in zebrafish. By transgenic lineage tracing, we found that a subset of cells within the forming somites emigrate ventromedially and mix with lateral plate mesoderm-derived primitive hematopoietic cells before the blood circulation starts...
August 2016: Journal of Molecular Cell Biology
P A McGettigan, J A Browne, S D Carrington, M A Crowe, T Fair, N Forde, B J Loftus, A Lohan, P Lonergan, K Pluta, S Mamo, A Murphy, J Roche, S W Walsh, C J Creevey, B Earley, S Keady, D A Kenny, D Matthews, M McCabe, D Morris, A O'Loughlin, S Waters, M G Diskin, A C O Evans
To compare gene expression among bovine tissues, large bovine RNA-seq datasets were used, comprising 280 samples from 10 different bovine tissues (uterine endometrium, granulosa cells, theca cells, cervix, embryos, leucocytes, liver, hypothalamus, pituitary, muscle) and generating 260 Gbases of data. Twin approaches were used: an information-theoretic analysis of the existing annotated transcriptome to identify the most tissue-specific genes and a de-novo transcriptome annotation to evaluate general features of the transcription landscape...
2016: Reproduction, Fertility, and Development
Wei Xiong, Jia Li, Erquan Zhang, Huanwei Huang
Transcription factors primarily regulate gene expression by determining which genes are transcribed at initiation and the extent to which those genes are transcribed during elongation. Brain and muscle Arnt-like protein-1 (BMAL1, ARNTL) is a well-characterized key activator of genes related to circadian rhythm that can specifically bind promoter boxes (E-boxes), cis-acting DNA elements. Previous genetic and biochemical studies have shown that BMAL1 regulates the circadian clock feedback loop, but the role of BMAL1 in transcription is still unclear...
May 13, 2016: Biochemical and Biophysical Research Communications
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