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muscle RNA-seq

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https://www.readbyqxmd.com/read/29138211/transcriptome-sequencing-of-the-naked-mole-rat-heterocephalus-glaber-and-identification-of-hypoxia-tolerance-genes
#1
Bang Xiao, Li Li, Chang Xu, Shanmin Zhao, Lifang Lin, Jishuai Cheng, Wenjing Yang, Wei Cong, Guanghan Kan, Shufang Cui
The naked mole rat (NMR; Heterocephalus glaber) is a small rodent species found in regions of Kenya, Ethiopia and Somalia. It has a high tolerance for hypoxia and is thus, considered one of the most important natural models for studying hypoxia tolerance mechanisms. The various mechanisms underlying the NMR's hypoxia tolerance are beginning to be understood at different levels of organization, and next-generation sequencing methods promise to expand this understanding to the level of gene expression. In this study, we examined the sequence and transcript abundance data of the muscle transcriptome of NMRs exposed to hypoxia using the Illumina HiSeq 2500 system to clarify the possible genomic adaptive responses to the hypoxic underground surroundings...
November 14, 2017: Biology Open
https://www.readbyqxmd.com/read/29128925/transcriptome-profile-analysis-reveals-cardiotoxicity-of-maduramicin-in-primary-chicken-myocardial-cells
#2
Xiuge Gao, Lin Peng, Xiangchun Ruan, Xin Chen, Hui Ji, Junxiao Ma, Han Ni, Shanxiang Jiang, Dawei Guo
Maduramicin, an excellent ionophore antibiotic, is extensively used to control coccidiosis in poultry. Numerous maduramicin intoxications have been reported in farm animal and human due to its relatively narrow safety range, with necrosis or degeneration of cardiac and skeletal muscles as hallmark. To date, the mechanisms of maduramicin-induced cardiotoxicity remain unclear in chicken and other animals. Maduramicin (5 µg/mL)-treated primary chicken myocardial cells were used for RNA sequencing (RNA-Seq) and bioinformatics analysis in this study...
November 11, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/29127356/a-transcriptomic-study-of-myogenic-differentiation-under-the-overexpression-of-ppar%C3%AE-by-rna-seq
#3
Kan He, Guoying Wu, Wen-Xing Li, Daogang Guan, Wenwen Lv, Mengting Gong, Shoudong Ye, Aiping Lu
To study the cellular and molecular function of peroxisome proliferator-activated receptor γ (PPARγ) in skeletal muscle differentiation, we have generated inducible gain-of-function to overexpress PPARγ in C2C12 myoblasts. In order to identify PPARγ targets, RNA sequencing (RNA-seq) was used to evaluate and quantify the transcriptomes and expression patterns during myogenic differentiation under the overexpression of PPARγ. The formation of myotubes and the expression of muscle-specific myogenic genes such as MyoD and MyoG may be inhibited by PPARγ overexpression...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29126880/a-heart-enriched-antisense-long-non-coding-rna-regulates-the-balance-between-cardiac-and-skeletal-muscle-triadin
#4
Lu Zhang, Antonio Salgado-Somoza, Melanie Vausort, Przemyslaw Leszek, Yvan Devaux
Non-coding RNAs play major roles in cardiac pathophysiology. Recent studies reported that long non-coding RNAs (lncRNAs) are dysregulated in the failing heart, but how they contribute to heart failure development is unclear. In this study, we aimed to identify heart-enriched lncRNAs and investigate their regulation and function in the failing heart. RESULTS: Analysis of a RNA-seq dataset of 15 Caucasian tissues allowed the identification of 415 heart-enriched lncRNAs. Fifty-three lncRNAs were located on the genome in close vicinity to protein-coding genes associated with cardiac function and disease...
November 7, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29121865/temporally-distinct-transcriptional-regulation-of-myocyte-dedifferentiation-and-myofiber-growth-during-muscle-regeneration
#5
Ke'ale W Louie, Alfonso Saera-Vila, Phillip E Kish, Justin A Colacino, Alon Kahana
BACKGROUND: Tissue regeneration requires a series of steps, beginning with generation of the necessary cell mass, followed by cell migration into damaged area, and ending with differentiation and integration with surrounding tissues. Temporal regulation of these steps lies at the heart of the regenerative process, yet its basis is not well understood. The ability of zebrafish to dedifferentiate mature "post-mitotic" myocytes into proliferating myoblasts that in turn regenerate lost muscle tissue provides an opportunity to probe the molecular mechanisms of regeneration...
November 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29120091/running-wheel-activity-delays-mitochondrial-respiratory-flux-decline-in-aging-mouse-muscle-via-a-post-transcriptional-mechanism
#6
Sarah Stolle, Jolita Ciapaite, Aaffien C Reijne, Alzbeta Talarovicova, Justina C Wolters, Raúl Aguirre-Gamboa, Pieter van der Vlies, Kim de Lange, Pieter B Neerincx, Gerben van der Vries, Patrick Deelen, Morris A Swertz, Yang Li, Rainer Bischoff, Hjalmar P Permentier, Peter L Horvatovitch, Albert K Groen, Gertjan van Dijk, Dirk-Jan Reijngoud, Barbara M Bakker
Loss of mitochondrial respiratory flux is a hallmark of skeletal muscle aging, contributing to a progressive decline of muscle strength. Endurance exercise alleviates the decrease in respiratory flux, both in humans and in rodents. Here, we dissect the underlying mechanism of mitochondrial flux decline by integrated analysis of the molecular network. Mice were given a lifelong ad libitum low-fat or high-fat sucrose diet and were further divided into sedentary and running-wheel groups. At 6, 12, 18 and 24 months, muscle weight, triglyceride content and mitochondrial respiratory flux were analysed...
November 9, 2017: Aging Cell
https://www.readbyqxmd.com/read/29108556/long-term-thermal-manipulation-in-the-late-incubation-period-can-inhibit-breast-muscle-development-by-activating-endoplasmic-reticulum-stress-in-duck-anasplatyrhynchos-domestica
#7
Xinxin Li, Jiamin Qiu, Hehe Liu, Yushi Wang, Jiwei Hu, Xiang Gan, Jiwen Wang
Poultry embryos are easily affected by environmental changings during incubation, thereinto, the temperature modification is the most important one, but the mechanism of temperature effects on bird eggs is not clear. By using RNA-seq, we have previously found that endoplasmic reticulum stress (ERS) may involve in regulating embryonic muscle development of duck under the influence of temperature alteration. To further clarify the role of ERS in the effect, in the present study, we detected the impact of increasing the incubation temperature by 1℃ during embryonic days 10-27 (E10-27) on the development of duck embryos, and investigated the changes in mRNA and protein expression of ERS marker genes and muscle-related genes under the thermal manipulation (TM)...
December 2017: Journal of Thermal Biology
https://www.readbyqxmd.com/read/29102726/differential-gene-expression-analysis-in-ageing-muscle-and-drug-discovery-perspectives
#8
REVIEW
Aicha Melouane, Abdelaziz Ghanemi, Simon Aubé, Mayumi Yoshioka, Jonny St-Amand
Identifying therapeutic target genes represents the key step in functional genomics-based therapies. Within this context, the disease heterogeneity, the exogenous factors and the complexity of genomic structure and function represent important challenges. The functional genomics aims to overcome such obstacles via identifying the gene functions and therefore highlight disease-causing genes as therapeutic targets. Genomic technologies promise to reshape the research on ageing muscle, exercise response and drug discovery...
November 1, 2017: Ageing Research Reviews
https://www.readbyqxmd.com/read/29093487/micrornas-promote-skeletal-muscle-differentiation-of-mesodermal-ipsc-derived-progenitors
#9
Giorgia Giacomazzi, Bryan Holvoet, Sander Trenson, Ellen Caluwé, Bojana Kravic, Hanne Grosemans, Álvaro Cortés-Calabuig, Christophe M Deroose, Danny Huylebroeck, Said Hashemolhosseini, Stefan Janssens, Elizabeth McNally, Mattia Quattrocelli, Maurilio Sampaolesi
Muscular dystrophies (MDs) are often characterized by impairment of both skeletal and cardiac muscle. Regenerative strategies for both compartments therefore constitute a therapeutic avenue. Mesodermal iPSC-derived progenitors (MiPs) can regenerate both striated muscle types simultaneously in mice. Importantly, MiP myogenic propensity is influenced by somatic lineage retention. However, it is still unknown whether human MiPs have in vivo potential. Furthermore, methods to enhance the intrinsic myogenic properties of MiPs are likely needed, given the scope and need to correct large amounts of muscle in the MDs...
November 1, 2017: Nature Communications
https://www.readbyqxmd.com/read/29073106/cardiovascular-homeostasis-dependence-on-micu2-a-regulatory-subunit-of-the-mitochondrial-calcium-uniporter
#10
Alexander G Bick, Hiroko Wakimoto, Kimberli J Kamer, Yasemin Sancak, Olga Goldberger, Anna Axelsson, Daniel M DeLaughter, Joshua M Gorham, Vamsi K Mootha, J G Seidman, Christine E Seidman
Comparative analyses of transcriptional profiles from humans and mice with cardiovascular pathologies revealed consistently elevated expression of MICU2, a regulatory subunit of the mitochondrial calcium uniporter complex. To determine if MICU2 expression was cardioprotective, we produced and characterized Micu2(-/-) mice. Mutant mice had left atrial enlargement and Micu2(-/-) cardiomyocytes had delayed sarcomere relaxation and cytosolic calcium reuptake kinetics, indicating diastolic dysfunction. RNA sequencing (RNA-seq) of Micu2(-/-) ventricular tissues revealed markedly reduced transcripts encoding the apelin receptor (Micu2(-/-) vs...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29044196/exercise-and-high-fat-feeding-remodel-transcript-metabolite-interactive-networks-in-mouse-skeletal-muscle
#11
Joaquín Pérez-Schindler, Aditi Kanhere, Lindsay Edwards, J William Allwood, Warwick B Dunn, Simon Schenk, Andrew Philp
Enhanced coverage and sensitivity of next-generation 'omic' platforms has allowed the characterization of gene, metabolite and protein responses in highly metabolic tissues, such as, skeletal muscle. A limitation, however, is the capability to determine interaction between dynamic biological networks. To address this limitation, we applied Weighted Analyte Correlation Network Analysis (WACNA) to RNA-seq and metabolomic datasets to identify correlated subnetworks of transcripts and metabolites in response to a high-fat diet (HFD)-induced obesity and/or exercise...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29024706/identification-of-circular-rnas-in-human-aortic-valves
#12
Jianle Chen, Jun Wang, Yun Jiang, Weidong Gu, Buqing Ni, Haoliang Sun, Wanjun Gu, Liang Chen, Yongfeng Shao
With the wide application of RNA-Seq technology, thousands of circular RNAs (circRNAs) have been identified in different type of tissues and cells in many organisms, but little is known on the human aortic valve expressed circRNAs. In this study, we identified all circRNAs in two calcified human aortic valves, and characterized the features of all circRNAs. A total of 5476 circRNAs were identified in human aortic valves, including 1412 (25.79%) aortic valve specific circRNAs. Next, we showed that most aortic valve specific circRNAs were derived from the exonic regions of their host genes, and majority of the host genes contained less than three circRNAs...
October 9, 2017: Gene
https://www.readbyqxmd.com/read/29024177/differential-regulation-of-two-flna-transcripts-explains-some-of-the-phenotypic-heterogeneity-in-the-loss-of-function-filaminopathies
#13
Zandra A Jenkins, Alison Macharg, Cheng-Yee Chang, Margriet van Kogelenberg, Tim Morgan, Sophia Frentz, Wenhua Wei, Jacek Pilch, Mark Hannibal, Nicola Foulds, George McGillivray, Richard J Leventer, Sixto García-Miñaúr, Stuart Sugito, Scott Nightingale, David M Markie, Tracy Dudding, Raj P Kapur, Stephen P Robertson
Loss-of-function mutations in the X-linked gene FLNA can lead to abnormal neuronal migration, vascular and cardiac defects, and congenital intestinal pseudo-obstruction (CIPO), the latter characterized by anomalous intestinal smooth muscle layering. Survival in male hemizygotes for such mutations is dependent on retention of residual FLNA function but it is unclear why a subgroup of males with mutations in the 5' end of the gene can present with CIPO alone. Here, we demonstrate evidence for the presence of two FLNA isoforms differing by 28 residues at the N-terminus initiated at ATG(+1) and ATG(+82) ...
October 12, 2017: Human Mutation
https://www.readbyqxmd.com/read/28993898/dynamic-transcriptomic-analysis-in-hircine-longissimus-dorsi-muscle-from-fetal-to-neonatal-development-stages
#14
Siyuan Zhan, Wei Zhao, Tianzeng Song, Yao Dong, Jiazhong Guo, Jiaxue Cao, Tao Zhong, Linjie Wang, Li Li, Hongping Zhang
Muscle growth and development from fetal to neonatal stages consist of a series of delicately regulated and orchestrated changes in expression of genes. In this study, we performed whole transcriptome profiling based on RNA-Seq of caprine longissimus dorsi muscle tissue obtained from prenatal stages (days 45, 60, and 105 of gestation) and neonatal stage (the 3-day-old newborn) to identify genes that are differentially expressed and investigate their temporal expression profiles. A total of 3276 differentially expressed genes (DEGs) were identified (Q value < 0...
October 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28981706/insights-into-interplay-between-rexinoid-signaling-and-myogenic-regulatory-factor-associated-chromatin-state-in-myogenic-differentiation
#15
Munerah Hamed, Saadia Khilji, Katherine Dixon, Alexandre Blais, Ilya Ioshikhes, Jihong Chen, Qiao Li
While skeletal myogenesis is tightly coordinated by myogenic regulatory factors including MyoD and myogenin, chromatin modifications have emerged as vital mechanisms of myogenic regulation. We have previously established that bexarotene, a clinically approved agonist of retinoid X receptor (RXR), promotes the specification and differentiation of skeletal muscle lineage. Here, we examine the genome-wide impact of rexinoids on myogenic differentiation through integral RNA-seq and ChIP-seq analyses. We found that bexarotene promotes myoblast differentiation through the coordination of exit from the cell cycle and the activation of muscle-related genes...
September 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28968511/rna-seq-analysis-of-the-head-kidney-transcriptome-response-to-handling-stress-in-the-red-cusk-eel-genypterus-chilensis
#16
Víctor Aballai, Jorge E Aedo, Jonathan Maldonado, Macarena Bastias-Molina, Herman Silva, Claudio Meneses, Sebastian Boltaña, Ariel Reyes, Alfredo Molina, Juan Antonio Valdés
Stress is a primary contributing factor of fish disease and mortality in aquaculture. We have previously reported that the red cusk-eel (Genypterus chilensis), an important farmed marine fish, demonstrates a handling-stress response that results in increased juvenile mortality, which is mainly associated with skeletal muscle atrophy and liver steatosis. To better understand the systemic effects of stress on red cusk-eel immune-related gene expression, the present study assessed the transcriptomic head-kidney response to handling-stress...
September 20, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28916639/small-rna-seq-during-acute-maximal-exercise-reveal-rnas-involved-in-vascular-inflammation-and-cardiometabolic-health
#17
Ravi Shah, Ashish S Yeri, Avash Das, Amanda Courtright-Lim, Olivia Ziegler, Ernest Gervino, Jeffrey Ocel, Pablo Quintero Pinzon, Luke Wooster, Cole Shields Bailey, Kahraman Tanriverdi, Lea Beaulieu, Jane E Freedman, Ionita Ghiran, Gregory D Lewis, Kendall Van Keuren-Jensen, Saumya Das
OBJECTIVE: Exercise improves cardiometabolic and vascular function, though mechanisms remain unclear. Our objective was to demonstrate the diversity of circulating extracellular RNA (ex-RNA) release during acute exercise in humans and its relevance to exercise-mediated benefits on vascular inflammation. Approach and Results: We performed plasma small RNA sequencing (RNA-seq) in 26 individuals undergoing symptom-limited maximal treadmill exercise, with replication of our top candidate miRNA in a separate cohort of 59 individuals undergoing bicycle ergometry...
September 15, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28915060/long-non-coding-rna-lnrpt-is-regulated-by-pdgf-bb-and-modulates-proliferation-of-pulmonary-artery-smooth-muscle-cells
#18
Jidong Chen, Jiao Guo, Xiaolei Cui, Yan Dai, Zhixiong Tang, Junle Qu, J Usha Raj, Qinghua Hu, Deming Gou
Pulmonary artery hypertension (PAH) is a rare and fatal disorder with extensive remodeling of pulmonary arteries mediated by hyperproliferation of pulmonary artery smooth muscle cell (PASMC). Aberrant platelet-derived growth factor (PDGF) activity can lead to hyperproliferation of PASMC, however, little is known about the role of long noncoding RNA (lncRNA) in this process. Using RNA sequencing (RNA-seq), we identified 725 lncRNAs in rat PASMC (RPASMC), 95 of which were expressed differentially in response to PDGF-BB treatment...
September 15, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28893664/single-cell-transcriptome-analysis-of-muscle-satellite-cells-reveals-widespread-transcriptional-heterogeneity
#19
Dong Seong Cho, Jason D Doles
Tissue specific stem cells are indispensable contributors to adult tissue maintenance, repair, and regeneration. In skeletal muscle, satellite cells (SCs) are the resident muscle stem cell population and are required to maintain skeletal muscle homeostasis throughout life. Increasing evidence suggests that SCs are a heterogeneous cell population with substantial biochemical and functional diversity. A major limitation in the field is an incomplete understanding of the nature and extent of this cellular heterogeneity...
December 15, 2017: Gene
https://www.readbyqxmd.com/read/28886574/comparative-transcriptome-analysis-of-fast-twitch-muscle-and-slow-twitch-muscle-in-takifugu-rubripes
#20
Kailun Gao, Zhicheng Wang, Xiaoxu Zhou, Haoze Wang, Derong Kong, Chen Jiang, Xiuli Wang, Zhiqiang Jiang, Xuemei Qiu
Fast twitch muscle and slow twitch muscle are two important organs of Takifugu rubripes. Both tissues are of ectodermic origin, and the differences between the two muscle fibers reflect the differences in their myofibril protein composition and molecular structure. In order to identify and characterize the gene expression profile in the two muscle fibers of T. rubripes, we generated 54 million and 44 million clean reads from the fast twitch muscle and slow twitch muscle, respectively, using RNA-Seq and identified a total of 580 fast-muscle-specific genes, 1533 slow-muscle-specific genes and 11,806 genes expressed by both muscles...
August 30, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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