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muscle RNA-seq

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https://www.readbyqxmd.com/read/29341863/distinct-gene-signatures-predict-insulin-resistance-in-young-mice-with-high-fat-diet-induced-obesity
#1
Katherine Chen, Alice Jih, Olivia Osborn, Sarah T Kavaler, Wenxian Fu, Roman Sasik, Rintaro Saito, Jane J Kim
Highly inbred C57BL/6 mice show wide variation in their degree of insulin resistance in response to diet-induced obesity even though they are almost genetically identical. Here we employed transcriptional profiling by RNA sequencing (RNA-Seq) of visceral adipose tissue (VAT) and liver in young mice to determine how gene expression patterns correlate with the later development of high-fat diet (HFD)-induced insulin resistance in adulthood. To accomplish this goal, we partially removed and banked tissues from pubertal mice...
January 8, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29324704/dissection-of-myogenic-differentiation-signatures-in-chickens-by-rna-seq-analysis
#2
Tingting Li, Genxi Zhang, Pengfei Wu, Lian Duan, Guohui Li, Qiuhong Liu, Jinyu Wang
A series of elaborately regulated and orchestrated changes in gene expression profiles leads to muscle growth and development. In this study, RNA sequencing was used to profile embryonic chicken myoblasts and fused myotube transcriptomes, long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs) at four stages of myoblast differentiation. Of a total of 2484 lncRNA transcripts, 2288 were long intergenic non-coding RNAs (lincRNAs) and 198 were antisense lncRNAs. Additionally, 1530 lncRNAs were neighboring 2041 protein-coding genes (<10 kb upstream and downstream) and functionally enriched in several pathways related to skeletal muscle development that have been extensively studied, indicating that these genes may be in cis-regulatory relationships...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29322263/comparative-transcriptomic-analysis-of-skeletal-muscle-tissue-during-prenatal-stages-in-tongcheng-and-yorkshire-pig-using-rna-seq
#3
Huijing Liu, Yu Xi, Guorong Liu, Yuqiang Zhao, Ji Li, Minggang Lei
Myogenesis is accompanied by a number of changes in gene expression in mammals, and the transcriptional events that underlie these processes have not been yet fully elucidated. In this study, RNA-seq was used to comprehensively compare the transcription profiles of skeletal muscle between Tongcheng (TC) and Yorkshire (YK) pigs at 40, 55, 63, 70, and 90 days of gestation. One thousand three hundred seventeen and 691 differentially expressed genes (DEGs) were detected in TC and YK, respectively, among which 321 DEGs were shown to be common in TC and YK...
January 10, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29321689/analysis-of-combined-transcriptomes-identifies-gene-modules-that-differentially-respond-to-pathogenic-stimulation-of-vascular-smooth-muscle-and-endothelial-cells
#4
Xiaokang Pan, Bowen Wang, Tiezheng Yuan, Mengxue Zhang, K Craig Kent, Lian-Wang Guo
Smooth muscle cells (SMCs) and endothelial cells (ECs) are vital cell types composing the vascular medial wall and the atheroprotective inner lining, respectively. Current treatments for cardiovascular disease inhibit SMC hyperplasia but compromise EC integrity, predisposing patients to thrombosis. Therapeutics targeting SMCs without collateral damage to ECs are highly desirable. However, differential (SMC versus EC) disease-associated regulations remain poorly defined. We conducted RNA-seq experiments to investigate SMC-versus-EC differential transcriptomic dynamics, following treatment of human primary SMCs and ECs with TNFα or IL-1β, both established inducers of SMC hyperplasia and EC dysfunction...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320759/identification-of-key-micrornas-affecting-drip-loss-in-porcine-longissimus-dorsi-by-rna-seq
#5
Wei Wei, Bojiang Li, Kaiqing Liu, Aiwen Jiang, Chao Dong, Chao Jia, Jie Chen, Honglin Liu, Wangjun Wu
MicroRNAs (miRNAs) are a class of ~22-nt non-coding small RNA that play an important role in various metabolic processes, mainly through suppressing the expression of protein coding genes at post-transcriptional level. Drip loss (DL) is one of the most important meat quality traits affecting the end product yield and quality of pork. To date, the underlying regulatory factors involved in DL trait are still incompletely understood. In the present study, we constructed two small RNA libraries with longissimus dorsi muscles from the higher (WJJ-H group) and the lower DL (WJJ-L group) individuals, and applied RNA-Seq technology to identify the differentially expressed miRNAs between the two extreme phenotypes of DL groups...
January 7, 2018: Gene
https://www.readbyqxmd.com/read/29314553/identification-of-mir-305-a-microrna-that-promotes-aging-and-its-target-mrnas-in-drosophila
#6
Makiko Ueda, Tetsuya Sato, Yasuyuki Ohkawa, Yoshihiro H Inoue
MicroRNAs (miRNAs) are involved in the regulation of important biological processes. Here, we describe a novel Drosophila miRNAs involved in aging. We selected eight Drosophila miRNAs, displaying high homology with seed sequences of aging-related miRNAs characterized in other species, and investigated whether the over-expression of these miRNAs affected aging in Drosophila adult flies. The lifespan of adults over-expressing miR-305, a miRNA showing high homology with miR-239 in C. elegans, was significantly shorter...
January 5, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/29304175/genome-scale-metabolic-models-as-tools-for-drug-design-and-personalized-medicine
#7
Vytautas Raškevičius, Valeryia Mikalayeva, Ieva Antanavičiūtė, Ieva Ceslevičienė, Vytenis Arvydas Skeberdis, Visvaldas Kairys, Sergio Bordel
In this work we aim to show how Genome Scale Metabolic Models (GSMMs) can be used as tools for drug design. By comparing the chemical structures of human metabolites (obtained using their KEGG indexes) and the compounds contained in the DrugBank database, we have observed that compounds showing Tanimoto scores higher than 0.9 with a metabolite, are 29.5 times more likely to bind the enzymes metabolizing the considered metabolite, than ligands chosen randomly. By using RNA-seq data to constrain a human GSMM it is possible to obtain an estimation of its distribution of metabolic fluxes and to quantify the effects of restraining the rate of chosen metabolic reactions (for example using a drug that inhibits the enzymes catalyzing the mentioned reactions)...
2018: PloS One
https://www.readbyqxmd.com/read/29273440/pitx1-promotes-chondrogenesis-and-myogenesis-in-mouse-hindlimbs-through-conserved-regulatory-targets
#8
Jialiang S Wang, Carlos R Infante, Sungdae Park, Douglas B Menke
The PITX1 transcription factor is expressed during hindlimb development, where it plays a critical role in directing hindlimb growth and the specification of hindlimb morphology. While it is known that PITX1 regulates hindlimb formation, in part, through activation of the Tbx4 gene, other transcriptional targets remain to be elucidated. We have used a combination of ChIP-seq and RNA-seq to investigate enhancer regions and target genes that are directly regulated by PITX1 in embryonic mouse hindlimbs. In addition, we have analyzed PITX1 binding sites in hindlimbs of Anolis lizards to identify ancient PITX1 regulatory targets...
December 19, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29262264/pde8-is-expressed-in-human-airway-smooth-muscle-and-selectively-regulates-camp-signaling-by-%C3%AE-2ar-ac6
#9
Timothy B Johnstone, Kaitlyn H Smith, Cynthia J Koziol-White, Fengying Li, Austin G Kazarian, Maia L Corpuz, Maya Shumyatcher, Frederick J Ehlert, Blanca E Himes, Reynold A Panettieri, Rennolds S Ostrom
Two cAMP signaling compartments centering around adenylyl cyclase (AC) exist in human airway smooth muscle (HASM) cells, one containing ß2AR-AC6 and another containing E prostanoid receptors (EPR)-AC2. We hypothesized that different phosphodiesterase (PDE) isozymes selectively regulate cAMP signaling in each compartment. According to RNA-seq data, 18 of 24 PDE genes were expressed in primary HASM cells derived from age- and gender-matched donors with and without asthma. PDE8A was the third most abundant of the cAMP-degrading PDE genes, after PDE4A and PDE1A...
December 20, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/29246115/training-the-salmon-s-genes-influence-of-aerobic-exercise-swimming-performance-and-selection-on-gene-expression-in-atlantic-salmon
#10
Nicholas A Robinson, Gerrit Timmerhaus, Matthew Baranski, Øivind Andersen, Harald Takle, Aleksei Krasnov
BACKGROUND: Farmed and wild Atlantic salmon are exposed to many infectious and non-infectious challenges that can cause mortality when they enter the sea. Exercise before transfer promotes growth, health and survival in the sea. Swimming performance in juveniles at the freshwater parr stage is positively associated with resistance to some diseases. Genetic variation is likely to affect response to exercise. In this study we map genetic differences associated with aerobic exercise, swimming performance and genetic origin...
December 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29236749/transcriptomic-analysis-of-chicken-myozenin-3-regulation-reveals-its-potential-role-in-cell-proliferation
#11
Maosen Ye, Fei Ye, Liutao He, Bin Luo, Fuling Yang, Can Cui, Xiaoling Zhao, Huadong Yin, Diyan Li, Hengyong Xu, Yan Wang, Qing Zhu
Embryonic muscle development and fibre type differentiation has always been a topic of great importance due to its impact on both human health and farm animal financial values. Myozenin3 (Myoz3) is an important candidate gene that may regulate these processes. In the current study, we knocked down and overexpressed Myoz3 in chicken embryonic fibroblasts (CEFs) and chicken myoblasts, then utilized RNA-seq technology to screen genes, pathways and biological processes associated with Myoz3. Multiple differentially expressed genes were identified, including MYH10, MYLK2, NFAM1, MYL4, MYL9, PDZLIM1; those can in turn regulate each other and influence the development of muscle fibres...
2017: PloS One
https://www.readbyqxmd.com/read/29228601/genome-wide-analysis-of-circular-rnas-in-prenatal-and-postnatal-muscle-of-sheep
#12
Cunyuan Li, Xiaoyue Li, Yang Yao, Qiman Ma, Wei Ni, Xiangyu Zhang, Yang Cao, Wureli Hazi, Dawei Wang, Renzhe Quan, Xiaoxu Hou, Zhijin Liu, Qianqian Zhan, Li Liu, Mengdan Zhang, Shuting Yu, Shengwei Hu
Circular RNAs (circRNAs), a type of non-coding RNA with circular structure, were generated by back splicing and widely expressed in animals and plants. Recent studies have shown that circRNAs extensively participate in cell proliferation, cell differentiation, cell autophagy and other biological processes. However, the role and expression of circRNAs in the development and growth of muscle have not been studied in sheep. In our study, we first used RNA-seq to study the circRNAs in prenatal and postnatal longissimus dorsi muscle of sheep...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228005/rna-seq-reveals-transcriptome-changes-in-goats-following-myostatin-gene-knockout
#13
Lamei Wang, Bei Cai, Shiwei Zhou, Haijing Zhu, Lei Qu, Xiaolong Wang, Yulin Chen
Myostatin (MSTN) is a powerful negative regulator of skeletal muscle mass in mammalian species that is primarily expressed in skeletal muscles, and mutations of its encoding gene can result in the double-muscling trait. In this study, the CRISPR/Cas9 technique was used to edit MSTN in Shaanbei Cashmere goats and generate knockout animals. RNA sequencing was used to determine and compare the transcriptome profiles of the muscles from three wild-type (WT) goats, three fibroblast growth factor 5 (FGF5) knockout goats (FGF5+/- group) and three goats with disrupted expression of both the FGF5 and MSTN genes (FM+/- group)...
2017: PloS One
https://www.readbyqxmd.com/read/29212859/human-hair-follicle-transcriptome-profiling-a-minimally-invasive-tool-to-assess-molecular-adaptations-upon-low-volume-high-intensity-interval-training
#14
Jing Zhang, Sarah J Wallace, Maria Y Shiu, Ingrid Smith, Shawn G Rhind, Valerie S Langlois
High-intensity interval training (HIIT) has become a popular fitness training approach under both civilian and military settings. Consisting of brief and intense exercise intervals, HIIT requires less time commitment yet is able to produce the consistent targeted physical adaptations as conventional endurance training. To effectively characterize and monitor HIIT-induced cellular and molecular responses, a highly accessible yet comprehensive biomarker discovery source is desirable. Both gene differential expression (DE) and gene set (GS) analyses were conducted using hair follicle transcriptome established from pre and postexercise subjects upon a 10-day HIIT program by RNA-Seq, Comparing between pre and posttraining groups, differentially expressed protein coding genes were identified...
December 2017: Physiological Reports
https://www.readbyqxmd.com/read/29202705/differences-in-global-gene-expression-in-muscle-tissue-of-nellore-cattle-with-divergent-meat-tenderness
#15
Larissa Fernanda Simielli Fonseca, Daniele Fernanda Jovino Gimenez, Danielly Beraldo Dos Santos Silva, Roger Barthelson, Fernando Baldi, Jesus Aparecido Ferro, Lucia Galvão Albuquerque
BACKGROUND: Meat tenderness is the consumer's most preferred sensory attribute. This trait is affected by a number of factors, including genotype, age, animal sex, and pre- and post-slaughter management. In view of the high percentage of Zebu genes in the Brazilian cattle population, mainly Nellore cattle, the improvement of meat tenderness is important since the increasing proportion of Zebu genes in the population reduces meat tenderness. However, the measurement of this trait is difficult once it can only be made after animal slaughtering...
December 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29189957/actin-genes-and-their-expression-in-pacific-white-shrimp-litopenaeus-vannamei
#16
Xiaoxi Zhang, Xiaojun Zhang, Jianbo Yuan, Jiangli Du, Fuhua Li, Jianhai Xiang
Actin is a multi-functional gene family that can be divided into muscle-type actins and non-muscle-type actins. In this study, 37 unigenes encoding actins were identified from RNA-Seq data of Pacific white shrimp, Litopenaeus vannamei. According to phylogenetic analysis, four and three cDNAs belong to cytoplasmic- and heart-type actins and were named LvActinCT and LvActinHT, respectively. 10 cDNAs belong to the slow-type skeletal muscle actins, and 18 belong to the fast-type skeletal muscle actins; they were designated LvActinSSK and LvActinFSK, respectively...
November 30, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29180763/identification-of-genes-expressed-in-a-mesenchymal-subset-regulating-prostate-organogenesis-using-tissue-and-single-cell-transcriptomics
#17
Nadia Boufaied, Claire Nash, Annie Rochette, Anthony Smith, Brigid Orr, O Cathal Grace, Yu Chang Wang, Dunarel Badescu, Jiannis Ragoussis, Axel A Thomson
Prostate organogenesis involves epithelial growth controlled by inductive signalling from specialised mesenchymal subsets. To identify pathways active in mesenchyme we used tissue and single cell transcriptomics to define mesenchymal subsets and subset-specific transcript expression. We documented transcript expression using Tag-seq and RNA-seq in female rat Ventral Mesenchymal Pad (VMP) as well as adjacent urethra comprised of smooth muscle and peri-urethral mesenchyme. Transcripts enriched in female VMP were identified with Tag-seq of microdissected tissue, RNA-seq of cell populations, and single cells...
November 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29163195/members-of-bitter-taste-receptor-cluster-tas2r143-tas2r135-tas2r126-are-expressed-in-the-epithelium-of-murine-airways-and-other-non-gustatory-tissues
#18
Shuya Liu, Shun Lu, Rui Xu, Ann Atzberger, Stefan Günther, Nina Wettschureck, Stefan Offermanns
The mouse bitter taste receptors Tas2r143, Tas2r135, and Tas2r126 are encoded by genes that cluster on chromosome 6 and have been suggested to be expressed under common regulatory elements. Previous studies indicated that the Tas2r143/Tas2r135/Tas2r126 cluster is expressed in the heart, but other organs had not been systematically analyzed. In order to investigate the expression of this bitter taste receptor gene cluster in non-gustatory tissues, we generated a BAC (bacterial artificial chromosome) based transgenic mouse line, expressing CreERT2 under the control of the Tas2r143 promoter...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29162882/sublethal-effects-of-imidacloprid-on-targeting-muscle-and-ribosomal-protein-related-genes-in-the-honey-bee-apis-mellifera-l
#19
Yan-Yan Wu, Qi-Hua Luo, Chun-Sheng Hou, Qiang Wang, Ping-Li Dai, Jing Gao, Yong-Jun Liu, Qing-Yun Diao
A sublethal concentration of imidacloprid can cause chronic toxicity in bees and can impact the behavior of honey bees. The nectar- and water-collecting, and climbing abilities of bees are crucial to the survival of the bees and the execution of responsibilities in bee colonies. Besides behavioral impact, data on the molecular mechanisms underlying the toxicity of imidacloprid, especially by the way of RNA-seq at the transcriptomic level, are limited. We treated Apis mellifera L. with sublethal concentrations of imidacloprid (0...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29155830/molecular-characterization-of-tsetse-s-proboscis-and-its-response-to-trypanosoma-congolense-infection
#20
Erick O Awuoche, Brian L Weiss, Aurélien Vigneron, Paul O Mireji, Emre Aksoy, Benson Nyambega, Geoffrey M Attardo, Yineng Wu, Michelle O'Neill, Grace Murilla, Serap Aksoy
Tsetse flies (Glossina spp.) transmit parasitic African trypanosomes (Trypanosoma spp.), including Trypanosoma congolense, which causes animal African trypanosomiasis (AAT). AAT detrimentally affects agricultural activities in sub-Saharan Africa and has negative impacts on the livelihood and nutrient availability for the affected communities. After tsetse ingests an infectious blood meal, T. congolense sequentially colonizes the fly's gut and proboscis (PB) organs before being transmitted to new mammalian hosts during subsequent feedings...
November 2017: PLoS Neglected Tropical Diseases
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