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muscle RNA-seq

Mariana P Berton, Larissa F S Fonseca, Daniela F J Gimenez, Bruno L Utembergue, Aline S M Cesar, Luiz L Coutinho, Marcos Vinicius A de Lemos, Carolyn Aboujaoude, Angélica S C Pereira, Rafael M de O Silva, Nedenia B Stafuzza, Fabieli L B Feitosa, Hermenegildo L J Chiaia, Bianca F Olivieri, Elisa Peripolli, Rafael L Tonussi, Daniel M Gordo, Rafael Espigolan, Adrielle M Ferrinho, Lenise F Mueller, Lucia G de Albuquerque, Henrique N de Oliveira, Susan Duckett, Fernando Baldi
BACKGROUND: Fatty acid type in beef can be detrimental to human health and has received considerable attention in recent years. The aim of this study was to identify differentially expressed genes in longissimus thoracis muscle of 48 Nellore young bulls with extreme phenotypes for fatty acid composition of intramuscular fat by RNA-seq technique. RESULTS: Differential expression analyses between animals with extreme phenotype for fatty acid composition showed a total of 13 differentially expressed genes for myristic (C14:0), 35 for palmitic (C16:0), 187 for stearic (C18:0), 371 for oleic (C18:1, cis-9), 24 for conjugated linoleic (C18:2 cis-9, trans11, CLA), 89 for linoleic (C18:2 cis-9,12 n6), and 110 genes for α-linolenic (C18:3 n3) fatty acids...
November 25, 2016: BMC Genomics
Xi Lan, John C F Hsieh, Carl J Schmidt, Qing Zhu, Susan J Lamont
BACKGROUND: High ambient temperatures cause stress in poultry, especially for broiler lines, which are genetically selected for rapid muscle growth. RNA-seq technology provides powerful insights into environmental response from a highly metabolic tissue, the liver. We investigated the effects of acute (3 h, 35 °C) and chronic (7d of 35 °C for 7 h/d) heat stress on the liver transcriptome of 3-week-old chicks of a heat-susceptible broiler line, a heat-resistant Fayoumi line, and their advanced intercross line (AIL)...
November 22, 2016: BMC Genomics
Richard S Sweat, David C Sloas, Scott A Stewart, Malwina Czarny-Ratajczak, Melody Baddoo, James R Eastwood, Ariana D Suarez-Martinez, Mohammad Sadegh Azimi, Hope E Burks, Lee O Chedister, Leann Myers, Walter Lee Murfee
A big problem associated with aging is thought to be impaired microvascular growth or angiogenesis. However, in order to link the evidence for impaired angiogenesis to microvascular dysfunction in aged tissues, we must compare adult versus aged microvascular networks in unstimulated scenarios. The objective of this study was to test the hypothesis that aged microvascular networks are characterized by both fewer vessels and the impaired ability to undergo angiogenesis. Mesentery tissues from adult (9 months) and aged (24 months) male Fischer 344 rats were harvested and immunolabeled for PECAM (an endothelial cell marker) according to two scenarios: unstimulated and stimulated...
November 18, 2016: American Journal of Physiology. Heart and Circulatory Physiology
Eman Badr, Mahmoud ElHefnawi, Lenwood S Heath
Alternative splicing is a vital process for regulating gene expression and promoting proteomic diversity. It plays a key role in tissue-specific expressed genes. This specificity is mainly regulated by splicing factors that bind to specific sequences called splicing regulatory elements (SREs). Here, we report a genome-wide analysis to study alternative splicing on multiple tissues, including brain, heart, liver, and muscle. We propose a pipeline to identify differential exons across tissues and hence tissue-specific SREs...
2016: PloS One
Dan Zhou, Ryan A Hlady, Marissa J Schafer, Thomas A White, Chen Liu, Jeong-Hyeon Choi, Jordan D Miller, Lewis R Roberts, Nathan K LeBrasseur, Keith D Robertson
High-fat diet consumption and sedentary life style elevates risk for obesity, non-alcoholic fatty liver disease, and cancer. Exercise training conveys health benefits in populations with or without these chronic conditions. Diet and exercise regulate gene expression by mediating epigenetic mechanisms in many tissues; however, such effects are poorly documented in the liver, a central metabolic organ. To dissect the consequences of diet and exercise on the liver epigenome, we measured DNA methylation, using reduced representation bisulfite sequencing, and transcription, using RNA-seq, in mice maintained on a fast food diet with sedentary lifestyle or exercise, compared to control diet with and without exercise...
November 18, 2016: Epigenetics: Official Journal of the DNA Methylation Society
Le Zhang, Yanfang Zhao, Yue Ning, Hongbao Wang, Linsen Zan
Fatty acid binding protein 4 (FABP4) plays a key role in Fatty acid catabolism in mammals. Findings from our previous studies have indicated that FABP4 neither affect the differentiation of bovine preadipocytes nor does it change the expression of upstream genes. To investigate whether ectopically expressed FABP4 can induces Muscle-Derived Stem Cells (MDSCs) lipid synthesis and understand the regulatory mechanism behind it. In this study, adenoviruses infection is achieved to ectopically expressed FABP4 in bovine MDSCs, RNA-seq analyses at the very early stages of induction were performed to reveal gene expression level changes during MDSCs transdifferentiation...
November 14, 2016: Biochemical and Biophysical Research Communications
J L Jo, J H Hwang, S G Kwon, D H Park, T W Kim, D G Kang, G E Yu, I S Kim, J G Ha, C W Kim
Single nucleotide polymorphisms (SNPs) are useful genetic markers that allow correlation of genetic sequences with phenotypic traits. It is shown here that HSD17B4, a bifunctional enzyme mediating dehydrogenation and anhydration during β-oxidation of long-chain fatty acids, contains a non-synonymous SNP (nsSNP) of chr2:128,825,976A>G, c.2137A>G, I690V, within the sterol carrier protein-2 domain of the HSD17B4 gene, by RNA-Seq of liver RNA. The HSD17B4 mRNA was highly expressed in the kidney and liver among various other tissues in four pig breeds, namely, Berkshire, Duroc, Landrace, and Yorkshire...
November 3, 2016: Genetics and Molecular Research: GMR
Mark P Polinski, Julia C Bradshaw, Sabrina M Inkpen, Jon Richard, Camilla Fritsvold, Trygve T Poppe, Matthew L Rise, Kyle A Garver, Stewart C Johnson
BACKGROUND: Piscine reovirus (PRV) has been associated with the serious disease known as Heart and Skeletal Muscle Inflammation (HSMI) in cultured Atlantic salmon Salmo salar in Norway. PRV is also prevalent in wild and farmed salmon without overt disease manifestations, suggesting multifactorial triggers or PRV variant-specific factors are required to initiate disease. In this study, we explore the head kidney transcriptome of Sockeye salmon Oncorhynchus nerka during early PRV infection to identify host responses in the absence of disease in hopes of elucidating mechanisms by which PRV may directly alter host functions and contribute to the development of a disease state...
November 2, 2016: BMC Genomics
Patricia Bianca Clissa, Rodrigo Pessôa, Karla Fernanda Ferraz, Daniela Raguer Valadão de Souza, Sabri Saeed Sanabani
This article describes the data on the global expression profile of small RNA (smRNAs) molecules in mice gastrocnemius muscle exposed to jararhagin, snake venom metalloproteinase. The data include smRNAs in mice gastrocnemius muscle challenged with Jararhagin (Jar; n=4) in the right paw or phosphate-buffered saline (PBS; control; n=4) in the left paw. smRNA-Seq libraries were generated after 24 h of exposure to PBS or jararhagin. The expression profiles of smRNAs including microRNA and snoRNA were compared between both groups...
December 2016: Data in Brief
Alicja Pacholewska, Núria Mach, Xavier Mata, Anne Vaiman, Laurent Schibler, Eric Barrey, Vincent Gerber
BACKGROUND: MiRNAs regulate multiple genes at the post-transcriptional level and therefore play an important role in many biological processes. It has been suggested that miRNA exported outside the cells contribute to inter-cellular communication. Consequently, circulating miRNAs are of particular interest and are promising biomarkers for many diseases. The number of miRNAs annotated in the horse genome is much lower compared to model organisms like human and mouse. We therefore aimed to identify novel equine miRNAs for tissue types and breed in serum...
October 26, 2016: BMC Genomics
Zi Yi Wan, Jun Hong Xia, Grace Lin, Le Wang, Valerie C L Lin, Gen Hua Yue
Sexual dimorphism is an interesting biological phenomenon. Previous studies showed that DNA methylation might play a role in sexual dimorphism. However, the overall picture of the genome-wide methylation landscape in sexually dimorphic species remains unclear. We analyzed the DNA methylation landscape and transcriptome in hybrid tilapia (Oreochromis spp.) using whole genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). We found 4,757 sexually dimorphic differentially methylated regions (DMRs), with significant clusters of DMRs located on chromosomal regions associated with sex determination...
October 26, 2016: Scientific Reports
Yongcheng Pan, Lusi Zhang, Qiong Liu, Ying Li, Hui Guo, Yu Peng, Hexiang Peng, Beisha Tang, Zhengmao Hu, Jingping Zhao, Kun Xia, Jia-Da Li
AMPD1 is an adenosine monophosphate deaminase that catalyzes the deamination of AMP to IMP. To understand the physiological function of AMPD1, we obtained a strain of Ampd1 mutant mice from KOMP repository, which was generated by a knockout-first strategy. An elevated AMP level and almost complete lack of IMP was detected in the skeletal muscle of E18.5 Ampd1(tm1a/tm1a) mice. However, Ampd1(tm1a/tm1a) mice died in 2 days postnatally, which was contradicting to previous reports. After removal of the knockout-first cassette and critical exon, mice homozygous for the Ampd1(tm1c/tm1c) and Ampd1(tm1d/tm1d) alleles survived to adulthood...
October 24, 2016: Scientific Reports
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 is central to the pathophysiology and treatment of metabolic disease through the receptors' 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...
November 1, 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 lncRNA discovery. However, no study on the overall expression patterns of lncRNAs during muscle development has been conducted. We reported here the first analysis of lncRNA 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...
November 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
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