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muscle RNA-seq

Katarzyna Ropka-Molik, Anna Bereta, Kacper Żukowski, Mirosław Tyra, Katarzyna Piórkowska, Grzegorz Żak, Maria Oczkowicz
Objective: The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants' effect on histological microstructure and production traits in a larger pig population. Methods: RNA-seq data was used to identify the panel of SNPs significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to QTLs regions...
March 13, 2018: Asian-Australasian Journal of Animal Sciences
Minlan Yang, Hairi Li, Yanru Li, Yang Ruan, Chengshi Quan
Multidrug resistance (MDR) is a major problem in the treatment of breast cancer. In the present study, next-generation sequencing technology was employed to identify differentially expressed genes in MCF‑7/MDR cells and MCF‑7 cells, and aimed to investigate the underlying molecular mechanisms of MDR in breast cancer. Differentially expressed genes between MCF‑7/MDR and MCF‑7 cells were selected using software; a total of 2085 genes were screened as differentially expressed in MCF‑7/MDR cells. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the DAVID database...
March 7, 2018: Molecular Medicine Reports
Bolin Cai, Manting Ma, Biao Chen, Zhenhui Li, Bahareldin Ali Abdalla, Qinghua Nie, Xiquan Zhang
The proliferation, apoptosis, and differentiation of myoblasts are essential processes in skeletal muscle development. During this developmental process, microRNAs (miRNAs) play crucial roles. In our previous RNA-seq study (accession number GSE62971), we found that miR-16-5p was differentially expressed between fast and slow growth in chicken. In this study, we report that miR-16-5p could inhibit myoblast proliferation, promote myoblast apoptosis, and repress myoblast differentiation by directly binding to the 3' UTR of SESN1, which is also differentially expressed...
March 6, 2018: Cell Death & Disease
Natalia A Stefanova, Kseniya Yi Maksimova, Ekaterina A Rudnitskaya, Natalia A Muraleva, Nataliya G Kolosova
BACKGROUND: Cerebrovascular dysfunction plays a critical role in the pathogenesis of Alzheimer's disease (AD): the most common cause of dementia in the elderly. The involvement of neurovasculature disorders in the progression of AD is now increasingly appreciated, but whether they represent initial factors or late-stage pathological changes during the disease is unclear. Using senescence-accelerated OXYS rats, which simulate key characteristics of sporadic AD, we evaluated contributions of cerebrovascular alterations to the disease development...
February 9, 2018: BMC Genomics
Claire Domenger, Marine Allais, Virginie François, Adrien Léger, Emilie Lecomte, Marie Montus, Laurent Servais, Thomas Voit, Philippe Moullier, Yann Audic, Caroline Le Guiner
Non-coding uridine-rich small nuclear RNAs (UsnRNAs) have emerged in recent years as effective tools for exon skipping for the treatment of Duchenne muscular dystrophy (DMD), a degenerative muscular genetic disorder. We recently showed the high capacity of a recombinant adeno-associated virus (rAAV)-U7snRNA vector to restore the reading frame of the DMD mRNA in the muscles of DMD dogs. We are now moving toward a phase I/II clinical trial with an rAAV-U7snRNA-E53, carrying an antisense sequence designed to hybridize exon 53 of the human DMD messenger...
March 2, 2018: Molecular Therapy. Nucleic Acids
Magdalena Harakalova, Folkert W Asselbergs
Dilated cardiomyopathy (DCM) is a form of severe failure of cardiac muscle caused by a long list of etiologies ranging from myocardial infarction, DNA mutations in cardiac genes, to toxics. Systems analysis integrating next-generation sequencing (NGS)-based omics approaches, such as the sequencing of DNA, RNA, and chromatin, provide valuable insights into DCM mechanisms. The outcome and interpretation of NGS methods can be affected by the localization of cardiac biopsy, level of tissue degradation, and variable ratios of different cell populations, especially in the presence of fibrosis...
February 27, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
Shengdi Li, Ziyi Chang, Tianqing Zhu, Yixue Li, Bruce A Freeman, Y Eugene Chen, Jifeng Zhang
Nitro-conjugated linoleic acid (NO2 -CLA) is formed by metabolic and inflammatory reactions of nitric oxide and nitrite, and represents the most abundant nitro-fatty acid species in humans. These electrophilic fatty acid nitroalkene derivatives mediate pleiotropic cell signaling responses. Here, we report a systematic approach to investigate the effect of NO2 -CLA on human coronary artery smooth muscle cells (hCASMC), based on the RNA-seq and bioinformatics analysis. There were extensive differentially expressed genes in NO2 -CLA vs...
February 23, 2018: Physiological Genomics
Mohammad Reza Bakhtiarizadeh, Abdolreza Salehi, Rocío Melissa Rivera
RNA editing increases the diversity of the transcriptome and proteome. Adenosine-to-inosine (A-to-I) editing is the predominant type of RNA editing in mammals and it is catalyzed by the adenosine deaminases acting on RNA (ADARs) family. Here, we used a largescale computational analysis of transcriptomic data from brain, heart, colon, lung, spleen, kidney, testes, skeletal muscle and liver, from three adult animals in order to identify RNA editing sites in bovine. We developed a computational pipeline and used a rigorous strategy to identify novel editing sites from RNA-Seq data in the absence of corresponding DNA sequence information...
2018: PloS One
Xiao Dong, Miao Shi, Moonsook Lee, Rafael Toro, Silvia Gravina, Weiguo Han, Shoya Yasuda, Tao Wang, Zhengdong Zhang, Jan Vijg, Yousin Suh, Simon D Spivack
Gene regulatory analysis of highly diverse human tissues in vivo is essentially constrained by the challenge of performing genome-wide, integrated epigenetic and transcriptomic analysis in small selected groups of specific cell types. Here we performed genome-wide bisulfite sequencing and RNA-seq from the same small groups of bronchial and alveolar cells isolated by laser capture microdissection from flash-frozen lung tissue of 12 donors and their peripheral blood T cells. Methylation and transcriptome patterns differed between alveolar and bronchial cells, while each of these epithelia showed more differences from mesodermally-derived T cells...
February 21, 2018: Epigenetics: Official Journal of the DNA Methylation Society
Ronald A Li, Wendy Keung, Timothy J Cashman, Peter C Backeris, Bryce V Johnson, Evan S Bardot, Andy O T Wong, Patrick K W Chan, Camie W Y Chan, Kevin D Costa
Tissue engineers and stem cell biologists have made exciting progress toward creating simplified models of human heart muscles or aligned monolayers to help bridge a longstanding gap between experimental animals and clinical trials. However, no existing human in vitro systems provide the direct measures of cardiac performance as a pump. Here, we developed a next-generation in vitro biomimetic model of pumping human heart chamber, and demonstrated its capability for pharmaceutical testing. From human pluripotent stem cell (hPSC)-derived ventricular cardiomyocytes (hvCM) embedded in collagen-based extracellular matrix hydrogel, we engineered a three-dimensional (3D) electro-mechanically coupled, fluid-ejecting miniature human ventricle-like cardiac organoid chamber (hvCOC)...
February 10, 2018: Biomaterials
Thomas Sanford, Maxwell V Meng, Reema Railkar, Piyush K Agarwal, Sima P Porten
Background: Elucidation of epigenetic alterations in bladder cancer will lead to further understanding of the biology of the disease and hopefully improved therapies. Our aim was to perform an integrative epigenetic analysis of invasive urothelial carcinoma of the bladder to identify the epigenetic abnormalities involved in the development and progression of this cancer. Methods: Pre-processed methylation data and RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) and processed using the R package TCGA-Assembler...
2018: Clinical Epigenetics
Tuanhui Ren, Zhuanjian Li, Yu Zhou, Xuelian Liu, Ruili Han, Yongcai Wang, Fengbin Yan, Guirong Sun, Hong Li, Xiangtao Kang
Chicken muscle quality is one of the most important factors determining the economic value of poultry, and muscle development and growth are affected by genetics, environment, and nutrition. However, little is known about the molecular regulatory mechanisms of long non-coding RNAs (lncRNAs) in chicken skeletal muscle development. Our study aimed to better understand muscle development in chickens and thereby improve meat quality. In this study, Ribo-Zero RNA-Seq was used to investigate differences in the expression profiles of muscle development-related genes and associated pathways between Gushi (GS) and Arbor Acres (AA) chickens...
February 15, 2018: Genome Génome / Conseil National de Recherches Canada
Sofia Garcia, Nadee Nissanka, Edson A Mareco, Susana Rossi, Susana Peralta, Francisca Diaz, Richard L Rotundo, Robson F Carvalho, Carlos T Moraes
PGC-1α is a transcriptional co-activator known as the master regulator of mitochondrial biogenesis. Its control of metabolism has been suggested to exert critical influence in the aging process. We have aged mice overexpressing PGC-1α in skeletal muscle to determine whether the transcriptional changes reflected a pattern of expression observed in younger muscle. Analyses of muscle proteins showed that Pax7 and several autophagy markers were increased. In general, the steady-state levels of several muscle proteins resembled that of muscle from young mice...
February 10, 2018: Aging Cell
Min Du, Na Li, Baozhen Niu, Yanhong Liu, Dongjing You, Defu Jiang, Congquan Ruan, Zhengquan Qin, Taowen Song, Wentao Wang
BACKGROUND: The yellow sisorid catfish (Bagarius yarrelli) is a carnivorous freshwater fish that inhabits the Honghe River, Lanchangjiang River and Nujiang River of southern China and other Southeast Asian countries. However, the publicly available genomic data for B. yarrelli are limited. METHODOLOGY AND PRINCIPAL FINDINGS: Illumina Solexa paired-end technology produced 1,706,456 raw reads from muscle, liver and caudal fin tissues of B. yarrelli. Nearly 5 Gb of data were acquired, and de novo assembly generated 14,607 unigenes, with an N50 of 2006 bp...
2018: PloS One
Xin Xie, Muhammedin Deliorman, Mohammad A Qasaimeh, Piergiorgio Percipalle
BACKGROUND: Cell surface mechanics is able to physically and biomechanically affect cell shape and motility, vesicle trafficking and actin dynamics. The biophysical properties of cell surface are strongly influenced by cytoskeletal elements. In mammals, tissue-specific expression of six actin isoforms is thought to confer differential biomechanical properties. However, the relative contribution of actin isoforms to cell surface properties is not well understood. Here, we sought to investigate whether and how the composition of endogenous actin isoforms directly affects the biomechanical features of cell surface and cellular behavior...
February 1, 2018: Biochimica et Biophysica Acta
Xiaoli Shi, Xianhong Meng, Jie Kong, Sheng Luan, Kun Luo, Baoxiang Cao, Xia Lu, Xupeng Li, Baolong Chen, Jiawang Cao
White spot syndrome (WSS) is one of the most damaging phenomena in the culturing of shrimp. To characterize the mechanisms of the molecular responses to WSSV infection in 'Huanghai No. 2'' Fenneropenaeus chinensis, we used next-generation sequencing to observe the transcriptome after oral infection. A total of 108.6 million clean reads were obtained and assembled into 64,103 final unigenes with an average length of 845 bp (N50 = 1534 bp). The assembled unigenes contained 14,263 significant unigenes after BLASTX against the Nr database (E-value cut-off of 10-5)...
January 30, 2018: Fish & Shellfish Immunology
Shaokun Guo, Zihua Zhao, Lijun Liu, Zhihong Li, Jie Shen
Flight capacity is important for invasive pests during entry, establishment and spreading. Both Bactroceradorsalis Hendel and Bactroceracorrecta Bezzi are invasive fruit flies but their flight capacities differ. Here, a tethered flight mill test demonstrated that B. dorsalis exhibits a greater flight capacity than B. correcta. RNA-Seq was used to determine the transcriptomic differences associated with the flight capacity of two Bactrocera species. Transcriptome data showed that 6392 unigenes were differentially expressed between the two species in the larval stage, whereas in the adult stage, 4104 differentially expressed genes (DEGs) were identified in females, and 3445 DEGs were observed in males...
January 30, 2018: International Journal of Molecular Sciences
Cun-Yuan Li, Xiaoyue Li, Zhijin Liu, Wei Ni, Xiangyu Zhang, Wureli Hazi, Qiman Ma, Yunfeng Zhang, Yang Cao, Jiangjiao Qi, Yang Yao, Lin Feng, Dawei Wang, Xiaoxu Hou, Shuting Yu, Li Liu, Mengdan Zhang, Shengwei Hu
lncRNAs are a class of transcriptional RNA molecules of >200 nucleotides in length. However, the overall expression pattern and function of lncRNAs in sheep muscle is not clear. Here, we identified 1566 lncRNAs and 404 differentially expressed lncRNAs in sheep muscle from prenatal (110 days of fetus) and postnatal (2 to 3 years old of adult sheep) developmental stages by using RNA-seq technology. Several lncRNAs were identified by using RT-PCR and DNA sequencing. The expression levels of several lncRNAs were confirmed by qRT-PCR...
January 20, 2018: Genomics
Zuchra Zakirova, Tomas Fanutza, Justine Bonet, Ben Readhead, Weijia Zhang, Zhengzi Yi, Genevieve Beauvais, Thomas P Zwaka, Laurie J Ozelius, Robert D Blitzer, Pedro Gonzalez-Alegre, Michelle E Ehrlich
Dystonia is characterized by involuntary muscle contractions. Its many forms are genetically, phenotypically and etiologically diverse and it is unknown whether their pathogenesis converges on shared pathways. Mutations in THAP1 [THAP (Thanatos-associated protein) domain containing, apoptosis associated protein 1], a ubiquitously expressed transcription factor with DNA binding and protein-interaction domains, cause dystonia, DYT6. There is a unique, neuronal 50-kDa Thap1-like immunoreactive species, and Thap1 levels are auto-regulated on the mRNA level...
January 24, 2018: PLoS Genetics
Ludwig Geistlinger, Vinicius Henrique da Silva, Aline Silva Mello Cesar, Polyana Cristine Tizioto, Levi Waldron, Ralf Zimmer, Luciana Correia de Almeida Regitano, Luiz Lehmann Coutinho
Copy number variation (CNV) is a frequently observed deviation from the diploid state due to duplication or deletion of genomic regions. Although intensively analyzed for association with diseases and production traits, the specific mechanisms and extent by which such variations affect the phenotype are incompletely understood. We present an integrative study on CNV and genome-wide gene expression in Brazilian Bos indicus cattle. We analyzed CNVs inferred from SNP-chip data for effects on gene expression measured with RNA-seq in skeletal muscle samples of 183 steers...
January 23, 2018: Scientific Reports
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