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muscle RNA-seq

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https://www.readbyqxmd.com/read/28717200/genome-wide-rna-sequencing-analysis-identifies-a-distinct-fibrosis-gene-signature-in-the-conjunctiva-after-glaucoma-surgery
#1
Cynthia Yu-Wai-Man, Nicholas Owen, Jonathan Lees, Aristides D Tagalakis, Stephen L Hart, Andrew R Webster, Christine A Orengo, Peng T Khaw
Fibrosis-related events play a part in most blinding diseases worldwide. However, little is known about the mechanisms driving this complex multifactorial disease. Here we have carried out the first genome-wide RNA-Sequencing study in human conjunctival fibrosis. We isolated 10 primary fibrotic and 7 non-fibrotic conjunctival fibroblast cell lines from patients with and without previous glaucoma surgery, respectively. The patients were matched for ethnicity and age. We identified 246 genes that were differentially expressed by over two-fold and p < 0...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28706492/lower-expression-of-slc27a1-enhances-intramuscular-fat-deposition-in-chicken-via-down-regulated-fatty-acid-oxidation-mediated-by-cpt1a
#2
Fengfang Qiu, Liang Xie, Jing-E Ma, Wen Luo, Li Zhang, Zhe Chao, Shaohao Chen, Qinghua Nie, Zhemin Lin, Xiquan Zhang
Intramuscular fat (IMF) is recognized as the predominant factor affecting meat quality due to its positive correlation with tenderness, juiciness, and flavor. Chicken IMF deposition depends on the balance among lipid synthesis, transport, uptake, and subsequent metabolism, involving a lot of genes and pathways, however, its precise molecular mechanisms remain poorly understood. In the present study, the breast muscle tissue of female Wenchang chickens (WC) (higher IMF content, 1.24 in D120 and 1.62 in D180) and female White Recessive Rock chickens (WRR; lower IMF content, 0...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28702480/dataset-on-transcriptional-profiles-and-the-developmental-characteristics-of-pdgfr%C3%AE-expressing-lung-fibroblasts
#3
Mehari Endale, Shawn Ahlfeld, Erik Bao, Xiaoting Chen, Jenna Green, Zach Bess, Matthew Weirauch, Yan Xu, Anne Karina Perl
The following data are derived from key stages of acinar lung development and define the developmental role of lung interstitial fibroblasts expressing platelet-derived growth factor alpha (PDGFRα). This dataset is related to the research article entitled "Temporal, spatial, and phenotypical changes of PDGFRα expressing fibroblasts during late lung development" (Endale et al., 2017) [1]. At E16.5 (canalicular), E18.5 (saccular), P7 (early alveolar) and P28 (late alveolar), PDGFRα(GFP) mice, in conjunction with immunohistochemical markers, were utilized to define the spatiotemporal relationship of PDGFRα(+) fibroblasts to endothelial, stromal and epithelial cells in both the proximal and distal acinar lung...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28688178/transcriptomic-analysis-identifies-a-role-of-pi3k-akt-signalling-in-the-responses-of-skeletal-muscle-to-acute-hypoxia-in-vivo
#4
Zhuohui Gan, Frank L Powell, Alexander C Zambon, Kyle S Buchholz, Zhenxing Fu, Karen Ocorr, Rolf Bodmer, Esteban A Moya, Jennifer C Stowe, Gabriel G Haddad, Andrew D McCulloch
The effects of acute hypoxia have been widely studied, but there are few studies of transcriptional responses to hours of hypoxia in vivo, especially in hypoxia-tolerant tissues like skeletal muscles. We used RNA-seq to analyse gene expression in plantaris muscles while monitoring respiration, arterial blood gases, and blood glucose in mice exposed to 8% O2 for 2 or 6 h. Rapid decreases in blood gases and a slower reduction in blood glucose suggest stress, which was accompanied by widespread changes in gene expression...
July 8, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28687512/recessive-mutation-in-exosc3-associates-with-mitochondrial-dysfunction-and-pontocerebellar-hypoplasia
#5
Gudrun Schottmann, Sylvie Picker-Minh, Jana Marie Schwarz, Esther Gill, Richard J T Rodenburg, Werner Stenzel, Angela M Kaindl, Markus Schuelke
Recessive mutations in EXOSC3, encoding a subunit of the human RNA exosome complex, cause pontocerebellar hypoplasia type 1b (PCH1B). We report a boy with severe muscular hypotonia, psychomotor retardation, progressive microcephaly, and cerebellar atrophy. Biochemical abnormalities comprised mitochondrial complex I and pyruvate dehydrogenase complex (PDHc) deficiency. Whole exome sequencing uncovered a known EXOSC3 mutation p.(D132A) as the underlying cause. In patient fibroblasts, a large portion of the EXOSC3 protein was trapped in the cytosol...
July 4, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28666194/dietary-cholesterol-induced-transcriptome-differences-in-the-intestine-hepatopancreas-and-muscle-of-oriental-river-prawn-macrobrachium-nipponense
#6
Xizhang Gu, Hongtuo Fu, Shengming Sun, Hui Qiao, Wenyi Zhang, Sufei Jiang, Yiwei Xiong, Shubo Jin, Yongsheng Gong, Yan Wu
Cholesterol is an important nutrient for crustaceans. In this study, we performed comparative transcriptome analyses to explore the transcriptome differences in the intestine, hepatopancreas, and muscle of Macrobrachium nipponense fed either a low cholesterol (LC) or high cholesterol (HC) diet (2.8 or 17.1g cholesterol per kg diet). High-throughput RNA-Seq was conducted, resulting in 7.65, 5.88, and 7.59G clean bases from the intestine, hepatopancreas, and muscle of the LC group, respectively, and 7.59, 6.73, and 6...
June 13, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28662063/rna-seq-and-cytof-immuno-profiling-of-regenerating-lacrimal-glands-identifies-a-novel-subset-of-cells-expressing-muscle-related-proteins
#7
Dillon Hawley, Jian Ding, Suharika Thotakura, Scott Haskett, Hema Aluri, Claire Kublin, Audrey Michel, Lisa Clapisson, Michael Mingueneau, Driss Zoukhri
The purpose of the present studies was to use CyTOF and RNA-Seq technologies to identify cells and genes involved in lacrimal gland repair that could be targeted to treat diseases of lacrimal gland dysfunction. Lacrimal glands of female BALB/c mice were experimentally injured by intra-glandular injection of interleukin 1 alpha (IL-1α). The lacrimal glands were harvested at various time points following injury (1 to 14 days) and used to either prepare single cell suspensions for CyTOF immuno-phenotyping analyses or to extract RNA for gene expression studies using RNA-Seq...
2017: PloS One
https://www.readbyqxmd.com/read/28575089/transcriptomic-analyses-on-muscle-tissues-of-litopenaeus-vannamei-provide-the-first-profile-insight-into-the-response-to-low-temperature-stress
#8
Wen Huang, Chunhua Ren, Hongmei Li, Da Huo, Yanhong Wang, Xiao Jiang, Yushun Tian, Peng Luo, Ting Chen, Chaoqun Hu
The Pacific white shrimp (Litopenaeus vannamei) is an important cultured crustacean species worldwide. However, little is known about the molecular mechanism of this species involved in the response to cold stress. In this study, four separate RNA-Seq libraries of L. vannamei were generated from 13°C stress and control temperature. Total 29,662 of Unigenes and overall of 19,619 annotated genes were obtained. Three comparisons were carried out among the four libraries, in which 72 of the top 20% of differentially-expressed genes were obtained, 15 GO and 5 KEGG temperature-sensitive pathways were fished out...
2017: PloS One
https://www.readbyqxmd.com/read/28554803/integrated-omics-approaches-to-characterize-a-nuclear-receptor-corepressor-associated-histone-deacetylase-in-mouse-skeletal-muscle
#9
REVIEW
Yingyun Gong, Rui Cao, Guolian Ding, Sungguan Hong, Wenjun Zhou, Wenyun Lu, Manashree Damle, Bin Fang, Chuhan C Wang, Justin Qian, Natasha Lie, Cristina Lanzillotta, Joshua D Rabinowitz, Zheng Sun
Nuclear receptors regulate gene expression by differentially binding to coactivators or corepressors in a ligand-dependent manner, which further recruits a set of epigenome-modifying enzymes that remodel chromatin conformation. Histone acetylation is a major epigenomic change controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs). HDAC3 is the only HDAC that confers the enzymatic activity to the complexes nucleated by nuclear receptor corepressors NCoR and SMRT. To address the metabolic function of HDAC3, we have deleted it specifically in mouse skeletal muscles...
May 26, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28545587/type-2-diabetes-and-obesity-induce-similar-transcriptional-reprogramming-in-human-myocytes
#10
Leif Väremo, Tora Ida Henriksen, Camilla Scheele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen, Jens Nielsen
BACKGROUND: Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to the disease alone. Therefore, here we set out to identify and characterize intrinsic properties of myocytes, associated independently with T2D or obesity. METHODS: We generated and analyzed RNA-seq data from primary differentiated myotubes from 24 human subjects, using a factorial design (healthy/T2D and non-obese/obese), to determine the influence of each specific factor on genome-wide transcription...
May 25, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28536000/an-analysis-of-myod-dependent-transcription-using-crispr-cas9-gene-targeting-in-xenopus-tropicalis-embryos
#11
Caitlin McQueen, Mary Elizabeth Pownall
Myogenic regulatory factors (MRFs) are known to have essential roles in both the establishment and differentiation of the skeletal muscle cell lineage. MyoD is expressed early in the Xenopus mesoderm where it is present and active several hours before the activation of muscle differentiation genes. Previous studies in cultured cells and in Xenopus laevis have identified sets of genes that require MyoD prior to differentiation of skeletal muscle. Here we report results from experiments using CRISPR/Cas9 to target the MyoD gene in the diploid frog Xenopus tropicalis, that are analysed by RNA-seq at gastrula stages...
August 2017: Mechanisms of Development
https://www.readbyqxmd.com/read/28504717/fibulin-3-promotes-muscle-invasive-bladder-cancer
#12
A L Han, B A Veeneman, L El-Sawy, K C Day, M L Day, S A Tomlins, E T Keller
Urothelial carcinoma is the most common type of bladder cancer and can be categorized as either non-muscle-invasive (Ta-T1) or muscle-invasive (⩾T2). The majority of bladder cancers are non-muscle-invasive at presentation; however, the recurrence rate for these tumors is high and a subset can progress to T2. In this study, we aimed to identify genes differentially expressed between T1 vs T2 bladder cancer to identify key regulators of bladder cancer progression and/or invasion. We performed RNA-Seq on T1 and T2 bladder cancer tissues and used publicly available bladder cancer profiling studies to prioritize differentially expressed genes for validation and functional assessment...
May 15, 2017: Oncogene
https://www.readbyqxmd.com/read/28473774/lncrna-six1-encodes-a-micropeptide-to-activate-six1-in-cis-and-is-involved-in-cell-proliferation-and-muscle-growth
#13
Bolin Cai, Zhenhui Li, Manting Ma, Zhijun Wang, Peigong Han, Bahareldin A Abdalla, Qinghua Nie, Xiquan Zhang
Long non-coding RNAs (lncRNAs) play important roles in epigenetic regulation of skeletal muscle development. In our previous RNA-seq study (accession number GSE58755), we found that lncRNA-Six1 is an lncRNA that is differentially expressed between White Recessive Rock (WRR) and Xinghua (XH) chicken. In this study, we have further demonstrated that lncRNA-Six1 is located 432 bp upstream of the gene encoding the protein Six homeobox 1 (Six1). A dual-luciferase reporter assay identified that lncRNA-Six1 overlaps the Six1 proximal promoter...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28472139/gene-expression-profiling-in-pekin-duck-embryonic-breast-muscle
#14
Tie-Shan Xu, Li-Hong Gu, Wei Huang, Wan-Liang Xia, Yun-Sheng Zhang, Ya-Ge Zhang, Guang Rong, Kyle Schachtschneider, Shui-Sheng Hou
Lean-type Pekin duck is a breed gained through long-term selection and great effort has been exerted to understand the mechanisms underlying increased muscle yields. However, the genes involved in Pekin duck embryonic breast muscle development have not been explored to date. In this study, we investigated gene expression profiles in Pekin Duck embryonic breast muscle at hatched day 13 (E13), E19, and E27 using RNA-seq. In total, we produced 519,312,178 raw reads resulting in 497,348,158 high-quality reads after filtering...
2017: PloS One
https://www.readbyqxmd.com/read/28455310/exercise-induced-modification-of-the-skeletal-muscle-transcriptome-in-arabian-horses
#15
Katarzyna Ropka-Molik, Monika Stefaniuk-Szmukier, Kacper Żukowski, Katarzyna Piórkowska, Monika Bugno-Poniewierska
It has been found that Arabian and Thoroughbred horses differ in muscle fiber structure and thus in physiological changes occurring in muscles during exercise. The aim of the present study was to identify the global gene expression modifications that occur in skeletal muscle following a training regime to prepare for flat racing. Whole transcriptomes of muscle (gluteus medius) were compared between three time points of tissue collection: T0 (untrained horses), T1 (horses after intense gallop phase) and T2 (horses at the end of racing season), 23 samples in total...
April 28, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28454518/transcriptome-wide-n-6-methyladenosine-methylome-profiling-of-porcine-muscle-and-adipose-tissues-reveals-a-potential-mechanism-for-transcriptional-regulation-and-differential-methylation-pattern
#16
Xuelian Tao, Jianning Chen, Yanzhi Jiang, Yingying Wei, Yan Chen, Huaming Xu, Li Zhu, Guoqing Tang, Mingzhou Li, Anan Jiang, Surong Shuai, Lin Bai, Haifeng Liu, Jideng Ma, Long Jin, Anxiang Wen, Qin Wang, Guangxiang Zhu, Meng Xie, Jiayun Wu, Tao He, Chunyu Huang, Xiang Gao, Xuewei Li
BACKGROUND: N (6) -methyladenosine (m(6)A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m(6)A methylation on mRNA have been revealed by mapping of m(6)A methylomes in several species. m(6)A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m(6)A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth...
April 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28453623/bayesian-inference-of-allele-specific-gene-expression-indicates-abundant-cis-regulatory-variation-in-natural-flycatcher-populations
#17
Mi Wang, Severin Uebbing, Hans Ellegren
Polymorphism in cis-regulatory sequences can lead to different levels of expression for the two alleles of a gene, providing a starting point for the evolution of gene expression. Little is known about the genome-wide abundance of genetic variation in gene regulation in natural populations but analysis of allele-specific expression (ASE) provides a means for investigating such variation. We performed RNA-seq of multiple tissues from population samples of two closely related flycatcher species and developed a Bayesian algorithm that maximizes data usage by borrowing information from the whole data set and combines several SNPs per transcript to detect ASE...
May 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28450296/endoglin-mediates-vascular-maturation-by-promoting-vascular-smooth-muscle-cell-migration-and-spreading
#18
Hongyu Tian, Tatiana Ketova, Duriel Hardy, Xiaojiang Xu, Xia Gao, Andries Zijlstra, Gerard C Blobe
OBJECTIVE: Endoglin, a transforming growth factor-β superfamily coreceptor, is predominantly expressed in endothelial cells and has essential roles in vascular development. However, whether endoglin is also expressed in vascular smooth muscle cells (VSMCs), especially in vivo, remains controversial. Furthermore, the roles of endoglin in VSMC biology remain largely unknown. Our objective was to examine the expression and determine the function of endoglin in VSMCs during angiogenesis...
June 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28448552/transcriptomic-analysis-of-the-hepatic-response-to-stress-in-the-red-cusk-eel-genypterus-chilensis-insights-into-lipid-metabolism-oxidative-stress-and-liver-steatosis
#19
Sebastian Naour, Brisa M Espinoza, Jorge E Aedo, Rodrigo Zuloaga, Jonathan Maldonado, Macarena Bastias-Molina, Herman Silva, Claudio Meneses, Cristian Gallardo-Escarate, Alfredo Molina, Juan Antonio Valdés
Teleosts exhibit a broad divergence in their adaptive response to stress, depending on the magnitude, duration, and frequency of stressors and the species receiving the stimulus. We have previously reported that the red cusk-eel (Genypterus chilensis), an important marine farmed fish, shows a physiological response to stress that results in increased skeletal muscle atrophy mediated by over-expression of components of the ubiquitin proteasome and autophagy-lysosomal systems. To better understand the systemic effects of stress on the red cusk-eel metabolism, the present study assessed the transcriptomic hepatic response to repetitive handling-stress...
2017: PloS One
https://www.readbyqxmd.com/read/28428068/comparative-analysis-of-gene-expression-profiles-for-several-migrating-cell-types-identifies-cell-migration-regulators
#20
Young-Kyung Bae, Frank Macabenta, Heather Leigh Curtis, Angelike Stathopoulos
Cell migration is an instrumental process that ensures cells are properly positioned to support the specification of distinct tissue types during development. To provide insight, we used fluorescence activated cell sorting (FACS) to isolate two migrating cell types from the Drosophila embryo: caudal visceral mesoderm (CVM) cells, precursors of longitudinal muscles of the gut, and hemocytes (HCs), the Drosophila equivalent of blood cells. ~350 genes were identified from each of the sorted samples using RNA-seq, and in situ hybridization was used to confirm expression within each cell type or, alternatively, within other interacting, co-sorted cell types...
April 18, 2017: Mechanisms of Development
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