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https://www.readbyqxmd.com/read/28545587/type-2-diabetes-and-obesity-induce-similar-transcriptional-reprogramming-in-human-myocytes
#1
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/28545555/the-complex-domain-architecture-of-samd9-family-proteins-predicted-stand-like-ntpases-suggests-new-links-to-inflammation-and-apoptosis
#2
Sergei L Mekhedov, Kira S Makarova, Eugene V Koonin
We report a comprehensive computational dissection of the domain architecture of the SAMD9 family proteins that are involved in antivirus and antitumor response in humans. We show that the SAMD9 protein family is represented in most animals and also, unexpectedly, in bacteria, in particular actinomycetes. From the N to C terminus, the core SAMD9 family architecture includes DNA/RNA-binding AlbA domain, a variant Sir2-like domain, a STAND-like P-loop NTPase, an array of TPR repeats and an OB-fold domain with predicted RNA-binding properties...
May 25, 2017: Biology Direct
https://www.readbyqxmd.com/read/28545501/pregnancy-induced-gene-expression-changes-in-vivo-among-women-with-rheumatoid-arthritis-a-pilot-study
#3
Dana E Goin, Mette Kiel Smed, Lior Pachter, Elizabeth Purdom, J Lee Nelson, Hanne Kjærgaard, Jørn Olsen, Merete Lund Hetland, Vibeke Zoffmann, Bent Ottesen, Damini Jawaheer
BACKGROUND: Little is known about gene expression changes induced by pregnancy in women with rheumatoid arthritis (RA) and healthy women because the few studies previously conducted did not have pre-pregnancy samples available as baseline. We have established a cohort of women with RA and healthy women followed prospectively from a pre-pregnancy baseline. In this study, we tested the hypothesis that pregnancy-induced changes in gene expression among women with RA who improve during pregnancy (pregDASimproved) overlap substantially with changes observed among healthy women and differ from changes observed among women with RA who worsen during pregnancy (pregDASworse)...
May 25, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28545403/long-lasting-effect-of-obesity-on-skeletal-muscle-transcriptome
#4
Ilhem Messaoudi, Mithila Handu, Maham Rais, Suhas Sureshchandra, Byung S Park, Suzanne S Fei, Hollis Wright, Ashley E White, Ruhee Jain, Judy L Cameron, Kerri M Winters-Stone, Oleg Varlamov
BACKGROUND: Reduced physical activity and increased intake of calorically-dense diets are the main risk factors for obesity, glucose intolerance, and type 2 diabetes. Chronic overnutrition and hyperglycemia can alter gene expression, contributing to long-term obesity complications. While caloric restriction can reduce obesity and glucose intolerance, it is currently unknown whether it can effectively reprogram transcriptome to a pre-obesity level. The present study addressed this question by the preliminary examination of the transcriptional dynamics in skeletal muscle after exposure to overnutrition and following caloric restriction...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28545146/transcriptomics-technologies
#5
Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan, Thomas Shafee
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst noncoding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28542811/integrative-analyses-reveal-biological-pathways-and-key-genes-in-psoriasis
#6
J Dou, L Zhang, X Xie, L Ye, C Yang, L Wen, C Shen, C Zhu, S Zhao, Z Zhu, B Liang, Z Wang, H Li, X Fan, S Liu, X Yin, X Zheng, L Sun, S Yang, Y Cui, F Zhou, X Zhang
BACKGROUND: Psoriasis is a complex disease that is influenced by both genetic and environmental factors with abnormal gene expression in lesional skin. However, no studies are available on genome-scale gene expression of psoriatic lesions in the Chinese population. In addition, systematic studies on the biological pathways, pathogenicity and interaction networks of psoriasis-related genes with abnormal expression profiles require further investigation. OBJECTIVES: To further explore the associated pathways in psoriasis by functional analysis and to identify the key genes by gene pathogenicity analysis...
May 25, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/28542617/inflammatory-and-apoptotic-remodeling-in-autonomic-nervous-system-following-myocardial-infarction
#7
Chen Gao, Kimberly Howard-Quijano, Christoph Rau, Tatsuo Takamiya, Yang Song, Kalyanam Shivkumar, Yibin Wang, Aman Mahajan
BACKGROUND: Chronic myocardial infarction (MI) triggers pathological remodeling in the heart and cardiac nervous system. Abnormal function of the autonomic nervous system (ANS), including stellate ganglia (SG) and dorsal root ganglia (DRG) contribute to increased sympathoexcitation, cardiac dysfunction and arrythmogenesis. ANS modulation is a therapeutic target for arrhythmia associated with cardiac injury. However, the molecular mechanism involved in the pathological remodeling in ANS following cardiac injury remains to be established...
2017: PloS One
https://www.readbyqxmd.com/read/28542579/transcriptomic-dissection-reveals-wide-spread-differential-expression-in-chickpea-during-early-time-points-of-fusarium-oxysporum-f-sp-ciceri-race-1-attack
#8
Sumanti Gupta, Anirban Bhar, Moniya Chatterjee, Amartya Ghosh, Sampa Das
Plants' reaction to underground microorganisms is complex as sessile nature of plants compels them to prioritize their responses to diverse microorganisms both pathogenic and symbiotic. Roots of important crops are directly exposed to diverse microorganisms, but investigations involving root pathogens are significantly less. Thus, more studies involving root pathogens and their target crops are necessitated to enrich the understanding of underground interactions. Present study reported the molecular complexities in chickpea during Fusarium oxysporum f...
2017: PloS One
https://www.readbyqxmd.com/read/28541580/genes-and-gene-clusters-related-to-genotype-and-drought-induced-variation-in-saccharification-potential-lignin-content-and-wood-anatomical-traits-in-populus-nigra%C3%A2
#9
Henning Wildhagen, Shanty Paul, Mike Allwright, Hazel K Smith, Marta Malinowska, Sabine K Schnabel, M João Paulo, Federica Cattonaro, Vera Vendramin, Simone Scalabrin, Dennis Janz, Cyril Douthe, Oliver Brendel, Cyril Buré, David Cohen, Irène Hummel, Didier Le Thiec, Fred van Eeuwijk, Joost J B Keurentjes, Jaume Flexas, Michele Morgante, Paul Robson, Marie-Béatrice Bogeat-Triboulot, Gail Taylor, Andrea Polle
Wood is a renewable resource that can be employed for the production of second generation biofuels by enzymatic saccharification and subsequent fermentation. Knowledge on how the saccharification potential is affected by genotype-related variation of wood traits and drought is scarce. Here, we used three Populus nigra L. genotypes from habitats differing in water availability to (i) investigate the relationships between wood anatomy, lignin content and saccharification and (ii) identify genes and co-expressed gene clusters related to genotype and drought-induced variation in wood traits and saccharification potential...
May 24, 2017: Tree Physiology
https://www.readbyqxmd.com/read/28541545/kr%C3%A3-ppel-like-factors-compete-for-promoters-and-enhancers-to-fine-tune-transcription
#10
Melissa D Ilsley, Kevin R Gillinder, Graham W Magor, Stephen Huang, Timothy L Bailey, Merlin Crossley, Andrew C Perkins
Krüppel-like factors (KLFs) are a family of 17 transcription factors characterized by a conserved DNA-binding domain of three zinc fingers and a variable N-terminal domain responsible for recruiting cofactors. KLFs have diverse functions in stem cell biology, embryo patterning, and tissue homoeostasis. KLF1 and related family members function as transcriptional activators via recruitment of co-activators such as EP300, whereas KLF3 and related members act as transcriptional repressors via recruitment of C-terminal Binding Proteins...
May 24, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28540674/microrna-expression-protein-participants-in-microrna-regulation
#11
Valeria M King, Glen M Borchert
MiRNAs are ~20 nt small RNAs that regulate networks of proteins using a seed region of nucleotides 2-8 to complement the 3' UTR of target mRNAs. The biogenesis and function of miRNAs as translational repressors is facilitated by protein counterparts that process primary and precursor miRNAs to maturity (Drosha/DCGR8 and Dicer/TRBP respectively) and incorporate miRNAs into the protein complex RISC to recognize and repress target mRNAs (RISC proteins: Ago/TRBP1/TRBP2/DICER). Similarly, siRNAs through comparable mechanisms are loaded into the protein complex RITS to heterochromatin formation of DNA and suppress transcription of particular genes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540181/dynamic-regulation-of-small-rnaome-during-the-early-stage-of-cardiac-differentiation-from-pluripotent-embryonic-stem-cells
#12
Yue Li, An Zeng, Ge Li, Ya-Na Guan, Huang-Tian Yang, Bairong Shen, Qing Jing
Embryonic stem cells (mESCs), having potential to differentiate into three germ-layer cells including cardiomyocytes, shall be a perfect model to help understanding heart development. Here, using small RNA deep sequencing, we studied the small RNAome in the early stage of mouse cardiac differentiation. We found that the expression pattern of most microRNA (miRNA) were highly enriched at the beginning and declined thereafter, some were still insufficiently expressed on day 6, and most miRNAs recovered in the following days...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28538214/profiling-and-bioinformatic-analysis-of-circular-rna-expression-regulated-by-c-myc
#13
Qiheng Gou, Ke Wu, Jian-Kang Zhou, Yuxin Xie, Lunxu Liu, Yong Peng
The c-Myc transcription factor is involved in cell proliferation, cell cycle and apoptosis by activating or repressing transcription of multiple genes. Circular RNAs (circRNAs) are widely expressed non-coding RNAs participating in the regulation of gene expression. Using a high-throughput microarray assay, we showed that Myc regulates the expression of certain circRNAs. A total of 309 up- and 252 down-regulated circRNAs were identified. Among them, randomly selected 8 circRNAs were confirmed by real-time PCR...
May 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28538170/yap-regulates-actin-dynamics-through-arhgap29-and-promotes-metastasis
#14
Yiting Qiao, Jianxiang Chen, Ying Bena Lim, Megan Louise Finch-Edmondson, Veerabrahma Pratap Seshachalam, Lei Qin, Tingting Jiang, Boon Chuan Low, Himanshu Singh, Chwee Teck Lim, Marius Sudol
Yes-associated protein (YAP) is regulated by mechanical cues via the interaction of the Hippo pathway with cytoskeleton. Previous studies showed that YAP plays a role in regulating the actomyosin network by suppressing Rho GTPase in medaka fish. Here, we identify Rho GTPase activating protein 29 (ARHGAP29) as a transcriptional target of YAP in a human gastric cancer cell line. YAP promotes the expression of ARHGAP29 to suppress the RhoA-LIMK-cofilin pathway, destabilizing F-actin. The overexpression of YAP causes cytoskeletal rearrangement by altering the dynamics of F-actin/G-actin turnover, thus promoting migration...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28536831/abnormal-expression-of-long-non-coding-rnas-in-myocardial-infarction
#15
Tao Wu, Huan-Dong Wu, Zao-Xian Xu, Fei Han, Bi-Qi Zhang, Jian Sun, Shen-Jiang Hu
Myocardial infarction (MI) is the leading cause of fatality worldwide. Our study aimed to investigate the dysregulated long non-coding RNA (lncRNA) in MI and elucidate the mechanism of it in MI. The lncRNA and mRNA expression profiling of the whole left ventricular tissue of MI mice model (8 mice) and Sham group (8 mice) was obtained based on microarray analysis. Differentially expressed lnRNAs/mRNA (DELs/DEMs) were identified in MI. DELs/DEMs co-expression network construction, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were conducted to predict the biological functions of DEMs...
May 23, 2017: Heart and Vessels
https://www.readbyqxmd.com/read/28536419/the-long-non-coding-rna-linc00152-is-essential-for-cell-cycle-progression-through-mitosis-in-hela-cells
#16
Linda Nötzold, Lukas Frank, Minakshi Gandhi, Maria Polycarpou-Schwarz, Matthias Groß, Manuel Gunkel, Nina Beil, Holger Erfle, Nathalie Harder, Karl Rohr, Jakob Trendel, Jeroen Krijgsveld, Thomas Longerich, Peter Schirmacher, Michael Boutros, Sylvia Erhardt, Sven Diederichs
In recent years, long non-coding RNA (lncRNA) research has identified essential roles of these transcripts in virtually all physiological cellular processes including tumorigenesis, but their functions and molecular mechanisms are poorly understood. In this study, we performed a high-throughput siRNA screen targeting 638 lncRNAs deregulated in cancer entities to analyse their impact on cell division by using time-lapse microscopy. We identified 26 lncRNAs affecting cell morphology and cell cycle including LINC00152...
May 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28536283/signal-integration-in-quorum-sensing-enables-cross-species-induction-of-virulence-in-pectobacterium-wasabiae
#17
Rita S Valente, Pol Nadal-Jimenez, André F P Carvalho, Filipe J D Vieira, Karina B Xavier
Bacterial communities can sense their neighbors, regulating group behaviors in response to cell density and environmental changes. The diversity of signaling networks in a single species has been postulated to allow custom responses to different stimuli; however, little is known about how multiple signals are integrated and the implications of this integration in different ecological contexts. In the plant pathogen Pectobacterium wasabiae (formerly Erwinia carotovora), two signaling networks-the N-acyl homoserine lactone (AHL) quorum-sensing system and the Gac/Rsm signal transduction pathway-control the expression of secreted plant cell wall-degrading enzymes, its major virulence determinants...
May 23, 2017: MBio
https://www.readbyqxmd.com/read/28535504/long-non-coding-rna-kcnq1ot1-promotes-cataractogenesis-via-mir-214-and-activation-of-the-caspase-1-pathway
#18
Xin Jin, Hao Jin, Yan Shi, Yiyuan Guo, Hong Zhang
BACKGROUND/AIMS: KCNQ1OT1 regulates the expression of tissue-specific imprinted genes within the Kcnq1 domain. Imprinted genes are positive regulators of apoptosis, one of the forms of cell death related to cataract formation, and thus may provide novel therapeutic targets for cataract treatment. Here, we studied the role of non-coding RNAs(ncRNA) in cataract formation. METHODS: Human lens epithelium cells (HLECs) were treated with H2O2, and the expression of KCNQ1OT1 and miR-214 was detected by qRT-PCR...
May 25, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28534948/dual-strands-of-pre-mir%C3%A2-150-mir%C3%A2-150%C3%A2-5p-and-mir%C3%A2-150%C3%A2-3p-act-as-antitumor-mirnas-targeting-spock1-in-na%C3%A3-ve-and-castration-resistant-prostate-cancer
#19
Atsushi Okato, Takayuki Arai, Satoko Kojima, Keiichi Koshizuka, Yusaku Osako, Tetsuya Idichi, Akira Kurozumi, Yusuke Goto, Mayuko Kato, Yukio Naya, Tomohiko Ichikawa, Naohiko Seki
Analysis of our microRNA (miRNA) expression signature in human cancers has shown that guide and passenger strands of pre-miR‑150, i.e., miR‑150‑5p and miR‑150‑3p, are significantly downregulated in cancer tissues. In miRNA biogenesis, the passenger strand of miRNA is degraded and is thought to have no functions. Thus, the aim of this study was to investigate the functional significance of miR‑150‑5p and miR‑150‑3p in naïve prostate cancer (PCa) and castration-resistant prostate cancer (CRPC)...
May 17, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28534714/profiling-and-bioinformatics-analyses-reveal-differential-circular-rna-expression-in-hypertensive-patients
#20
Na Wu, Ling Jin, Jun Cai
OBJECTIVES: CircRNAs, a novel class of noncoding RNAs, have been reported in many diseases. However, their role in hypertension remains unclear. Here, we aimed to determine the circRNA expression profile in hypertension patients and further construct a circRNA-miRNA-mRNA network for mechanism exploration. METHODS: Plasma circRNA expression profiles were screened by circRNA microarrays and verified by qRT-PCR method. CircRNA-miRNA-mRNA network was established to predict the circRNA targets...
May 23, 2017: Clinical and Experimental Hypertension: CHE
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