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3' utr intron

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https://www.readbyqxmd.com/read/29143945/one-evidence-of-cocaine-and-amphetamine-regulated-transcript-cart-has-the-bidirectional-effects-on-appetite-in-siberian-sturgeon-acipenser-baerii
#1
Xin Zhang, Yundi Gao, Ni Tang, Jinwen Qi, Yuanbing Wu, Jin Hao, Shuyao Wang, Defang Chen, Zhiqiong Li
Cocaine- and amphetamine-regulated transcript (CART), discovered in 1995, with various biological functions, has received much attention recently due to its role in the regulation of appetite in mammals. However, the function of CART on the appetite control in fish species is still not very clear. In this study, Siberian sturgeon (Acipenser baerii Brandt) cart gene was cloned for the first time, and the cart mRNA levels in 11 feeding-related tissues was investigated. The Siberian sturgeon cart gene sequence was 1459 base pairs (bp), including a 3'-terminal untranslated region (3'-UTR) of 39 bp, a 5'-terminal untranslated region (5'-UTR) of 52 bp, and an open reading frame (ORF) of 348 bp encoding 115 amino acids...
November 16, 2017: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/29141666/intron-retention-enhances-gene-regulatory-complexity-in-vertebrates
#2
Ulf Schmitz, Natalia Pinello, Fangzhi Jia, Sultan Alasmari, William Ritchie, Maria-Cristina Keightley, Shaniko Shini, Graham J Lieschke, Justin J-L Wong, John E J Rasko
BACKGROUND: While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of IR, we performed an exhaustive phylogenetic analysis in a highly purified and functionally defined cell type comprising neutrophilic granulocytes from five vertebrate species spanning 430 million years of evolution. RESULTS: Our RNA-sequencing-based analysis suggests that IR increases gene regulatory complexity, which is indicated by a strong anti-correlation between the number of genes affected by IR and the number of protein-coding genes in the genome of individual species...
November 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/29073727/mouse-double-minute-4-variants-modify-susceptibility-to-risk-of-recurrence-in-patients-with-squamous-cell-carcinoma-of-the-oropharynx
#3
Zhongming Lu, Erich M Sturgis, Lijun Zhu, Hua Zhang, Ye Tao, Peng Wei, Qingyi Wei, Guojun Li
Given the crucial role of Mouse double minute 4 (MDM4) oncoprotein in p53 pathway, single nucleotide polymorphisms (SNPs) could serve as such biomarkers for prediction of SCCOP recurrence. Thus, we investigated associations between three tagging putatively functional variants of MDM4, two in the 3' untranslated region of 3' UTR [rs11801299 (NC_000001.10:g.204529084G>A) and rs10900598(NC_000001.10:g.204525568G>T)] and one in intron 1 [rs1380576(NC_000001.10:g.204488278G>C)], and recurrence risk of SCCOP in 1,008 incident patients...
October 26, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/29039460/characterization-of-tree-shrew-tupaia-belangeri-interleukin-6-and-its-expression-pattern-in-response-to-exogenous-challenge
#4
Yuanyuan Han, Xiaomei Sun, Dexuan Kuang, Pinfen Tong, Caixia Lu, Wenguang Wang, Na Li, Yang Chen, Xiaoping Wang, Jiejie Dai, Huatang Zhang
Tree shrews, one of the closest relatives of primates, have attracted increasing attention as a model of human diseases, particularly for viral infections. As the first line of defense against microbial pathogens, the innate immune system is crucial in tree shrews. Interleukin-6 (IL-6) is important in the pathophysiology of infection, inflammation and cancer, where it promotes disease development or sustains immune reactions. The present study aimed to obtain further insight into the tree shrew IL-6 (tsIL-6) system, and the function of tsIL-6 in the antiviral and antibacterial response...
October 2, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28951221/a-novel-stimulator-of-interferon-gene-sting-from-larimichthys-crocea-and-their-involvement-in-immune-response-to-ectoparasite-cryptocaryon-irritans-infection
#5
Li-Bing Zheng, Jun Wang, Yong Mao, Ruan-Ni Chen, Yong-Quan Su, Jia Chen, Qiao-Zhen Ke, Wei-Qiang Zheng
The marine white spot disease caused by protozoan ectoparasite Cryptocaryon irritans is a severe problem to the large yellow croaker farming industry. To understand the molecular immune mechanisms and improve its immune capacity are particular important. STING, one of the important second messengers in innate immune response process, plays pivotal roles in defensing against different pathogenic microorganisms. Many reports have pointed that STING could not only combine the uncovered dsDNA, ssDNA directly in the cytoplasm from the pathogens or biology itself, but it also could recognize cyclic diguanylate monophosphate (c-di-GMP), cyclic diadenylate monophosphate (c-di-AMP)...
September 23, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28926398/association-of-a-3-untranslated-region-polymorphism-in-pcsk9-with-hiv-viral-load-and-cd4-levels-in-hiv-hepatitis-c-virus-co-infected-women
#6
Mark H Kuniholm, Hua Liang, Kathryn Anastos, Deborah Gustafson, Seble Kassaye, Marek Nowicki, Beverly E Sha, Emilia J Pawlowski, Stephen J Gange, Bradley E Aouizerat, Tatiana Pushkarsky, Michael I Bukrinsky, Vinayaka R Prasad
OBJECTIVE: To assess variation in genes that regulate cholesterol metabolism in relation to the natural history of HIV infection. DESIGN: Cross-sectional and longitudinal analysis of the Women's Interagency HIV Study (WIHS). METHODS: We examined 2,050 single nucleotide polymorphisms (SNPs) in 19 genes known to regulate cholesterol metabolism in relation to HIV viral load and CD4 T cell levels in a multiracial cohort of 1,066 antiretroviral therapy (ART) naïve women...
September 18, 2017: AIDS
https://www.readbyqxmd.com/read/28901494/molecular-mechanisms-of-pathogenesis-in-hepatocellular-carcinoma-revealed-by-rna%C3%A2-sequencing
#7
Yao Liu, Zhe Yang, Feng Du, Qiao Yang, Jie Hou, Xiaohong Yan, Yi Geng, Yaning Zhao, Hua Wang
The present study aimed to explore the underlying molecular mechanisms of hepatocellular carcinoma (HCC). RNA‑sequencing profiles GSM629264 and GSM629265, from the GSE25599 data set, were downloaded from the Gene Expression Omnibus database and processed by quality evaluation. GSM629264 and GSM629265 were from HCC and adjacent non‑cancerous tissues, respectively. TopHat software was used for alignment analysis, followed by the detection of novel splicing sites. In addition, the Cufflinks software package was used to analyze gene expressions, and the Cuffdiff program was used to screen for differently expressed genes (DEGs) and differentially expressed splicing variants...
November 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28886202/fuchs-endothelial-corneal-dystrophy-and-rna-foci-in-patients-with-myotonic-dystrophy
#8
V Vinod Mootha, Brock Hansen, Ziye Rong, Pradeep P Mammen, Zhengyang Zhou, Chao Xing, Xin Gong
Purpose: The most common cause of Fuchs' endothelial corneal dystrophy (FECD) is an intronic CTG repeat expansion in TCF4. Expanded CUG repeat RNA colocalize with splicing factor, muscleblind-like 1 (MBNL1), in nuclear foci in endothelium as a molecular hallmark. Myotonic dystrophy type 1 (DM1) is a neuromuscular disorder caused by a CTG repeat expansion in the 3'-untranslated region (UTR) of DMPK. In this study, we examine for RNA-MBNL1 foci in endothelial cells of FECD subjects with DM1, test the hypothesis that DM1 patients are at risk for FECD, and determine prevalence of TCF4 and DMPK expansions in a FECD cohort...
September 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28867604/characterization-and-genomic-localization-of-a-smad4-processed-pseudogene
#9
Christopher M Watson, Nick Camm, Laura A Crinnion, Agne Antanaviciute, Julian Adlard, Alexander F Markham, Ian M Carr, Ruth Charlton, David T Bonthron
Like many clinical diagnostic laboratories, the Yorkshire Regional Genetics Service undertakes routine investigation of cancer-predisposed individuals by high-throughput sequencing of patient DNA that has been target-enriched for genes associated with hereditary cancer. Accurate diagnosis using such reagents requires alertness regarding rare nonpathogenic variants that may interfere with variant calling. In a cohort of 2042 such cases, we identified 5 that initially appeared to be carriers of a 95-bp deletion of SMAD4 intron 6...
September 1, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28821541/targeting-mir-423-5p-reverses-exercise-training-induced-hcn4-channel-remodeling-and-sinus-bradycardia
#10
Alicia D'Souza, Charles M Pearman, Yanwen Wang, Shu Nakao, Sunil Jit R J Logantha, Charlotte Cox, Hayley Bennett, Yu Zhang, Anne Berit Johnsen, Nora Linscheid, Pi Camilla Poulsen, Jonathan Elliott, Jessica Coulson, Jamie McPhee, Abigail Robertson, Paula A da Costa Martins, Ashraf Kitmitto, Ulrik Wisløff, Elizabeth J Cartwright, Oliver Monfredi, Alicia Lundby, Halina Dobrzynski, Delvac Oceandy, Gwilym M Morris, Mark R Boyett
RATIONALE: Downregulation of the pacemaking ion channel, HCN4 (hyperpolarization-activated cyclic nucleotide gated channel 4), and the corresponding ionic current, If, underlies exercise training-induced sinus bradycardia in rodents. If this occurs in humans, it could explain the increased incidence of bradyarrhythmias in veteran athletes, and it will be important to understand the underlying processes. OBJECTIVE: To test the role of HCN4 in the training-induced bradycardia in human athletes and investigate the role of microRNAs (miRs) in the repression of HCN4...
October 13, 2017: Circulation Research
https://www.readbyqxmd.com/read/28815537/from-heterochromatin-to-long-noncoding-rnas-in-drosophila-expanding-the-arena-of-gene-function-and-regulation
#11
Subhash C Lakhotia
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28807314/a-candidate-gene-approach-to-study-nematode-resistance-traits-in-naturally-infected-sheep
#12
Hazel Wilkie, Valentina Riggio, Oswald Matika, Louise Nicol, Kathryn A Watt, Rona Sinclair, Alexandra M Sparks, Daniel H Nussey, Josephine M Pemberton, Ross D Houston, John Hopkins
Sheep naturally acquire a degree of resistant immunity to parasitic worm infection through repeated exposure. However, the immune response and clinical outcome vary greatly between animals. Genetic polymorphisms in genes integral to differential T helper cell polarization may contribute to variation in host response and disease outcome. A total of twelve single nucleotide polymorphisms (SNPs) were sequenced in IL23R, RORC2 and TBX21 from genomic DNA of Scottish Blackface lambs. Of the twelve SNPs, six were non-synonymous (missense), four were within the 3' UTRs and two were intronic...
August 30, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28765142/a-retained-intron-in-the-3-utr-of-calm3-mrna-mediates-its-staufen2-and-activity-dependent-localization-to-neuronal-dendrites
#13
Tejaswini Sharangdhar, Yoichiro Sugimoto, Jacqueline Heraud-Farlow, Sandra M Fernández-Moya, Janina Ehses, Igor Ruiz de Los Mozos, Jernej Ule, Michael A Kiebler
Dendritic localization and hence local mRNA translation contributes to synaptic plasticity in neurons. Staufen2 (Stau2) is a well-known neuronal double-stranded RNA-binding protein (dsRBP) that has been implicated in dendritic mRNA localization. The specificity of Stau2 binding to its target mRNAs remains elusive. Using individual-nucleotide resolution CLIP (iCLIP), we identified significantly enriched Stau2 binding to the 3'-UTRs of 356 transcripts. In 28 (7.9%) of those, binding occurred to a retained intron in their 3'-UTR The strongest bound 3'-UTR intron was present in the longest isoform of Calmodulin 3 (Calm3L ) mRNA Calm3L 3'-UTR contains six Stau2 crosslink clusters, four of which are in this retained 3'-UTR intron...
October 2017: EMBO Reports
https://www.readbyqxmd.com/read/28728506/microsatellite-instability-and-promoter-hypermethylation-of-dna-repair-genes-in-hematologic-malignancies-a-forthcoming-direction-toward-diagnostics
#14
Priyanjali Bhattacharya, Trupti N Patel
OBJECTIVE: The objective of our review is to highlight the significance of microsatellite hypervariation in diagnostics of hematologic malignancies. METHODS: For the past few decades, extensive experiments in cancer research have explored all the possible pathways and a number of deleterious mutations that either make the tumor suppressor genes (TSGs) dysfunctional or cause the proto-oncogenes to behave abnormally by changing the cellular phenotype hence rendering disease...
July 20, 2017: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/28698179/a-novel-regulatory-mechanism-of-smooth-muscle-%C3%AE-actin-expression-by-nrg-1-circacta2-mir-548f-5p-axis
#15
Yan Sun, Zhan Yang, Bin Zheng, Xin-Hua Zhang, Man-Li Zhang, Xue-Shan Zhao, Hong-Ye Zhao, Toru Suzuki, Jin-Kun Wen
RATIONALE: Neuregulin-1 (NRG-1) includes an extracellular epidermal growth factor-like domain and an intracellular domain (NRG-1-ICD). In response to transforming growth factor-β1, its cleavage by proteolytic enzymes releases a bioactive fragment, which suppresses the vascular smooth muscle cell (VSMC) proliferation by activating ErbB (erythroblastic leukemia viral oncogene homolog) receptor. However, NRG-1-ICD function in VSMCs remains unknown. OBJECTIVE: Here, we characterize the function of NRG-1-ICD and underlying mechanisms in VSMCs...
September 1, 2017: Circulation Research
https://www.readbyqxmd.com/read/28697396/novel-mutations-in-the-exon-5-intron-2-and-3-utr-regions-of-il-12b-gene-were-observed-in-clinically-proven-tuberculosis-patients-of-south-india
#16
Pallipamu Prakash Babu, Pasupuleti Santhosh Kumar, Alladi Mohan, Bhattaram Siddhartha Kumar, Potukuchi Venkata Gurunadha Krishna Sarma
Interleukin-12 (IL-12) is formed by the interaction of IL-12p35 and IL-12p40 expressed independently from IL-12A and IL-12B genes. This interleukin plays prominent role in the T-helper type-1 (Th1) response against intracellular pathogens. Variations in IL-12B gene causes disruption of various activities one of them is suppression of Th1 response and is one of the characteristic features observed in patients with active tuberculosis. Hence, in the present study IL-12B gene status was evaluated in 50 new sputum smear-positive pulmonary tuberculosis patients (NSP-PTB) as identified by Ziehl-Nielsen (ZN) staining and 50 apparently healthy control subjects (HCS) who were sputum smear-negative...
July 8, 2017: Cytokine
https://www.readbyqxmd.com/read/28651633/improved-methods-and-resources-for-paramecium-genomics-transcription-units-gene-annotation-and-gene-expression
#17
Olivier Arnaiz, Erwin Van Dijk, Mireille Bétermier, Maoussi Lhuillier-Akakpo, Augustin de Vanssay, Sandra Duharcourt, Erika Sallet, Jérôme Gouzy, Linda Sperling
BACKGROUND: The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigenetics of Paramecium acquired over the last century, this species complex offers a uniquely powerful system to investigate the consequences of whole genome duplication in a unicellular eukaryote as well as the genetic and epigenetic mechanisms that drive speciation. High quality Paramecium gene models are important for research using this system...
June 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28620087/daily-activity-of-the-housefly-musca-domestica-is-influenced-by-temperature-independent-of-3-utr-period-gene-splicing
#18
Olga Bazalova, David Dolezel
Circadian clocks orchestrate daily activity patterns and free running periods of locomotor activity under constant conditions. While the first often depends on temperature, the latter is temperature-compensated over a physiologically relevant range. Here, we explored the locomotor activity of the temperate housefly Musca domestica Under low temperatures, activity was centered round a major and broad afternoon peak, while high temperatures resulted in activity throughout the photophase with a mild midday depression, which was especially pronounced in males exposed to long photoperiods...
August 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28559476/noncanonical-alternative-polyadenylation-contributes-to-gene-regulation-in-response-to-hypoxia
#19
Laura de Lorenzo, Reed Sorenson, Julia Bailey-Serres, Arthur G Hunt
Stresses from various environmental challenges continually confront plants, and their responses are important for growth and survival. One molecular response to such challenges involves the alternative polyadenylation of mRNA. In plants, it is unclear how stress affects the production and fate of alternative mRNA isoforms. Using a genome-scale approach, we show that in Arabidopsis thaliana, hypoxia leads to increases in the number of mRNA isoforms with polyadenylated 3' ends that map to 5'-untranslated regions (UTRs), introns, and protein-coding regions...
June 2017: Plant Cell
https://www.readbyqxmd.com/read/28555142/oligodeoxynucleotides-can-transiently-up-and-downregulate-chs-gene-expression-in-flax-by-changing-dna-methylation-in-a-sequence-specific-manner
#20
Magdalena Dzialo, Jan Szopa, Tadeusz Czuj, Magdalena Zuk
Chalcone synthase (CHS) has been recognized as an essential enzyme in the phenylpropanoid biosynthesis pathway. Apart from the leading role in the production of phenolic compounds with many valuable biological activities beneficial to biomedicine, CHS is well appreciated in science. Genetic engineering greatly facilitates expanding knowledge on the function and genetics of CHS in plants. The CHS gene is one of the most intensively studied genes in flax. In our study, we investigated engineering of the CHS gene through genetic and epigenetic approaches...
2017: Frontiers in Plant Science
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