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3' utr intron

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https://www.readbyqxmd.com/read/28815537/from-heterochromatin-to-long-noncoding-rnas-in-drosophila-expanding-the-arena-of-gene-function-and-regulation
#1
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
#2
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
#3
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...
August 1, 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
#4
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
#5
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 EGF-like domain and an intracellular domain (NRG-1-ICD). In response to transforming growth factor (TGF)-β1,its cleavage by proteolytic enzymes releases a bioactive fragment, which suppresses the vascular smooth muscle cell (VSMC) proliferation by activating ErbB 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. Methods and Results: Immunofluorescence staining, Western blotting and quantitative real-time polymerase chain reaction (qRT-PCR) showed that NRG-1 was expressed in rat, mouse and human VSMCs and was upregulated and cleaved in response to TGF-β1...
July 11, 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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28547825/dual-redundant-sequencing-strategy-full-length-gene-characterisation-of-1056-novel-and-confirmatory-hla-alleles
#11
V Albrecht, C Zweiniger, V Surendranath, K Lang, G Schöfl, A Dahl, S Winkler, V Lange, I Böhme, A H Schmidt
The high-throughput department of DKMS Life Science Lab encounters novel human leukocyte antigen (HLA) alleles on a daily basis. To characterise these alleles, we have developed a system to sequence the whole gene from 5'- to 3'-UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory - European Nucleotide Archive (EMBL-ENA) and the IPD-IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and single molecule real-time (SMRT) sequencing on a PacBio RS II instrument, we are able to achieve highly accurate HLA full-length consensus sequences...
May 25, 2017: HLA
https://www.readbyqxmd.com/read/28525753/the-u6-snrna-m-6-a-methyltransferase-mettl16-regulates-sam-synthetase-intron-retention
#12
Kathryn E Pendleton, Beibei Chen, Kuanqing Liu, Olga V Hunter, Yang Xie, Benjamin P Tu, Nicholas K Conrad
Maintenance of proper levels of the methyl donor S-adenosylmethionine (SAM) is critical for a wide variety of biological processes. We demonstrate that the N(6)-adenosine methyltransferase METTL16 regulates expression of human MAT2A, which encodes the SAM synthetase expressed in most cells. Upon SAM depletion by methionine starvation, cells induce MAT2A expression by enhanced splicing of a retained intron. Induction requires METTL16 and its methylation substrate, a vertebrate conserved hairpin (hp1) in the MAT2A 3' UTR...
May 18, 2017: Cell
https://www.readbyqxmd.com/read/28464846/sequence-variations-of-the-egr4-gene-in-korean-men-with-spermatogenesis-impairment
#13
Se Ra Sung, Seung Hun Song, Kyung Min Kang, Ji Eun Park, Yeo Jung Nam, Yun-Jeong Shin, Dong Hyun Cha, Ju Tae Seo, Tae Ki Yoon, Sung Han Shim
BACKGROUND: Egr4 is expressed in primary and secondary spermatocytes in adult mouse testes and has a crucial role in regulating germ cell maturation. The functional loss of Egr4 blocks spermatogenesis, significantly reducing the number of spermatozoa that are produced. In this study, we examined whether EGR4 variants are present in Korean men with impaired spermatogenesis. METHODS: A total 170 Korean men with impaired spermatogenesis and 272 normal controls were screened...
May 2, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28400126/targeted-sequencing-of-abca7-identifies-splicing-stop-gain-and-intronic-risk-variants-for-alzheimer-disease
#14
B W Kunkle, R M Carney, M A Kohli, A C Naj, K L Hamilton-Nelson, P L Whitehead, L Wang, R Lang, M L Cuccaro, J M Vance, G S Byrd, G W Beecham, J R Gilbert, E R Martin, J L Haines, M A Pericak-Vance
Several variants in the gene ABCA7 have been identified as potential causal variants for late-onset Alzheimer's disease (LOAD). In order to replicate these findings, and search for novel causal variants, we performed targeted sequencing of this gene in cohorts of non-Hispanic White (NHW) and African-American (AA) LOAD cases and controls. We sequenced the gene ABCA7 in 291 NHW LOAD cases and 103 controls. Variants were prioritized for rare, damaging variants and previously reported variants associated with LOAD, and were follow-up genotyped in 4076 NHW and 1157 AA cases and controls...
April 8, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28272483/snp-snp-interactions-between-wnt4-and-wnt5a-were-associated-with-obesity-related-traits-in-han-chinese-population
#15
Shan-Shan Dong, Wei-Xin Hu, Tie-Lin Yang, Xiao-Feng Chen, Han Yan, Xiang-Ding Chen, Li-Jun Tan, Qing Tian, Hong-Wen Deng, Yan Guo
Considering the biological roles of WNT4 and WNT5A involved in adipogenesis, we aimed to investigate whether SNPs in WNT4 and WNT5A contribute to obesity related traits in Han Chinese population. Targeted genomic sequence for WNT4 and WNT5A was determined in 100 Han Chinese subjects and tag SNPs were selected. Both single SNP and SNP × SNP interaction association analyses with body mass index (BMI) were evaluated in the 100 subjects and another independent sample of 1,627 Han Chinese subjects. Meta-analyses were performed and multiple testing corrections were carried out using the Bonferroni method...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28215743/a-nlrc3-like-gene-from-blunt-snout-bream-megalobrama-amblycephala-molecular-characterization-expression-and-association-with-resistance-to-aeromonas-hydrophila-infection
#16
Fengjuan Zhou, Qifeng Zhan, Zhujin Ding, Lina Su, Jun Fan, Lei Cui, Nan Chen, Weimin Wang, Hong Liu
NLRC (the nucleotide-oligomerization domain (NOD)-like receptor subfamily C) consists of teleost-specific NLRs (NOD-like receptors) and plays pivotal roles in microbial recognition and regulation of innate immune response. In this study, we cloned and characterized a NLRC3-like gene (MamNLRC3-like) from blunt snout bream (Megalobrama amblycephala) by using the quantitative real-time PCR method, and analyzed the correlation between its polymorphisms and resistance to Aeromonas hydrophila infection. The full length cDNA of MamNLRC3-like was 2863 bp, with a 5'-UTR of 169 bp, ORF of 2301 bp and 3'-UTR of 393 bp, encoding 766 amino acid residues...
April 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28102759/antisense-transcription-of-the-myotonic-dystrophy-locus-yields-low-abundant-rnas-with-and-without-cag-n-repeat
#17
Anke E E G Gudde, Simon J van Heeringen, Amanda I de Oude, Ingeborg D G van Kessel, Joseph Estabrook, Eric T Wang, Bé Wieringa, Derick G Wansink
The unstable (CTG·CAG)n trinucleotide repeat in the myotonic dystrophy type 1 (DM1) locus is bidirectionally transcribed from genes with terminal overlap. By transcription in the sense direction, the DMPK gene produces various alternatively spliced mRNAs with a (CUG)n repeat in their 3' UTR. Expression in opposite orientation reportedly yields (CAG)n-repeat containing RNA, but both structure and biologic significance of this antisense gene (DM1-AS) are largely unknown. Via a combinatorial approach of computational and experimental analyses of RNA from unaffected individuals and DM1 patients we discovered that DM1-AS spans >6 kb, contains alternative transcription start sites and uses alternative polyadenylation sites up- and downstream of the (CAG)n repeat...
January 19, 2017: RNA Biology
https://www.readbyqxmd.com/read/28059001/possible-association-of-3-utr-357-a-g-ivs11-nt-93-t-c-c-1311-c-t-polymorphism-with-g6pd-deficiency
#18
Mahmoud M Sirdah, Mohammad E Shubair, Mustafa S Al-Kahlout, Jamal M Al-Tayeb, Josef T Prchal, N Scott Reading
BACKGROUND: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common X-linked inherited enzymopathic disorder affecting more than 500 million people worldwide. It has so far been linked to 217 distinct genetic variants in the exons and exon-intron boundaries of the G6PD gene, giving rise to a wide range of biochemical heterogeneity and clinical manifestations. OBJECTIVES: Reports from different settings suggested the association of intronic and other mutations outside the reading frame of the G6PD gene with reduced enzyme activity and presenting clinical symptoms...
July 2017: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/28006787/role-of-mir-215-in-hirschsprung-s-disease-pathogenesis-by-targeting-siglec-8
#19
Hao Lei, Hongxing Li, Hua Xie, Chunxia Du, Yankai Xia, Weibing Tang
BACKGROUND/AIMS: Hirschsprung's disease (HSCR), known as aganglionosis, is an infrequent congenital gut motility disorder characterized by absence of enteric neurons. In this study, we focus on the role of the intronic miR-215 and its host gene isoleucyl-tRNA synthetase 2 (IARS2) in the pathogenesis of HSCR. METHODS: Quantitative real time PCR and Western blot were used to detect the miRNA, mRNAs, and proteins levels. The dual-luciferase reporter gene assay confirmed the direct regulation of the specific mRNA and miRNAs in cell lines...
2016: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28003160/regulatory-factor-x1-depresses-apoe-dependent-a%C3%AE-uptake-by-mirna-124-in-microglial-response-to-oxidative-stress
#20
Chen-Zhuo Feng, Jin-Bo Yin, Jian-Jun Yang, Lin Cao
Decreased proteolytic clearance of soluble amyloid β (Aβ) in microglia affects Aβ accumulation on Alzheimer's disease progression. However, the potential molecular mechanism by which microglial Aβ uptake is regulated remains unclear. In this study, we identified a microRNA, miR-124, that was down-regulated in aging with a function in regulating apolipoprotein E (ApoE)-dependent Aβ uptake by targeting regulatory factor X1 (RFX1) transcripts on BV2 microglia cell. Decreased expression of miRNA-124 in BV2 cells exposed to mild hydrogen peroxide increased RFX1 protein level and decreased the expression of ApoE, a gene which has been suggested to enhance cellular Aβ uptake in microglia...
March 6, 2017: Neuroscience
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