keyword
MENU ▼
Read by QxMD icon Read
search

upstream open reading frame

keyword
https://www.readbyqxmd.com/read/27864472/transcriptome-wide-identification-of-nmd-targeted-human-mrnas-reveals-extensive-redundancy-between-smg6-and-smg7-mediated-degradation-pathways
#1
Martino Colombo, Evangelos D Karousis, Joël Bourquin, Rémy Bruggmann, Oliver Mühlemann
Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6 and SMG7. We provide evidence that this combinatorial approach identifies NMD-targeted transcripts more reliably than previous attempts that focused on inactivation of single NMD factors...
November 18, 2016: RNA
https://www.readbyqxmd.com/read/27846320/an-inhibitory-motif-on-the-5-utr-of-several-rotavirus-genome-segments-affects-protein-expression-and-reverse-genetics-strategies
#2
Giuditta De Lorenzo, Marija Drikic, Guido Papa, Catherine Eichwald, Oscar R Burrone, Francesca Arnoldi
Rotavirus genome consists of eleven segments of dsRNA, each encoding one single protein. Viral mRNAs contain an open reading frame (ORF) flanked by relatively short untranslated regions (UTRs), whose role in the viral cycle remains elusive. Here we investigated the role of 5'UTRs in T7 polymerase-driven cDNAs expression in uninfected cells. The 5'UTRs of eight genome segments (gs3, gs5-6, gs7-11) of the simian SA11 strain showed a strong inhibitory effect on the expression of viral proteins. Decreased protein expression was due to both compromised transcription and translation and was independent of the ORF and the 3'UTR sequences...
2016: PloS One
https://www.readbyqxmd.com/read/27800707/characterization-of-tilapia-oreochromis-niloticus-aldehyde-reductase-akr1a1-gene-promoter-and-expression-pattern-in-benzo-a-pyrene-exposed-fish
#3
Abeer Hassanin, Yoshio Kaminishi, Takao Itakura
This study planned to isolation and characterization of AKR1A1 cDNA from Bap injected nile tilapia (Oreochromis niloticus), comparison of its characteristic structures with those of other species, characterization of AKR1A1 gene and promoter, and investigation of AKR1A1 mRNA expression in various organs of Bap injected tilapia. The cDNA was 1172 bp long which includes an open reading frame of 975 bp encoding a 324 amino acids protein and a stop codon. The sequence showed 3' and 5' non-coding regions of 179 and 18 bp...
November 1, 2016: Toxicology Mechanisms and Methods
https://www.readbyqxmd.com/read/27790092/upstream-open-reading-frames-located-in-the-leader-of-protein-kinase-m%C3%AE-mrna-regulate-its-translation
#4
Natalia V Bal, Denis Susorov, Ekaterina Chesnokova, Artem Kasianov, Tatiana Mikhailova, Elena Alkalaeva, Pavel M Balaban, Peter Kolosov
For protein synthesis that occurs locally in dendrites, the translational control mechanisms are much more important for neuronal functioning than the transcription levels. Here, we show that uORFs (upstream open reading frames) in the 5' untranslated region (5'UTR) play a critical role in regulation of the translation of protein kinase Mζ (PKMζ). Elimination of these uORFs activates translation of the reporter protein in vitro and in primary cultures of rat hippocampal neurons. Using cell-free translation systems, we demonstrate that translational initiation complexes are formed only on uORFs...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/27789685/hnrnps-and-elavl1-cooperate-with-uorfs-to-inhibit-protein-translation
#5
Jiewen Zhang, Lijuan Kong, Sichao Guo, Mengmeng Bu, Qian Guo, Yuan Xiong, Ning Zhu, Chuan Qiu, Xuejing Yan, Qian Chen, Hongfei Zhang, Junling Zhuang, Qiong Wang, Samuel S Zhang, Yan Shen, Meihong Chen
Most of our knowledge about translation regulatory mechanisms comes from studies on lower organisms. However, the translation control system of higher organisms is less understood. Here we find that in 5' untranslated region (5'UTR) of human Annexin II receptor (AXIIR) mRNA, there are two upstream open reading frames (uORFs) acting in a fail-safe manner to inhibit the translation from the main AUG. These uORFs are unfavorable for re-initiation after termination of uORF translation. Heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1), hnRNPA0 and ELAV like RNA binding protein 1 (ELAVL1) bind to the 5'UTR of AXIIR mRNA...
October 26, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27775442/release-kinetics-of-high-sensitivity-cardiac-troponins-i-and-t-and-troponin-t-upstream-open-reading-frame-peptide-tntuorf-in-clinically-induced-acute-myocardial-infarction
#6
Christoph Liebetrau, Luise Gaede, J Sebastian Wolter, Julia Homann, Alexander Meyer, Oliver Dörr, Holger M Nef, Christian Troidl, Christian W Hamm, Helge Möllmann, A Mark Richards, Chris J Pemberton
CONTEXT: Troponin T upstream open reading frame peptide (TnTuORF) may be useful as a novel biomarker in acute cardiac syndromes. OBJECTIVE: The study examined the early release kinetics of TnTuORF. MATERIALS AND METHODS: We analyzed the time course of the release of cardiac troponins I and T and TnTuORF in patients (n = 31) with hypertrophic obstructive cardiomyopathy undergoing transcoronary ablation of septal hypertrophy (TASH). RESULTS: Fifteen minutes after TASH the levels of both troponins increased significantly (cTnT median: 18 ng/L vs...
October 24, 2016: Biomarkers: Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals
https://www.readbyqxmd.com/read/27768772/de-novo-transcriptomes-of-forsythia-koreana-using-a-novel-assembly-method-insight-into-tissue-and-species-specific-expression-of-lignan-biosynthesis-related-gene
#7
Akira Shiraishi, Jun Murata, Erika Matsumoto, Shin Matsubara, Eiichiro Ono, Honoo Satake
Forsythia spp. are perennial woody plants which are one of the most extensively used medicinal sources of Chinese medicines and functional diets owing to their lignan contents. Lignans have received widespread attention as leading compounds in the development of antitumor drugs and healthy diets for reducing the risks of lifestyle-related diseases. However, the molecular basis of Forsythia has yet to be established. In this study, we have verified de novo deep transcriptome of Forsythia koreana leaf and callus using the Illumina HiSeq 1500 platform...
2016: PloS One
https://www.readbyqxmd.com/read/27760805/the-minimum-open-reading-frame-aug-stop-induces-boron-dependent-ribosome-stalling-and-mrna-degradation
#8
Mayuki Tanaka, Naoyuki Sotta, Yusuke Yamazumi, Yui Yamashita, Kyoko Miwa, Katsunori Murota, Yukako Chiba, Masami Yokota Hirai, Tetsu Akiyama, Hitoshi Onouchi, Satoshi Naito, Toru Fujiwara
Upstream open reading frames (uORFs) are often translated ahead of the main ORF of a gene and regulate gene expression, sometimes in a condition-dependent manner, but such a role for the minimum uORF (hereafter referred to as 'AUG-stop') in living organisms is currently unclear. Here, we show that AUG-stop plays an important role in the boron (B)-dependent regulation of NIP5;1, encoding a boric acid channel required for normal growth under low B conditions in Arabidopsis thaliana. High B enhanced ribosome stalling at AUG-stop, which was accompanied by the suppression of translation and mRNA degradation...
October 19, 2016: Plant Cell
https://www.readbyqxmd.com/read/27758893/genome-wide-mapping-of-uncapped-and-cleaved-transcripts-reveals-a-role-for-the-nuclear-mrna-cap-binding-complex-in-cotranslational-rna-decay-in-arabidopsis
#9
Xiang Yu, Matthew R Willmann, Stephen J Anderson, Brian D Gregory
RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5' end to the 3' end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames...
October 2016: Plant Cell
https://www.readbyqxmd.com/read/27742800/global-analysis-of-truncated-rna-ends-reveals-new-insights-into-ribosome-stalling-in-plants
#10
Cheng-Yu Hou, Wen-Chi Lee, Hsiao-Chun Chou, Ai-Ping Chen, Shu-Jen Chou, Ho-Ming Chen
High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied to analyze and validate cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome other than miRNA targets is currently largely uncharacterized, and this limits the application of RNA degradome studies. We conducted a global analysis of 5'-truncated mRNA ends that mapped to coding sequences (CDSs) of Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max)...
October 2016: Plant Cell
https://www.readbyqxmd.com/read/27733338/construction-of-ctcf-degradation-cell-line-by-crispr-cas9-mediated-genome-editing
#11
Xie Dejian, Shi Minglei, Zhang Yan, Wang Tianyi, Shen Wenlong, Ye Bingyu, Li Ping, He Chao, Zhang Xiangyuan, Zhao Zhihu
The CCCTC-binding factor (CTCF) is the main insulator protein described in vertebrates. It plays fundamental roles during diverse cellular processes. CTCF gene knockout mice led to death during embryonic development. To further explore the functions of CTCF, we employed a CRISPR/Cas9-based genome engineering strategy to in-frame insert the mitosis-special degradation domain (MD) of cyclin B into the upstream open reading frame of CTCF gene. Fusion protein is designed to degrade during mitosis leaded by MD. As a control group, mutation of a single arginine (R42A) within the destruction box inactivates the MD leading to constitutive expression of MD(*)-CTCF...
July 20, 2016: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/27712622/coronavirus-cis-acting-rna-elements
#12
R Madhugiri, M Fricke, M Marz, J Ziebuhr
Coronaviruses have exceptionally large RNA genomes of approximately 30 kilobases. Genome replication and transcription is mediated by a multisubunit protein complex comprised of more than a dozen virus-encoded proteins. The protein complex is thought to bind specific cis-acting RNA elements primarily located in the 5'- and 3'-terminal genome regions and upstream of the open reading frames located in the 3'-proximal one-third of the genome. Here, we review our current understanding of coronavirus cis-acting RNA elements, focusing on elements required for genome replication and packaging...
2016: Advances in Virus Research
https://www.readbyqxmd.com/read/27649606/cloning-and-characterization-of-a-squalene-synthase-gene-from-the-chaga-medicinal-mushroom-inonotus-obliquus-agaricomycetes
#13
Panpan Zhang, Xiaoying Cao, Changgen Li, Zhujun Zheng, Sun Yong, Ji-Hong Jiang
Squalene synthase catalyzes the condensation of 2 molecules of farnesyl diphosphate to produce squalene, the first committed precursor for sterol, brassinosteroid, and triterpene biosynthesis. A squalene synthase gene, designated IoSQS, was isolated from Inonotus obliquus, a medicinal mushroom that produces a plethora of bioactive triterpenes. IoSQS complementary DNA was found to contain an open reading frame of 1476 bp, encoding a protein of 491 amino acids with a calculated molecular mass of 55.85 kDa. The IoSQS genomic DNA sequence consisted of 1813 bp and contained 4 exons and 3 introns...
2016: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/27592105/characterization-of-a-rolling-circle-replication-plasmid-pm411-from-lactobacillus-plantarum-1-3
#14
Xvchuan Ma, Jinhua Li, Yao Xiong, Zhengyuan Zhai, Fazheng Ren, Yanling Hao
A cryptic plasmid pM411 isolated from Lactobacillus plantarum 1-3 consisted of a 2303-bp circular molecule with a G + C content 32.96 %. Sequence analysis of pM411 revealed four putative open reading frames (ORFs). ORF1 shared 99 and 94 % similarities, respectively, with the Rep proteins of plasmids pLC2 and pYC2, which belong to the rolling-circle replication pMV158 family. A typical pMV158 family double-strand origin (dso) and a putative single-strand origin (sso) located upstream of the rep gene. Southern hybridization confirmed the presence of single-strand DNA (ssDNA) intermediates, suggesting that pM411 belongs to the RCR pMV158 family...
December 2016: Current Microbiology
https://www.readbyqxmd.com/read/27539672/subtypes-of-hypoxia-responsive-cells-differentiate-into-neurons-in-spinal-cord-of-zebrafish-embryos-after-hypoxic-stress
#15
Chih-Wei Zeng, Yasuhiro Kamei, Chih-Tien Wang, Huai-Jen Tsai
BACKGROUND INFORMATION: Neuron stem/progenitor cells (NSPCs) of zebrafish central nervous system (CNS) are known to thrive during oxygen recovery after hypoxia, but not all cell types have been fully characterised due to their heterogeneities. In addition, an in vivo model system is not available that can help us to identify what type-specific cell populations that are involved in neural regeneration and to track their cell fate after regeneration. To solve these issues, we employed a zebrafish transgenic line, huORFZ, which harbours an inhibitory upstream open reading frame of human chop mRNA fused downstream with GFP reporter and driven by cytomegalovirus promoter...
December 2016: Biology of the Cell
https://www.readbyqxmd.com/read/27526386/arabidopsis-polyamine-oxidase-2-uorf-is-required-for-downstream-translational-regulation
#16
María de la Luz Guerrero-González, María Azucena Ortega-Amaro, Margarita Juárez-Montiel, Juan Francisco Jiménez-Bremont
In eukaryotic mRNAs, small upstream open reading frames (uORFs) located in the 5'-untranslated region control the translation of the downstream main ORF. Polyamine oxidase (PAO) enzymes catalyze the oxidation of higher polyamines such as spermidine and spermine, and therefore contribute to the maintenance of intracellular polyamine content and to the regulation of physiological processes through their catabolic products. Recently, we reported that the Arabidopsis thaliana Polyamine Oxidase 2 (AtPAO2) is post-transcriptionally regulated by its 5'-UTR region through an uORF...
August 5, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27525887/effect-of-dual-bt-expression-transformation-vectors-on-transgene-expression-in-tobacco
#17
L N Xu, Y Dong, J Zhang, R X Wang, H M Liu, Q Yang, M S Yang
This study aimed to determine the influence of vector structure on dual Bt gene expression and establish an efficient expression vector using Cry1Ac and Cry3A genes. Four vectors (N4, N5, N10, and S23) were developed and used for genetic transformation of tobacco to obtain insect-resistant transgenic lines. The vectors were constructed using the MAR structure, applying different promoter and enhancer sequences, and changing the transgene open-reading frame sequence. The average Cry1Ac toxalbumin expression quantity was 67 times higher in N5 than in N4 transgenic lines (8...
2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27515280/the-human-olfactory-transcriptome
#18
Tsviya Olender, Ifat Keydar, Jayant M Pinto, Pavlo Tatarskyy, Anna Alkelai, Ming-Shan Chien, Simon Fishilevich, Diego Restrepo, Hiroaki Matsunami, Yoav Gilad, Doron Lancet
BACKGROUND: Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-characterized human olfactory epithelial samples and compared the results to novel and published mouse olfactory epithelium as well as 16 human control tissues. RESULTS: We identified 194 non-olfactory receptor (OR) genes that are overexpressed in human olfactory tissues vs...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27467758/5-terminal-augs-in-escherichia-coli-mrnas-with-shine-dalgarno-sequences-identification-and-analysis-of-their-roles-in-non-canonical-translation-initiation
#19
Heather J Beck, Ian M C Fleming, Gary R Janssen
Analysis of the Escherichia coli transcriptome identified a unique subset of messenger RNAs (mRNAs) that contain a conventional untranslated leader and Shine-Dalgarno (SD) sequence upstream of the gene's start codon while also containing an AUG triplet at the mRNA's 5'- terminus (5'-uAUG). Fusion of the coding sequence specified by the 5'-terminal putative AUG start codon to a lacZ reporter gene, as well as primer extension inhibition assays, reveal that the majority of the 5'-terminal upstream open reading frames (5'-uORFs) tested support some level of lacZ translation, indicating that these mRNAs can function both as leaderless and canonical SD-leadered mRNAs...
2016: PloS One
https://www.readbyqxmd.com/read/27422166/characterization-of-a-potential-abc-type-bacteriocin-exporter-protein-from-treponema-denticola
#20
Kimiko Tanaka-Kumazawa, Yuichiro Kikuchi, Yumiko Sano-Kokubun, Seikou Shintani, Masashi Yakushiji, Howard K Kuramitsu, Kazuyuki Ishihara
BACKGROUND: Treponema denticola is strongly associated with the development of periodontal disease. Both synergistic and antagonistic effects are observed among bacterial species in the process of biofilm formation. Bacteriocin-related genes have not yet been fully characterized in periodontopathic bacteria. The aim of this study was to detect and characterize bacteriocin-associated proteins in T. denticola. METHODS: The whole genome sequence of T. denticola ATCC 35405 was screened with a Streptococcus mutans bacteriocin immunity protein (ImmA/Bip) sequence...
2016: BMC Oral Health
keyword
keyword
95619
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"