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Bridget P Bannerman, Susanne Kramer, Richard G Dorrell, Mark Carrington
The degree of conservation and evolution of cytoplasmic mRNA metabolism pathways across the eukaryotes remains incompletely resolved. In this study, we describe a comprehensive genome and transcriptome-wide analysis of proteins involved in mRNA maturation, translation, and mRNA decay across representative organisms from the six eukaryotic super-groups. We demonstrate that eukaryotes share common pathways for mRNA metabolism that were almost certainly present in the last eukaryotic common ancestor, and show for the first time a correlation between intron density and a selective absence of some Exon Junction Complex (EJC) components in eukaryotes...
2018: PloS One
Patrycja Plewka, Agnieszka Thompson, Maciej Szymanski, Przemyslaw Nuc, Katarzyna Knop, Agnieszka Rasinska, Aleksandra Bialkowska, Zofia Szweykowska-Kulinska, Wojciech M Karlowski, Artur Jarmolowski
The Arabidopsis GUT15 RNA belongs to a class of noncoding RNAs that are expressed from the intergenic regions of protein-coding genes. We show that the RNA polymerase II transcribed GUT15 transcript serves as a precursor for two stable RNA species, a tRNA-like molecule and GUT15-tRF-F5, which are both encoded by the final intron in the GUT15 gene. The GUT15-encoded tRNA-like molecule cannot be autonomously transcribed by RNA polymerase III. However, this molecule contains a CCA motif, suggesting that it may enter the tRNA maturation pathway...
March 21, 2018: RNA Biology
Andreas Kompatscher, J H F de Baaij, Karam Aboudehen, Shayan Farahani, Lex H J Van Son, Susanne Milatz, Nina Himmerkus, Gert Jan C Veenstra, René J M Bindels, Joost G J Hoenderop
Mutations in HNF1β cause autosomal dominant tubulointerstitial kidney disease (ADTKD-HNF1β), and patients tend to develop renal cysts, maturity-onset diabetes of the young (MODY), and suffer from electrolyte disturbances, including hypomagnesemia, hypokalemia and hypocalciuria. Previous HNF1β research focused on the renal distal convoluted tubule (DCT) to elucidate the ADTKD-HNF1β electrolyte phenotype, although 70% of Mg2+ is reabsorbed in the thick ascending limb of Henle's loop (TAL). An important regulator of Mg2+ reabsorption in the TAL is the calcium-sensing receptor (CaSR)...
March 21, 2018: American Journal of Physiology. Renal Physiology
Weijing Wang, Dongfeng Zhang, Chunsheng Xu, Yili Wu, Haiping Duan, Shuxia Li, Qihua Tan
Serum uric acid (SUA), as the end product of purine metabolism, has proven emerging roles in human disorders. Here based on a sample of 379 middle and old-aged Chinese twin pairs, we aimed to explore the magnitude of genetic impact on SUA variation by performing sex-limitation twin modeling analyses and further detect specific genetic variants related to SUA by conducting a genome-wide association study. Monozygotic (MZ) twin correlation for SUA level (rMZ = 0.56) was larger than for dizygotic (DZ) twin correlation (rDZ = 0...
2018: Frontiers in Endocrinology
Chang Liu, Xueqin Ran, Jiafu Wang, Sheng Li, Jianfeng Liu
Genomic structural variation (SV) is noticed for the contribution to genetic diversity and phenotypic changes. Guizhou indigenous pig (GZP) has been raised for hundreds of years with many special characteristics. The present paper aimed to uncover the influence of SV on gene polymorphism and the genetic mechanisms of phenotypic traits for GZP. Eighteen GZPs were chosen for resequencing by Illumina sequencing platform. The confident SVs of GZP were called out by both programs of pindel and softSV simultaneously and compared with the SVs deduced from the genomic data of European pig (EUP) and the native pig outside of Guizhou, China (NPOG)...
2018: PloS One
Thaís B Alves, Tatiana M Souza-Moreira, Sandro R Valentini, Cleslei F Zanelli, Maysa Furlan
Triterpenes are interesting compounds because they play an important role in cell homeostasis and a wide variety exhibiting defense functions is produced by plant secondary metabolism. Those same plant secondary metabolites also exhibit biological properties with promising therapeutic potential as anti-inflammatory and antitumor agents. Friedelin is a triterpene ketone with anti-inflammatory and gastroprotective activities and it is a precursor of relevant antitumor quinonemethides. Although many triterpene synthases have been described, only two friedelin synthases were characterized and there is no information about their genomic features and alleles...
March 20, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Ozlem Kurnaz-Gomleksiz, Ozlem Kucukhuseyin, Elif Ozkok, Zehra Bugra, Oguz Ozturk, Hulya Yilmaz-Aydogan
BACKGROUND: The OLR1 gene has been identified as a candidate gene for coronary artery disease (CAD). Six single-nucleotide polymorphisms (SNPs) of the OLR1 gene located within intron 4 (IVS4-27G>C, IVS4-73C>T, IVS4-14A>G), intron 5 (IVS5-70A>G, IVS5-27G>T) and 3'UTR (188C>T) comprise a linkage disequilibrium (LD) block, which is strongly associated with the elevated risk of CAD. OBJECTIVES: We aimed to investigate the effects of the OLR1 IVS4-14A>G and -73C>T SNPs on metabolic parameters in Turkish CAD patients, and the linkage between these 2 genetic variants...
March 20, 2018: Advances in Clinical and Experimental Medicine: Official Organ Wroclaw Medical University
Qi Wang, Qian Wang, Yan-Le Zhou, Shuang Shan, Huan-Huan Cui, Yong Xiao, Kun Dong, Adel Khashaveh, Liang Sun, Yong-Jun Zhang
The phytophagous mirid bugs of Apolygus lucorum, Lygus pratensis as well as three Adelphocoris spp., including Adelphocoris lineolatus, A. suturalis , and A. fasciaticollis are major pests of multiple agricultural crops in China, which have distinct geographical distribution and occurrence ranges. Like many insect species, these bugs heavily rely on olfactory cues to search preferred host plants, thereby investigation on functional co-evolution and divergence of olfactory genes seems to be necessary and is of great interest...
2018: Frontiers in Physiology
Achal Rastogi, Uma Maheswari, Richard G Dorrell, Fabio Rocha Jimenez Vieira, Florian Maumus, Adam Kustka, James McCarthy, Andy E Allen, Paul Kersey, Chris Bowler, Leila Tirichine
Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes...
March 19, 2018: Scientific Reports
Tomohiko Yamamura, Kandai Nozu, Hiroaki Ueda, Rika Fujimaru, Ryutaro Hisatomi, Yoko Yoshida, Hideki Kato, Masaomi Nangaku, Toshiyuki Miyata, Toshihiro Sawai, Shogo Minamikawa, Hiroshi Kaito, Masafumi Matsuo, Kazumoto Iijima
Pathogenic variants in specific complement-related genes lead to atypical hemolytic uremic syndrome (aHUS). Some reports have indicated that patients with digenic variants in these genes might present severer phenotypes. Upon detecting novel intronic variants, transcriptional analysis is necessary to prove pathogenicity; however, when intronic variants are located in intron 1 and, as a result, no transcript is produced, no appropriate method had been established to reveal the pathogenicity. Recently, the minigene assay was used to assess the pathogenicity of intronic variants...
March 19, 2018: Journal of Human Genetics
Juan F Aranda, Stefan Rathjen, Ludger Johannes, Carlos Fernández-Hernando
Retrograde transport (RT) allows cells the retrieval of receptors and other cellular cargoes to the Golgi contributing to the maintenance of cellular homeostasis. This transport route is also commonly used by several bacterial toxins to exert their deleterious actions on eukaryotic cells. While the retrograde transport process has been well characterized, the contribution of microRNAs (miRNAs) in regulating this cellular transport mechanism remains unknown. Here, we identified that the intronic miRNA family, miR-199a/b , coordinate genes regulating RT and endosome trafficking...
March 19, 2018: Molecular and Cellular Biology
Xinyan Wang, Linyong Du, He Wei, Anying Zhang, Kun Yang, Hong Zhou
Signal transducer and activator of transcription 3 (STAT3) is a member of the STAT family in response to cytokines and growth factors. In mammals, alternative splicing of STAT3 generates STAT3α and STAT3β, which have distinct and overlapping functions. In the previous study, we have identified two spliceforms of Stat3α (Stat3α1 and Stat3α2) possessing all functional domains of Stat3 in grass carp (Ctenopharyngodon idella). In the present study, two Stat3β variants (Stat3β1 and Stat3β2) without C-terminal transactivation domain were isolated from this species, and their transcripts were ubiquitously expressed in all examined tissues with the highest levels in liver...
March 16, 2018: Fish & Shellfish Immunology
M Koruyucu, J Kang, Y J Kim, F Seymen, Y Kasimoglu, Z H Lee, T J Shin, H K Hyun, Y J Kim, S H Lee, J C C Hu, J P Simmer, J W Kim
Tooth enamel, the hardest tissue in the human body, is formed after a complex series of interactions between dental epithelial tissue and the underlying ectomesenchyme. Nonsyndromic amelogenesis imperfecta (AI) is a rare genetic disorder affecting tooth enamel without other nonoral symptoms. In this study, we identified 2 novel ENAM mutations in 2 families with hypoplastic AI by whole exome sequencing. Family 1 had a heterozygous splicing donor site mutation in intron 4, NM_031889; c.123+2T>G. Affected individuals had hypoplastic enamel with or without the characteristic horizontal hypoplastic grooves in some teeth...
March 1, 2018: Journal of Dental Research
Ali R Keramati, Lisa R Yanek, Kruthika Iyer, Margaret A Taub, Ingo Ruczinski, Diane M Becker, Lewis C Becker, Nauder Faraday, Rasika A Mathias
Coronary artery disease (CAD) remains a major cause of mortality and morbidity worldwide. The aggregation of activated platelets on a ruptured atherosclerotic plaque is a critical step in most acute cardiovascular events like myocardial infarction. Platelet aggregation both at baseline and after aspirin is highly heritable. Genome-wide association studies (GWAS) have identified a common variant within the first intron of the platelet endothelial aggregation receptor1 (PEAR1), to be robustly associated with platelet aggregation...
March 19, 2018: Platelets
Guomin Li, Qian Shen, Li Sun, Haimei Liu, Yu An, Hong Xu
Branchio-oto-renal (BOR) syndrome is a rare autosomal dominant disorder characterized by branchial cleft fistulae or cysts, preauricular pits, ear malformations, hearing loss, and renal anomalies. Mutations in the human homologue of the Drosophila eyes absent gene ( EYA1 ) are the most common cause of BOR syndrome. PCR and direct sequencing were used to investigate all of the exons and exon-intron boundaries in the EYA1 gene in a patient with BOR syndrome from China. The patient was a child who displayed clinical features of BOR syndrome...
February 2018: Intractable & Rare Diseases Research
Naixiang Zhai, Yanqin Lu, Yanzhou Wang, Xiuzhi Ren, Jinxiang Han
Circular RNA (circRNA) is a non-linear form of RNA derived from exonic, intronic, and exon-intron gene regions. circRNAs are characterized by covalent closed loops, highly stable nuclease resistance, and specific expression in species and developmental stages. CircRNA molecules have been identified as playing roles in the regulation of cell transcription, transcriptional expression after translation, interactions with microRNAs, and protein coding. A high stability and tissue- and disease-specific expression allow circRNAs to serve as potential biomarkers both for diseases and prognosis...
February 2018: Intractable & Rare Diseases Research
Ping Jin, Caiyun Lv, Shuangli Peng, Lu Cai, Jiu Zhu, Fei Ma
The COMMD (COpper Metabolism gene MURR1 Domain) gene family with ten members participates in various biological processes, such as the regulation of copper and sodium transport, NF-κB activity and cell cycle progression. However, studies on the COMMD gene family in amphioxus (Branchiostoma belcheri) are yet largely unknown. In this study, we have identified and characterized the ten COMMD family members from amphioxus (designated as AmphiCOMMDs). Firstly, we clone the full length of AmphiCOMMDs, and all AmphiCOMMD proteins contain the conserved COMM domain with two NES (Nuclear Export Signal) motifs...
March 15, 2018: Fish & Shellfish Immunology
Daniel B Hawcutt, Ben Francis, Daniel F Carr, Andrea L Jorgensen, Peng Yin, Naomi Wallin, Natalie O'Hara, Eunice J Zhang, Katarzyna M Bloch, Amitava Ganguli, Ben Thompson, Laurence McEvoy, Matthew Peak, Andrew A Crawford, Brian R Walker, Joanne C Blair, Jonathan Couriel, Rosalind L Smyth, Munir Pirmohamed
BACKGROUND: A serious adverse effect of corticosteroid therapy is adrenal suppression. Our aim was to identify genetic variants affecting susceptibility to corticosteroid-induced adrenal suppression. METHODS: We enrolled children with asthma who used inhaled corticosteroids as part of their treatment from 25 sites across the UK (discovery cohort), as part of the Pharmacogenetics of Adrenal Suppression with Inhaled Steroids (PASS) study. We included two validation cohorts, one comprising children with asthma (PASS study) and the other consisting of adults with chronic obstructive pulmonary disorder (COPD) who were recruited from two UK centres for the Pharmacogenomics of Adrenal Suppression in COPD (PASIC) study...
March 15, 2018: Lancet Respiratory Medicine
Zhangbiao Long, Yali Du, Hongmin Li, Bing Han
Patients with paroxysmal nocturnal hemoglobinuria (PNH) who have minor allele of the complement receptor 1 (CR1) gene, displayed more sub-optimal responder to eculizumab compared with major allele. To investigate polymorphism of the CR1 gene in Chinese patients with PNH and its correlation with clinical features and the potential impact on eculizumab efficiency, we genotyped CR1 rs2274567, rs3811381 and the intron 27 Hind III restriction fragment length polymorphism in 95patients with PNH and 96 controls. The results indicated that the genotypes of CR1 rs2274567, rs3811381 and the intron 27 Hind III in PNH patients and controls both consist with Hardy-Weinberg equilibrium...
March 15, 2018: Gene
Yue Yao, Ping Gao, Lili Chen, Wei Wang, Jinchao Zhang, Qiang Li, Yi Xu
Recently, long noncoding RNAs (lncRNAs) have been emerged as pivotal regulators in various human cancers, including pancreatic ductal adenocarcinoma (PDAC). SPRY4-intronic transcript 1 (SPRY4-IT1) was reported to be upregulated in some kind of human cancers. Here, we elucidated the biological functions and possible clinical values of SPRY4-IT1 on PDAC. In present study, expression of SPRY4-IT1 in PDAC tissues and corresponding normal tissues were explored by qRT-PCR experiments. The link between SPRY4-IT1 expression levels and clinicopathological significance was further analyzed...
March 15, 2018: Gene
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