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3' utr intron

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https://www.readbyqxmd.com/read/29779243/co-occurrence-of-schwannomatosis-and-rhabdoid-tumor-predisposition-syndrome-1
#1
Hildegard Kehrer-Sawatzki, Uwe Kordes, Simone Seiffert, Anna Summerer, Christian Hagel, Ulrich Schüller, Said Farschtschi, Reinhard Schneppenheim, Martin Bendszus, Tim Godel, Victor-Felix Mautner
BACKGROUND: The clinical phenotype associated with germline SMARCB1 mutations has as yet not been fully documented. It is known that germline SMARCB1 mutations may cause rhabdoid tumor predisposition syndrome (RTPS1) or schwannomatosis. However, the co-occurrence of rhabdoid tumor and schwannomas in the same patient has not so far been reported. METHODS: We investigated a family with members harboring a germline SMARCB1 deletion by means of whole-body MRI as well as high-resolution microstructural magnetic resonance neurography (MRN)...
May 20, 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29766417/the-fto-gene-is-associated-with-growth-and-omega-3-6-ratio-in-asian-seabass
#2
Fei Sun, Rongjian Tu, Jun Hong Xia, Xiao Jun Liu, Gen Hua Yue
Polymorphisms in the FTO gene are associated with obesity and body mass index in humans and livestock. Little information of whether FTO plays an important role in aquaculture fish species is available. We cloned and characterized the FTO gene in an economically important food fish species: Asian seabass (Lates calcarifer). The full-length cDNA of the gene is 3679 bp, containing an ORF of 1935 bp encoding 644 amino acids, a 216 bp 5' UTR and a 1538 bp 3' UTR. The gene consisted of nine exons and eight introns and was 117,679 bp in length...
May 16, 2018: Marine Biotechnology
https://www.readbyqxmd.com/read/29755318/arc-3-utr-splicing-leads-to-dual-and-antagonistic-effects-in-fine-tuning-arc-expression-upon-bdnf-signaling
#3
Chiara Paolantoni, Simona Ricciardi, Veronica De Paolis, Chinenye Okenwa, Caterina Catalanotto, Maria T Ciotti, Antonino Cattaneo, Carlo Cogoni, Corinna Giorgi
Activity-regulated cytoskeletal associated protein (Arc) is an immediate-early gene critically involved in synaptic plasticity and memory consolidation. Arc mRNA is rapidly induced by synaptic activation and a portion is locally translated in dendrites where it modulates synaptic strength. Being an activity-dependent effector of homeostatic balance, regulation of Arc is uniquely tuned to result in short-lived bursts of expression. Cis -Acting elements that control its transitory expression post-transcriptionally reside primarily in Arc mRNA 3' UTR...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29703141/genome-wide-identification-and-characterization-of-the-sbp-box-gene-family-in-petunia
#4
Qin Zhou, Sisi Zhang, Feng Chen, Baojun Liu, Lan Wu, Fei Li, Jiaqi Zhang, Manzhu Bao, Guofeng Liu
BACKGROUND: SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box genes encode a family of plant-specific transcription factors (TFs) that play important roles in many growth and development processes including phase transition, leaf initiation, shoot and inflorescence branching, fruit development and ripening etc. The SBP-box gene family has been identified and characterized in many species, but has not been well studied in Petunia, an important ornamental genus. RESULTS: We identified 21 putative SPL genes of Petunia axillaris and P...
March 12, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29702237/molecular-characterization-and-functional-analysis-of-two-phospholipid-hydroperoxide-isoforms-from-larimichthys-crocea-under-vibrio-parahaemolyticus-challenge
#5
Xiaoze Xie, Mengnan Chen, Aiyi Zhu
Glutathione peroxidases family is a key role in the antioxidant system in oxybiotic organisms for cell redox homeostasis. One of their members, phospholipid hydroperoxide glutathione peroxidase (GPx4) have unique monomeric structure and can directly react with complex lipid and membrane-bound peroxides under the presence of glutathione(GSH). In this paper, two complete GPx4 cDNAs (designated as LcGPx4a and LcGPx4b) from Larimichthys crocea are identified by rapid amplification of cDNA ends. The cDNA of LcGPx4a was consisted of a 5'-untranslated region (UTR) of 258 bp, a 3'-UTR of 330 bp, and an open reading frame (ORF) of 561 bp encoding 186 amino acid (aa) polypeptides...
April 24, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29691780/combinatory-rna-sequencing-analyses-reveal-a-dual-mode-of-gene-regulation-by-adar1-in-gastric-cancer
#6
Charles J Cho, Jaeeun Jung, Lushang Jiang, Eun Ji Lee, Dae-Soo Kim, Byung Sik Kim, Hee Sung Kim, Hwoon-Yong Jung, Ho-June Song, Sung Wook Hwang, Yangsoon Park, Min Kyo Jung, Chan Gi Pack, Seung-Jae Myung, Suhwan Chang
BACKGROUND: Adenosine deaminase acting on RNA 1 (ADAR1) is known to mediate deamination of adenosine-to-inosine through binding to double-stranded RNA, the phenomenon known as RNA editing. Currently, the function of ADAR1 in gastric cancer is unclear. AIMS: This study was aimed at investigating RNA editing-dependent and editing-independent functions of ADAR1 in gastric cancer, especially focusing on its influence on editing of 3' untranslated regions (UTRs) and subsequent changes in expression of messenger RNAs (mRNAs) as well as microRNAs (miRNAs)...
April 25, 2018: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/29651162/quantitative-methods-to-monitor-rna-biomarkers-in-myotonic-dystrophy
#7
Marzena Wojciechowska, Krzysztof Sobczak, Piotr Kozlowski, Saam Sedehizadeh, Agnieszka Wojtkowiak-Szlachcic, Karol Czubak, Robert Markus, Anna Lusakowska, Anna Kaminska, J David Brook
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are human neuromuscular disorders associated with mutations of simple repetitive sequences in affected genes. The abnormal expansion of CTG repeats in the 3'-UTR of the DMPK gene elicits DM1, whereas elongated CCTG repeats in intron 1 of ZNF9/CNBP triggers DM2. Pathogenesis of both disorders is manifested by nuclear retention of expanded repeat-containing RNAs and aberrant alternative splicing. The precise determination of absolute numbers of mutant RNA molecules is important for a better understanding of disease complexity and for accurate evaluation of the efficacy of therapeutic drugs...
April 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29601527/sequence-and-haplotypes-variation-of-the-ovine-uncoupling-protein-1-gene-ucp1-and-their-association-with-growth-and-carcass-traits-in-new-zealand-romney-lambs
#8
Qingming An, Huitong Zhou, Jiang Hu, Yuzhu Luo, Jon G H Hickford
Uncoupling protein-1 gene ( UCP1 ) plays an important role in the regulation of thermogenesis, energy expenditure, and protection against oxidative stress. In this study, six separate UCP1 regions: region-1 and region-2 (two parts of the promoter), region-3 and region-4 (two parts of intron 1), region-5 (spanning part of intron 5 and part of exon 6), and region-6 (spanning part of exon 6 and part of the 3'-UTR) from a variety of sheep breeds, were analysed using polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP) analyses...
March 30, 2018: Genes
https://www.readbyqxmd.com/read/29592900/genome-sequencing-and-rna-motif-analysis-reveal-novel-damaging-non-coding-mutations-in-human-tumors
#9
Babita Singh, Juan L Trincado, P J Tatlow, Stephen R Piccolo, Eduardo Eyras
A major challenge in cancer research is to determine the biological and clinical significance of somatic mutations in non-coding regions. This has been studied in terms of recurrence, functional impact, and association to individual regulatory sites, but the combinatorial contribution of mutations to common RNA regulatory motifs has not been explored. Therefore, we developed a new method, MIRA (Mutation Identification for RNA Alterations), to perform an unbiased and comprehensive study of significantly mutated regions (SMRs) affecting binding sites for RNA-binding proteins (RBPs) in cancer...
March 28, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29569734/remarkable-genetic-diversity-detected-at-river-buffalo-prolactin-receptor-prlr-gene-and-association-studies-with-milk-fatty-acid-composition
#10
G Cosenza, M Iannaccone, B Auzino, N P P Macciotta, A Kovitvadhi, I Nicolae, A Pauciullo
Prolactin is an anterior pituitary peptide hormone involved in many different endocrine activities and is essential for reproductive performance. This action is mediated by its receptor, the prolactin receptor, encoded by the PRLR gene. In this study, we sequenced and characterized the Mediterranean river buffalo PRLR gene (from exon 3 to 10), and we found remarkable genetic diversity. In particular, we found 24 intronic polymorphisms and 13 exonic SNPs, seven of which were non-synonymous. Furthermore, the polymorphisms identified in the 3'-UTR were investigated to establish their possible influence on microRNA binding sites...
March 23, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29568389/computational-modeling-suggests-impaired-interactions-between-nkx2-5-and-gata4-in-individuals-carrying-a-novel-pathogenic-d16n-nkx2-5-mutation
#11
Saidulu Mattapally, Mrityunjay Singh, Kona Samba Murthy, Shailendra Asthana, Sanjay K Banerjee
NKX2.5 , a homeobox containing gene, plays an important role in embryonic heart development and associated mutations are linked with various cardiac abnormalities. We sequenced the NKX2.5 gene in 100 congenital heart disease (CHD) patients and 200 controls. Our analysis revealed a total of 7 mutations, 3 in intronic region, 3 in coding region and 1 in 3' UTR. Of the above mutations, one mutation was found to be associated with tetralogy of fallot (TOF) and two (rs2277923 and a novel mutation, D16N) were strongly associated with VSD...
March 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29518015/capturing-the-alternative-cleavage-and-polyadenylation-sites-of-14-nac-genes-in-populus-using-a-combination-of-3-race-and-high-throughput-sequencing
#12
Haoran Wang, Mingxiu Wang, Qiang Cheng
Detection of complex splice sites (SSs) and polyadenylation sites (PASs) of eukaryotic genes is essential for the elucidation of gene regulatory mechanisms. Transcriptome-wide studies using high-throughput sequencing (HTS) have revealed prevalent alternative splicing (AS) and alternative polyadenylation (APA) in plants. However, small-scale and high-depth HTS aimed at detecting genes or gene families are very few and limited. We explored a convenient and flexible method for profiling SSs and PASs, which combines rapid amplification of 3'-cDNA ends (3'-RACE) and HTS...
March 8, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29472695/deficiency-of-a-pyrroline-5-carboxylate-reductase-produces-the-yellowish-green-cocoon-ryokuken-of-the-silkworm-bombyx-mori
#13
Chikara Hirayama, Keisuke Mase, Tetsuya Iizuka, Yoko Takasu, Eiji Okada, Kimiko Yamamoto
The silkworm cocoon colour has attracted researchers involved in genetics, physiology and ecology for a long time. 'Ryokuken' cocoons are yellowish green in colour due to unusual flavonoids, prolinylflavonols, while 'Sasamayu' cocoons are light green and contain only simple flavonol glucosides. We found a novel gene associated with the cocoon colour change resulting from a change in flavonoid composition and named it Lg (light green cocoon). In the middle silk glands of the + Lg /+ Lg larvae, 1-pyrroline-5-carboxylic acid (P5C) was found to accumulate due to a decrease in the activity of pyrroline-5-carboxylate reductase (P5CR), an enzyme reducing P5C to proline...
May 2018: Heredity
https://www.readbyqxmd.com/read/29429924/the-tia1-rna-binding-protein-family-regulates-eif2ak2-mediated-stress-response-and-cell-cycle-progression
#14
Cindy Meyer, Aitor Garzia, Michael Mazzola, Stefanie Gerstberger, Henrik Molina, Thomas Tuschl
TIA1 and TIAL1 encode a family of U-rich element mRNA-binding proteins ubiquitously expressed and conserved in metazoans. Using PAR-CLIP, we determined that both proteins bind target sites with identical specificity in 3' UTRs and introns proximal to 5' as well as 3' splice sites. Double knockout (DKO) of TIA1 and TIAL1 increased target mRNA abundance proportional to the number of binding sites and also caused accumulation of aberrantly spliced mRNAs, most of which are subject to nonsense-mediated decay. Loss of PRKRA by mis-splicing triggered the activation of the double-stranded RNA (dsRNA)-activated protein kinase EIF2AK2/PKR and stress granule formation...
February 15, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29413897/the-au-rich-element-landscape-across-human-transcriptome-reveals-a-large-proportion-in-introns-and-regulation-by-elavl1-hur
#15
Tala Bakheet, Edward Hitti, Maher Al-Saif, Walid N Moghrabi, Khalid S A Khabar
Adenylate-uridylate (AU)-rich elements (AREs) are sequence instability elements that are known to be located in the 3' untranslated regions (UTR) in thousands of human transcripts. AREs regulate the expression of many genes at the post-transcriptional level, and they are essential for many normal cellular functions. We conducted a transcriptome-wide screen for AREs and found that they are most abundant in introns, with up to 25% of introns containing AREs corresponding to 58% of human genes. Clustering studies of ARE size, complexity, and distribution revealed that, in introns, longer AREs with two or more overlapping repeats are more abundant than in the 3'UTR, and only introns can contain very long AREs with 6-14 overlapping AUUUA pentamers...
February 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29413755/association-of-agtr1-a1166c-and-ace-i-d-polymorphisms-with-breast-cancer-risk-in-north-indian-population
#16
Anukriti Singh, Nidhi Srivastava, Sonal Amit, S N Prasad, M P Misra, Bushra Ateeq
Renin angiotensin system (RAS) comprising Angiotensin converting enzyme (ACE), Angiotensin II (Ang II) and its receptor Angiotensin II receptor type I (AGTR1), plays a critical role in several diseases including cancer. A single nucleotide polymorphism (SNP) A1166C located in 3' untranslated region (UTR) of AGTR1 and an insertion/deletion (I/D) polymorphism present in intron 16 of ACE gene have been associated with many diseases, but their association with Breast cancer (BCa) is still debatable. Here, we for the first time investigated the association of these polymorphisms in a North Indian BCa cohort including 161 patients and 152 healthy women...
April 2018: Translational Oncology
https://www.readbyqxmd.com/read/29394137/genetic-effects-of-prnp-gene-insertion-deletion-indel-on-phenotypic-traits-in-sheep
#17
Jie Li, Sarantsetseg Erdenee, Shaoli Zhang, Zhenyu Wei, Meng Zhang, Yunyun Jin, Hui Wu, Hong Chen, Xiuzhu Sun, Hongwei Xu, Yong Cai, Xianyong Lan
Prion protein (PRNP) gene is well known for affecting mammal transmissible spongiform encephalopathies (TSE), and is also reported to regulate phenotypic traits (e.g. growth traits) in healthy ruminants. To identify the insertion/deletion (indel) variations of the PRNP gene and evaluate their effects on growth traits, 768 healthy individuals from five sheep breeds located in China and Mongolia were identified and analyzed. Herein, four novel indel polymorphisms, namely, Intron-1-insertion-7bp (I1-7bp), Intron-2-insertion-15bp (I2-15bp), Intron-2-insertion-19bp (I2-19bp), and 3' UTR-insertion-7bp (3' UTR-7bp), were found in the sheep PRNP gene...
January 2, 2018: Prion
https://www.readbyqxmd.com/read/29388067/oncogenic-and-tumor-suppressive-roles-of-micrornas-with-special-reference-to-apoptosis-molecular-mechanisms-and-therapeutic-potential
#18
REVIEW
Dharambir Kashyap, Hardeep Singh Tuli, Vivek Kumar Garg, Neelam Goel, Anupam Bishayee
MicroRNAs (miRNAs) are the non-coding class of minute RNA molecules that negatively control post-transcriptional regulation of various functional genes. These miRNAs are transcribed from the loci present in the introns of functional or protein-coding genes, exons of non-coding genes, or even in the 3'-untranslated region (3'-UTR). They have potential to modulate the stability or translational efficiency of a variety of target RNA [messenger RNA (mRNA)]. The regulatory function of miRNAs has been elucidated in several pathological conditions, including neurological (Alzheimer's disease and Parkinson's disease) and cardiovascular conditions, along with cancer...
February 1, 2018: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/29382842/the-sr-protein-b52-srp55-regulates-splicing-of-the-period-thermosensitive-intron-and-mid-day-siesta-in-drosophila
#19
Zhichao Zhang, Weihuan Cao, Isaac Edery
Similar to many diurnal animals, Drosophila melanogaster exhibits a mid-day siesta that is more robust as temperature increases, an adaptive response that aims to minimize the deleterious effects from exposure to heat. This temperature-dependent plasticity in mid-day sleep levels is partly based on the thermal sensitive splicing of an intron in the 3' untranslated region (UTR) of the circadian clock gene termed period (per). In this study, we evaluated a possible role for the serine/arginine-rich (SR) splicing factors in the regulation of dmpi8 splicing efficiency and mid-day siesta...
January 30, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352395/association-between-crp-genetic-diversity-and-bipolar-disorder-comorbid-complications
#20
Wahid Boukouaci, José Oliveira, Bruno Etain, Meriem Bennabi, Christina Mariaselvam, Nora Hamdani, Céline Manier, Djaouida Bengoufa, Frank Bellivier, Chantal Henry, Jean-Pierre Kahn, Dominique Charron, Rajagopal Krishnamoorthy, Marion Leboyer, Ryad Tamouza
BACKGROUND: Chronic low-grade inflammation is believed to contribute, at least in a subset of patients, to the development of bipolar disorder (BD). In this context, the most investigated biological marker is the acute phase response molecule, C-reactive protein (CRP). While the genetic diversity of CRP was amply studied in various pathological settings, little is known in BD. METHODS: 568 BD patients along with 163 healthy controls (HC) were genotyped for the following single-nucleotide polymorphisms (SNPs) on the CRP gene: intron rs1417938 (+ 29) T/A, 3'-UTR rs1130864 (+ 1444) G/A, and downstream rs1205 (+ 1846) (C/T)...
January 20, 2018: International Journal of Bipolar Disorders
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