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Gene splicing

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https://www.readbyqxmd.com/read/28091775/developmental-and-sex-specific-differences-in-expression-of-neuropeptides-derived-from-allatotropin-gene-in-the-silkmoth-bombyx-mori
#1
Branislav Bednár, Ladislav Roller, Daniel Čižmár, Diana Mitrová, Dušan Žitňan
Allatotropin (AT) and related neuropeptides are widespread bioactive molecules that regulate development, food intake and muscle contractions in insects and other invertebrates. In moths, alternative splicing of the at gene generates three mRNA precursors encoding AT with different combinations of three structurally similar AT-like peptides (ATLI-III). We used in situ hybridization and immunohistochemistry to map the differential expression of these transcripts during the postembryonic development of Bombyx mori...
January 16, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28091594/functional-analysis-reveals-that-rbm10-mutations-contribute-to-lung-adenocarcinoma-pathogenesis-by-deregulating-splicing
#2
Jiawei Zhao, Yue Sun, Yin Huang, Fan Song, Zengshu Huang, Yufang Bao, Ji Zuo, David Saffen, Zhen Shao, Wen Liu, Yongbo Wang
RBM10 is an RNA splicing regulator that is frequently mutated in lung adenocarcinoma (LUAD) and has recently been proposed to be a cancer gene. How RBM10 mutations observed in LUAD affect its normal functions, however, remains largely unknown. Here integrative analysis of RBM10 mutation and RNA expression data revealed that LUAD-associated RBM10 mutations exhibit a mutational spectrum similar to that of tumor suppressor genes. In addition, this analysis showed that RBM10 mutations identified in LUAD patients lacking canonical oncogenes are associated with significantly reduced RBM10 expression...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28090405/transcriptomic-analysis-of-diplomonad-parasites-reveals-a-trans-spliced-intron-in-a-helicase-gene-in-giardia
#3
Scott William Roy
BACKGROUND: The mechanisms by which DNA sequences are expressed is the central preoccupation of molecular genetics. Recently, ourselves and others reported that in the diplomonad protist Giardia lamblia, the coding regions of several mRNAs are produced by ligation of independent RNA species expressed from distinct genomic loci. Such trans-splicing of introns was found to affect nearly as many genes in this organism as does classical cis-splicing of introns. These findings raised questions about the incidence of intron trans-splicing both across the G...
2017: PeerJ
https://www.readbyqxmd.com/read/28090092/the-clonal-origins-of-leukemic-progression-of-myelodysplasia
#4
T H Kim, M S Tyndel, H J Kim, J-S Ahn, S H Choi, H J Park, Y-K Kim, D-H Yang, J-J Lee, S-H Jung, S Y Kim, Y H Min, J-W Cheong, S K Sohn, J H Moon, M Choi, M Lee, Z Zhang, D Dong Hwan Kim
The genetics behind the progression of myelodysplasia to secondary acute myeloid leukemia (sAML) is poorly understood. In this study, we profiled somatic mutations and their dynamics using next generation sequencing on serial samples from a total of 124 patients, consisting of a 31 patient discovery cohort and 93 patients from two validation cohorts. Whole-exome analysis on the discovery cohort revealed that 29 of 31 patients carry mutations related to at least one of 8 commonly mutated pathways in AML. Mutations in genes related to DNA methylation and splicing machinery were found in T-cell samples, which expand at the initial diagnosis of the myelodysplasia, suggesting their importance as early disease events...
January 16, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28089922/x-linked-elliptocytosis-with-impaired-growth-is-related-to-mutated-ammecr1
#5
Lina Basel-Vanagaite, Nir Pillar, Ofer Isakov, Pola Smirin-Yosef, Irina Lagovsky, Naama Orenstein, Mali Salmon-Divon, Hannah Tamary, Tami Zaft, Lily Bazak, Joseph Meyerovitch, Tal Pelli, Shay Botchan, Luba Farberov, Daphna Weissglas, Noam Shomron
In this study, we report a family with X-linked recessive syndrome caused by mutated AMMECR1 and characterized by elliptocytosis with or without anemia, midface hypoplasia, proportionate short stature and hearing loss. Recently, mutations in AMMECR1 were reported in two maternal half-brothers, presenting with nephrocalcinosis, midface hypoplasia and, in one of the siblings, deafness and elliptocytosis. AMMECR1 gene is localized in the critical region of contiguous deletion syndrome on Xq22.3 implicated in Alport syndrome, mental retardation, midface hypoplasia, and elliptocytosis (AMME complex)...
January 9, 2017: Gene
https://www.readbyqxmd.com/read/28089820/deregulated-expression-of-vhl-mrna-variants-in-papillary-thyroid-cancer
#6
Enke Baldini, Chiara Tuccilli, Yannick Arlot-Bonnemains, Frank Chesnel, Salvatore Sorrenti, Corrado De Vito, Antonio Catania, Eleonora D'Armiento, Alessandro Antonelli, Poupak Fallahi, Sara Watutantrige-Fernando, Francesco Tartaglia, Susi Barollo, Caterina Mian, Marco Bononi, Stefano Arceri, Domenico Mascagni, Massimo Vergine, Daniele Pironi, Massimo Monti, Angelo Filippini, Salvatore Ulisse
Recent findings demonstrated that a subset of papillary thyroid cancers (PTCs) is characterized by reduced expression of the von Hippel-Lindau (VHL) tumor suppressor gene, and that lowest levels associated with more aggressive PTCs. In the present study, the levels of the two VHL mRNA splicing variants, VHL-213 (V1) and VHL-172 (V2), were measured in a series of 96 PTC and corresponding normal matched tissues by means of quantitative RT-PCR. Variations in the mRNA levels were correlated with patients' clinicopathological parameters and disease-free interval (DFI)...
January 12, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28089691/orcokinin-neuropeptides-regulate-ecdysis-in-the-hemimetabolous-insect-rhodnius-prolixus
#7
Juan Pedro Wulff, Ivana Sierra, Marcos Sterkel, Michiel Holtof, Pieter Van Wielendaele, Flavio Francini, Jozef Vanden Broeck, Sheila Ons
To grow and develop insects must undergo ecdysis. During this process, the individual sheds the old cuticle to emerge as the following developmental stage. During ecdysis, different programed behaviors are regulated by neuropeptidergic pathways. In general, components of these pathways are better characterized in crustacean and holometabolous insects than in hemimetabola. In insects, the orkoninin gene produces two different neuropeptide precursors by alternative splicing: orcokinin A and orcokinin B. Although orcokinins are well conserved in insect species, their physiological role remains elusive...
January 9, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28088760/usp15-regulates-dynamic-protein-protein-interactions-of-the-spliceosome-through-deubiquitination-of-prp31
#8
Tanuza Das, Joon Kyu Park, Jinyoung Park, Eunji Kim, Michael Rape, Eunice EunKyeong Kim, Eun Joo Song
Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified with K63-linked ubiquitin chains by the PRP19 complex and deubiquitinated by USP15 and its substrate targeting factor SART3. USP15(SART3) makes a complex with USP4 and this ternary complex serves as a platform to deubiquitinate PRP31 and PRP3...
January 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28088503/evidence-for-splice-transcript-variants-of-tmem165-a-gene-involved-in-cdg
#9
Marie-Ange Krzewinski-Recchi, Sven Potelle, Anne Marie-Mir, Dorothée Vicogne, Eudoxie Dulary, Sandrine Duvet, Willy Morelle, Geoffroy de Bettignies, François Foulquier
BACKGROUND: Defects in TMEM165 gene cause a type-II Congenital Disorder of Glycosylation affecting Golgi glycosylation processes. TMEM165 patients exhibit psychomotor retardation, important osteoporosis, scoliosis, irregular epiphyses and thin bone cortex. Human TMEM165 protein is highly conserved in evolution and belongs to the family of UPF0016 membrane proteins which could be an unique group of Ca(2+)/H(+) antiporters regulating Ca(2+) and pH homeostasis and mainly localized in the Golgi apparatus...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088441/resveratrol-limits-epithelial-to-mesenchymal-transition-through-modulation-of-khsrp-hnrnpa1-dependent-alternative-splicing-in-mammary-gland-cells
#10
Arfa Moshiri, Margherita Puppo, Martina Rossi, Roberto Gherzi, Paola Briata
Resveratrol (RESV) is a natural polyphenolic compound endowed with anti-inflammatory, anti-proliferative, as well as pro-apoptotic activities that make it a potential anti-tumor compound. Here we show that RESV counteracts the TGF-β-induced Epithelial to Mesenchymal Transition (EMT) phenotype in mammary gland cells and affects the alternative exon usage of pre-mRNAs that encode crucial factors in adhesion and migration -including CD44, ENAH, and FGFR2- in a panel of immortalized and transformed mammary gland cells...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28087881/role-of-stim2-in-cell-function-and-physiopathology
#11
Alejandro Berna-Erro, Isaac Jardin, Gines M Salido, Juan A Rosado
An endoplasmic reticulum (ER)-resident protein that regulates cytosolic and ER free-Ca(2+) concentration by induction of store-operated calcium entry. That is the original definition of STIM2 and its function. While its activity strongly depends on the amount of calcium stored in the ER, its function goes further to intracellular signalling and gene expression. Initially undercovered by the prominent function of STIM1, STIM2 became to be vital in mice, gradually emerging as an important player in the nervous system, and cooperating with STIM1 in the immune system...
January 14, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28087732/novel-gnb1-mutations-disrupt-assembly-and-function-of-g-protein-heterotrimers-and-cause-global-developmental-delay-in-humans
#12
Katja Lohmann, Ikuo Masuho, Dipak N Patil, Hauke Baumann, Eva Hebert, Sofia Steinrücke, Daniel Trujillano, Nickolas K Skamangas, Valerija Dobricic, Irina Hüning, Gabriele Gillessen-Kaesbach, Ana Westenberger, Dusanka Savic-Pavicevic, Alexander Münchau, Gabriela Oprea, Christine Klein, Arndt Rolfs, Kirill A Martemyanov
Global developmental delay (GDD), often accompanied by intellectual disability, seizures and other features is a severe, clinically and genetically highly heterogeneous childhood-onset disorder. In cases where genetic causes have been identified, de-novo mutations in neuronally expressed genes are a common scenario. These mutations can be best identified by exome sequencing of parent-offspring trios. De novo mutations in the guanine nucleotide-binding protein, beta 1 (GNB1) gene, encoding the Gβ1 subunit of heterotrimeric G proteins, have recently been identified as a novel genetic cause of GDD...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28087625/faithful-mrna-splicing-depends-on-the-prp19-complex-subunit-faint-sausage-and-is-required-for-tracheal-branching-morphogenesis-in-drosophila
#13
Julia Sauerwald, Charlotte Soneson, Mark D Robinson, Stefan Luschnig
Morphogenesis requires the dynamic regulation of gene expression, including transcription, mRNA maturation and translation. Dysfunction of the general mRNA splicing machinery can cause surprisingly specific cellular phenotypes, but the basis for these effects is not clear. Here we show that the Drosophila faint sausage (fas) locus, implicated in epithelial morphogenesis and previously reported to encode a secreted immunoglobulin domain protein, in fact encodes a subunit of the spliceosome-activating Prp19 complex, which is essential for efficient pre-mRNA splicing...
January 13, 2017: Development
https://www.readbyqxmd.com/read/28086949/nek2-promotes-aerobic-glycolysis-in-multiple-myeloma-through-regulating-splicing-of-pyruvate-kinase
#14
Zhimin Gu, Jiliang Xia, Hongwei Xu, Ivana Frech, Guido Tricot, Fenghuang Zhan
BACKGROUND: Aerobic glycolysis, a hallmark of cancer, is characterized by increased metabolism of glucose and production of lactate in normaxia. Recently, pyruvate kinase M2 (PKM2) has been identified as a key player for regulating aerobic glycolysis and promoting tumor cell proliferation and survival. METHODS: Tandem affinity purification followed up by mass spectrometry (TAP-MS) and co-immunoprecipitation (Co-IP) were used to study the interaction between NIMA (never in mitosis gene A)-related kinase 2 (NEK2) and heterogeneous nuclear ribonucleoproteins (hnRNP) A1/2...
January 13, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28077658/a-cytoplasmic-rna-virus-alters-the-function-of-the-cell-splicing-protein-srsf2
#15
Efraín E Rivera-Serrano, Ethan J Fritch, Elizabeth H Scholl, Barbara Sherry
: To replicate efficiently, viruses must create favorable cell conditions and overcome cell antiviral responses. We previously reported that the reovirus protein μ2 from strain T1L, but not strain T3D, represses one antiviral response: interferon-α/β (IFN-β) signaling. We report here that T1L but not T3D μ2 localizes to nuclear speckles where it forms a complex with the mRNA splicing factor SRSF2 and alters its sub-nuclear localization. Reovirus replicates in cytoplasmic viral factories and there is no evidence that reovirus genomic or messenger RNAs are spliced, suggesting that T1L μ2 might target splicing of cell RNAs...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28077597/muscle-developmental-defects-in-heterogeneous-nuclear-ribonucleoprotein-a1-knockout-mice
#16
Ting-Yuan Liu, Yu-Chia Chen, Yuh-Jyh Jong, Huai-Jen Tsai, Chien-Chin Lee, Ya-Sian Chang, Jan-Gowth Chang, Yung-Fu Chang
Heterogeneous ribonucleoprotein A1 (hnRNP A1) is crucial for regulating alternative splicing. Its integrated function within an organism has not, however, been identified. We generated hnRNP A1 knockout mice to study the role of hnRNP A1 in vivo The knockout mice, hnRNP A1(-/-), showed embryonic lethality because of muscle developmental defects. The blood pressure and heart rate of the heterozygous mice were higher than those of the wild-type mice, indicating heart function defects. We performed mouse exon arrays to study the muscle development mechanism...
January 2017: Open Biology
https://www.readbyqxmd.com/read/28077579/neuron-enriched-rna-binding-proteins-regulate-pancreatic-beta-cell-function-and-survival
#17
Jon Agraves Juan-Mateu, Tatiana H Rech, Olatz Villate, Esther Lizarraga-Mollinedo, Anna Wendt, Jean-Valery Turatsinze, Leticia A Brondani, Tarlliza R Nardelli, Tatiane C Nogueira, Jonatan L S Esguerra, Maria In Ecircs Alvelos, Piero Marchetti, Lena Eliasson, D Eacutecio L Eizirik
Pancreatic beta cell failure is the central event leading to diabetes. Beta cells share many phenotypic traits with neurons, and proper beta cell function relies on the activation of several neuronal-like transcription programs. Regulation of gene expression by alternative splicing plays a pivotal role in brain, where it affects neuronal development, function and disease. The role of alternative splicing in beta cells remains unclear, but recent data indicate that splicing alterations modulated by both inflammation and susceptibility genes for diabetes contribute to beta cell dysfunction and death...
January 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28077403/gene-co-expression-analysis-for-functional-classification-and-gene-disease-predictions
#18
Sipko van Dam, Urmo Võsa, Adriaan van der Graaf, Lude Franke, João Pedro de Magalhães
Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28077248/alternative-splicing-at-exon-2-results-in-the-loss-of-the-catalytic-activity-of-mouse-dna-polymerase-iota-in-vitro
#19
Konstantin Y Kazachenko, Nataliya A Miropolskaya, Leonid V Gening, Vyacheslav Z Tarantul, Alena V Makarova
Y-family DNA polymerase iota (Pol ι) possesses both DNA polymerase and dRP lyase activities and was suggested to be involved in DNA translesion synthesis and base excision repair in mammals. The 129 strain of mice and its derivatives have a natural nonsense codon mutation in the second exon of the Pol ι gene resulting in truncation of the Pol ι protein. These mice were widely used as a Pol ι-null model for in vivo studies of the Pol ι function. However whether 129-derived strains of mice are fully deficient in the Pol ι functions was a subject of discussion since Pol ι mRNA undergoes alternative splicing at exon 2...
January 4, 2017: DNA Repair
https://www.readbyqxmd.com/read/28077092/phylogenetic-analysis-of-ionotropic-l-glutamate-receptor-genes-in-the-bilateria-with-special-notes-on-aplysia-californica
#20
Justin B Greer, Sawsan Khuri, Lynne A Fieber
BACKGROUND: The neurotransmitter L-Glutamate (L-Glu) acting at ionotropic L-Glu receptors (iGluR) conveys fast excitatory signal transmission in the nervous systems of all animals. iGluR-dependent neurotransmission is a key component of the synaptic plasticity that underlies learning and memory. During learning, two subtypes of iGluR, α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPAR) and N-methyl-D-aspartate receptors (NMDAR), are dynamically regulated postsynaptically in vertebrates...
January 11, 2017: BMC Evolutionary Biology
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