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Alternative splicing

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https://www.readbyqxmd.com/read/28811331/targeting-a-single-alternative-polyadenylation-site-coordinately-blocks-expression-of-androgen-receptor-mrna-splice-variants-in-prostate%C3%A2-cancer
#1
Jamie L Van Etten, Michael Nyquist, Yingming Li, Rendong Yang, Yeung Ho, Rachel M Johnson, Olivia Ondigi, Daniel F Voytas, Christine Henzler, Scott M Dehm
Prostate cancer is the second leading cause of male cancer deaths due to disease progression to castration resistant prostate cancer (CRPC). Androgen receptor (AR) splice variants including AR-V7 function as constitutively active transcription factors in CRPC cells, thereby promoting resistance to AR-targeted therapies. To date, there are no AR variant specific treatments for CRPC. Here we report that the splicing of AR variants AR-V7 as well as AR-V1 and AR-V9 is regulated coordinately by a single polyadenylation signal in AR intron 3...
August 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28810306/-alternative-splicing-and-tumor
#2
Y Liu, H H Zhang, E P Xu
No abstract text is available yet for this article.
August 8, 2017: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
https://www.readbyqxmd.com/read/28809392/mettl3-mediated-m-6-a-regulates-spermatogonial-differentiation-and-meiosis-initiation
#3
Kai Xu, Ying Yang, Gui-Hai Feng, Bao-Fa Sun, Jun-Qing Chen, Yu-Fei Li, Yu-Sheng Chen, Xin-Xin Zhang, Chen-Xin Wang, Li-Yuan Jiang, Chao Liu, Ze-Yu Zhang, Xiu-Jie Wang, Qi Zhou, Yun-Gui Yang, Wei Li
METTL3 catalyzes the formation of N(6)-methyl-adenosine (m(6)A) which has important roles in regulating various biological processes. However, the in vivo function of Mettl3 remains largely unknown in mammals. Here we generated germ cell-specific Mettl3 knockout mice and demonstrated that Mettl3 was essential for male fertility and spermatogenesis. The ablation of Mettl3 in germ cells severely inhibited spermatogonial differentiation and blocked the initiation of meiosis. Transcriptome and m(6)A profiling analysis revealed that genes functioning in spermatogenesis had altered profiles of expression and alternative splicing...
August 15, 2017: Cell Research
https://www.readbyqxmd.com/read/28807867/impairment-of-different-protein-domains-causes-variable-clinical-presentation-within-pitt-hopkins-syndrome-and-suggests-intragenic-molecular-syndromology-of-tcf4
#4
Maria Francesca Bedeschi, Giuseppe Marangi, Maria Rosaria Calvello, Stefania Ricciardi, Francesca Pia Chiara Leone, Marco Baccarin, Silvana Guerneri, Daniela Orteschi, Marina Murdolo, Serena Lattante, Silvia Frangella, Beth Keena, Margaret H Harr, Elaine Zackai, Marcella Zollino
Pitt-Hopkins syndrome is a neurodevelopmental disorder characterized by severe intellectual disability and a distinctive facial gestalt. It is caused by haploinsufficiency of the TCF4 gene. The TCF4 protein has different functional domains, with the NLS (nuclear localization signal) domain coded by exons 7-8 and the bHLH (basic Helix-Loop-Helix) domain coded by exon 18. Several alternatively spliced TCF4 variants have been described, allowing for translation of variable protein isoforms. Typical PTHS patients have impairment of at least the bHLH domain...
August 11, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28806747/low-lamin-a-expression-in-lung-adenocarcinoma-cells-from-pleural-effusions-is-a-pejorative-factor-associated-with-high-number-of-metastatic-sites-and-poor-performance-status
#5
Elise Kaspi, Diane Frankel, Julien Guinde, Sophie Perrin, Sophie Laroumagne, Andrée Robaglia-Schlupp, Kevin Ostacolo, Karim Harhouri, Rachid Tazi-Mezalek, Joelle Micallef, Hervé Dutau, Pascale Tomasini, Annachiara De Sandre-Giovannoli, Nicolas Lévy, Pierre Cau, Philippe Astoul, Patrice Roll
The type V intermediate filament lamins are the principal components of the nuclear matrix, including the nuclear lamina. Lamins are divided into A-type and B-type, which are encoded by three genes, LMNA, LMNB1, and LMNB2. The alternative splicing of LMNA produces two major A-type lamins, lamin A and lamin C. Previous studies have suggested that lamins are involved in cancer development and progression. A-type lamins have been proposed as biomarkers for cancer diagnosis, prognosis, and/or follow-up. The aim of the present study was to investigate lamins in cancer cells from metastatic pleural effusions using immunofluorescence, western blotting, and flow cytometry...
2017: PloS One
https://www.readbyqxmd.com/read/28802831/validation-of-a-targeted-rna-sequencing-assay-for-kinase-fusion-detection-in-solid-tumors
#6
Julie W Reeser, Dorrelyn Martin, Jharna Miya, Esko A Kautto, Ezra Lyon, Eliot Zhu, Michele R Wing, Amy Smith, Matthew Reeder, Eric Samorodnitsky, Hannah Parks, Karan R Naik, Joseph Gozgit, Nicholas Nowacki, Kurtis D Davies, Marileila Varella-Garcia, Lianbo Yu, Aharon G Freud, Joshua Coleman, Dara L Aisner, Sameek Roychowdhury
Kinase gene fusions are important drivers of oncogenic transformation and can be inhibited with targeted therapies. Clinical grade diagnostics using RNA sequencing to detect gene rearrangements in solid tumors are limited, and the few that are available require prior knowledge of fusion break points. To address this, we have analytically validated a targeted RNA sequencing assay (OSU-SpARKFuse) for fusion detection that interrogates complete transcripts from 93 kinase and transcription factor genes. From a total of 74 positive and 36 negative control samples, OSU-SpARKFuse had 93...
August 8, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28801986/persistent-detection-of-alternatively-spliced-bcr-abl-variant-results-in-a-failure-to-achieve-deep-molecular-response
#7
Junichiro Yuda, Toshihiro Miyamoto, Jun Odawara, Yasuyuki Ohkawa, Yuichiro Semba, Masayasu Hayashi, Koichi Miyamura, Mitsune Tanimoto, Kazuhito Yamamoto, Masafumi Taniwaki, Koichi Akashi
Treatment with tyrosine kinase inhibitors (TKIs) may sequentially induce TKI-resistant BCR-ABL mutants in chronic myeloid leukemia (CML). Conventional polymerase chain reaction (PCR) monitoring of BCR-ABL is an important indicator to determine therapeutic intervention for preventing disease progression. However, PCR cannot quantify separately amounts of BCR-ABL and its mutants, including alternatively spliced BCR-ABL with an insertion of 35 intronic nucleotides (BCR-ABL(I)(ns35bp) ) between ABL exons 8 and 9 which introduces the premature termination and loss of kinase activity...
August 12, 2017: Cancer Science
https://www.readbyqxmd.com/read/28801530/rhythmic-behavior-is-controlled-by-the-srm160-splicing-factor-in-drosophila-melanogaster
#8
Esteban J Beckwith, Carlos E Hernando, Sofía Polcowñuk, Agustina P Bertolin, Estefania Mancini, M Fernanda Ceriani, Marcelo J Yanovsky
Circadian clocks organize the metabolism, physiology, and behavior of organisms throughout the day-night cycle by controlling daily rhythms in gene expression at the transcriptional and post-transcriptional levels. While many transcription factors underlying circadian oscillations are known, the splicing factors that modulate these rhythms remain largely unexplored. A genome-wide assessment of the alterations of gene expression in a null mutant of the alternative splicing regulator SR-related matrix protein of 160 kD (SRm160) revealed the extent to which alternative splicing impacts on behavior-related genes...
August 11, 2017: Genetics
https://www.readbyqxmd.com/read/28800142/alcohol-mediated-missplicing-of-mcl-1-pre-mrna-is-involved-in-neurotoxicity
#9
Rahsan Sariyer, Francesca I De Simone, Martina Donadoni, Jan B Hoek, Sulie L Chang, Ilker Kudret Sariyer
BACKGROUND: Heavy and chronic ethanol (EtOH) exposure can cause significant structural and functional damage to the adult brain. The most devastating consequence of EtOH exposure is the neurotoxicity associated with the depletion of neurons. Regulation of splice variants in the brain can modulate protein functions, which may ultimately affect behaviors associated with alcohol dependence and EtOH-mediated neurotoxicity. Since alcohol consumption is associated with neurotoxicity, it is possible that altered splicing of survival and pro-survival factors during the development of alcoholism may contribute to the neurotoxicity...
August 11, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28798723/structural-perspectives-of-insulin-receptor-isoform-selective-insulin-analogs
#10
Jiří Jiráček, Lenka Žáková
A significant drawback of the exogenous administration of insulin to diabetics is the non-physiological profile of insulin action resulting in the insufficient suppression of hepatic glucose production, which is the main contributing factor to diabetic hyperglycemia under fasting conditions and the basis of the challenge to restore a more physiological glucose profile in diabetes. The insulin receptor (IR) exists in two alternatively spliced variants, IR-A and IR-B, with different tissue distribution. While peripheral tissues contain different proportions of both isoforms, hepatic cells almost exclusively contain IR-B...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/28798494/identification-and-functional-characterization-of-the-sex-determining-gene-doublesex-in-the-sawfly-athalia-rosae%C3%A2-hymenoptera-tenthredinidae
#11
Shotaro Mine, Megumi Sumitani, Fugaku Aoki, Masatsugu Hatakeyama, Masataka G Suzuki
Sexual fate of the sawfly, Athalia rosae (Hymenoptera: Tenthredinidae) is determined by the complementary sex determination (CSD) mechanism as is the case in honeybees. However, to date, genes involved in sex determination have not been identified in this species. In this study, we attempted to identify orthologs of complementary sex-determiner (csd), feminizer (fem), and doublesex (dsx) from the A. rosae genome, all of which are crucial components of the sex determination cascade in the honeybee. As a result, we identified a sawfly ortholog of dsx (designated as Ardsx)...
2017: Applied Entomology and Zoology
https://www.readbyqxmd.com/read/28798351/snap-25b-deficiency-increases-insulin-secretion-and-changes-spatiotemporal-profile-of-ca-2-oscillations-in-%C3%AE-cell-networks
#12
Teresa Daraio, Lidija Križančić Bombek, Marko Gosak, Ismael Valladolid-Acebes, Maša Skelin Klemen, Essam Refai, Per-Olof Berggren, Kerstin Brismar, Marjan Slak Rupnik, Christina Bark
SNAP-25 is a protein of the core SNARE complex mediating stimulus-dependent release of insulin from pancreatic β cells. The protein exists as two alternatively spliced isoforms, SNAP-25a and SNAP-25b, differing in 9 out of 206 amino acids, yet their specific roles in pancreatic β cells remain unclear. We explored the effect of SNAP-25b-deficiency on glucose-stimulated insulin release in islets and found increased secretion both in vivo and in vitro. However, slow photo-release of caged Ca(2+) in β cells within pancreatic slices showed no significant differences in Ca(2+)-sensitivity, amplitude or rate of exocytosis between SNAP-25b-deficient and wild-type littermates...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28794490/a-transcriptome-atlas-of-rabbit-revealed-by-pacbio-single-molecule-long-read-sequencing
#13
Shi-Yi Chen, Feilong Deng, Xianbo Jia, Cao Li, Song-Jia Lai
It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexity. However, it still remains a huge challenge for obtaining full-length transcripts because of difficulties in the short read-based assembly. In the present study we employ PacBio single-molecule long-read sequencing technology for whole-transcriptome profiling in rabbit (Oryctolagus cuniculus)...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28793859/investigating-knockdown-resistance-kdr-mechanism-against-pyrethroids-ddt-in-the-malaria-vector-anopheles-funestus-across-africa
#14
Helen Irving, Charles S Wondji
BACKGROUND: Understanding the molecular basis of insecticide resistance is key to improve the surveillance and monitoring of malaria vector populations under control. In the major malaria vector Anopheles funestus, little is currently known about the role of the knockdown resistance (kdr) mechanism. Here, we investigated the presence and contribution of knockdown resistance (kdr) to pyrethroids/DDT resistance observed in Anopheles funestus across Africa. RESULTS: Pyrosequencing genotyping and sequencing of the voltage gated sodium channel (VGSC) gene did not detect the common L1014F mutation in field collected An...
August 9, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28790308/transcriptome-profiling-of-mouse-brains-with-qki-deficient-oligodendrocytes-reveals-major-alternative-splicing-defects-including-self-splicing
#15
Lama Darbelli, Karine Choquet, Stéphane Richard, Claudia L Kleinman
The qkI gene encodes a family of RNA binding proteins alternatively spliced at its 3' end, giving rise to three major spliced isoforms: QKI-5, QKI-6 and QKI-7. Their expression is tightly regulated during brain development with nuclear QKI-5 being the most abundant during embryogenesis followed by QKI-6 and QKI-7 that peak during myelination. Previously, we generated a mouse conditional qkI allele where exon 2 is excised using Olig2-Cre resulting in QKI-deficient oligodendrocytes (OLs). These mice have dysmyelination and die at the third post-natal week...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28790111/amiloride-an-old-diuretic-drug-is-a-potential-therapeutic-agent-for-multiple-myeloma
#16
Elizabeta Rojas, Luis Corchete, Laura San Segundo, Juan F Martínez-Blanch, Francisco M Codoñer, Teresa Paíno, Noemi Puig, Ramón García-Sanz, Maria Victoria Mateos, Enrique M Ocio, Irena Misiewicz-Krzeminska, Norma C Gutiérrez
<br />The search for new drugs that control the continuous relapses of multiple myeloma is still required. Here, we report for the first time the potent anti-myeloma activity of amiloride, an old potassium-sparing diuretic approved for the treatment of hypertension and edema due to heart failure.<br /><br />Experimental Design:  <p>Myeloma cell lines and primary samples were used to evaluate cytotoxicity of amiloride. In vivo studies were carried out in a xenograft mouse model. The mechanisms of action were investigated using RNA-Seq, qRT-PCR, immunoblotting and immunofluorescence assays...
August 8, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28789987/regulation-of-splicing-and-circularisation-of-rna-in-epithelial-mesenchymal-plasticity
#17
REVIEW
Daniel P Neumann, Gregory J Goodall, Philip A Gregory
Interconversions between epithelial and mesenchymal states, often referred to as epithelial mesenchymal transition (EMT) and its reverse MET, play important roles in embryonic development and are recapitulated in various adult pathologies including cancer progression. These conversions are regulated by complex transcriptional and post-transcriptional mechanisms including programs of alternative splicing which are orchestrated by specific splicing factors. This review will focus on the latest developments in our understanding of the splicing factors regulating epithelial mesenchymal plasticity associated with cancer progression and the induction of pluripotency, including potential roles for circular RNAs (circRNAs) which have been recently implicated in these processes...
August 5, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28780165/the-na-ca-2-exchanger-and-the-plasma-membrane-ca-2-atpase-in-%C3%AE-cell-function-and-diabetes
#18
REVIEW
André Herchuelz, Nathalie Pachera
The rat pancreatic β-cell expresses 6 splice variants of the Plasma Membrane Ca(2+)-ATPase (PMCA) and two splice variants of the Na(+)/Ca(2+) exchanger 1 (NCX1). In the β-cell Na(+)/Ca(2+) exchange displays a high capacity, contributes to both Ca(2+) outflow and influx and participates to the control of insulin release. Gain of function studies show that overexpression of PMCA2 or NCX1 leads to endoplasmic reticulum (ER) Ca(2+) depletion with subsequent ER stress, decrease in β-cell proliferation and β-cell death by apoptosis...
August 2, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28776436/chimeric-nup98-nsd1-transcripts-from-the-cryptic-t-5-11-q35-2-p15-4-in-adult-de-novo-acute-myeloid-leukemia
#19
Jarno L Kivioja, Jesus M Lopez Martí, Ashwini Kumar, Mika Kontro, Henrik Edgren, Alun Parsons, Tuija Lundán, Maija Wolf, Kimmo Porkka, Caroline A Heckman
The t(5;11)(q35;p15.4) is a clinically significant marker of poor prognosis in acute myeloid leukemia (AML), which is difficult to detect due to sub-telomeric localization of the breakpoints. To facilitate the detection of this rearrangement, we studied NUP98-NSD1 transcript variants in patients with the t(5;11) using paired-end RNA sequencing and standard molecular biology techniques. We discovered three NUP98-NSD1 transcripts with two fusion junctions (NUP98 exon 11-12/NSD1 exon 6), alternative 5' donor site in NUP98 exon 7, and NSD1 exon 7 skipping...
August 4, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28776286/bypassing-mirna-mediated-gene-regulation-under-drought-stress-alternative-splicing-affects-csd1-gene-expression
#20
So-Yon Park, Elizabeth Grabau
The binding site for miR398 in an isoform of Cu/Zn superoxide dismutase (CSD1) is eliminated by alternative splicing to bypass miR398-mediated gene down-regulation under drought stress. MicroRNA (miRNA) binding sites (MBSs) are frequently interrupted by introns and therefore require proper splicing to generate functional MBSs in target transcripts. MBSs can also be excluded during splicing of pre-messenger RNA, leading to different regulation among isoforms. Previous studies have shown that levels of Cu/Zn superoxide dismutase (CSD) are down-regulated by miR398...
August 3, 2017: Plant Molecular Biology
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