Identification of Sequence Variants
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Mir-125 in Normal and Malignant Hematopoiesis
Leukemia (2012) 26, 2011–2018 & 2012 Macmillan Publishers Limited All rights reserved 0887-6924/12 www.nature.com/leu SPOTLIGHT REVIEW MiR-125 in normal and malignant hematopoiesis L Shaham1,2, V Binder3,4,NGefen1,5, A Borkhardt3 and S Izraeli1,5 MiR-125 is a highly conserved microRNA throughout many different species from nematode to humans. In humans, there are three homologs (hsa-miR-125b-1, hsa-miR-125b-2 and hsa-miR-125a). Here we review a recent research on the role of miR-125 in normal and malignant hematopoietic cells. Its high expression in hematopoietic stem cells (HSCs) enhances self-renewal and survival. Its expression in specific subtypes of myeloid and lymphoid leukemias provides resistance to apoptosis and blocks further differentiation. A direct oncogenic role in the hematopoietic system has recently been demonstrated by several mouse models. Targets of miR-125b include key proteins regulating apoptosis, innate immunity, inflammation and hematopoietic differentiation. Leukemia (2012) 26, 2011–2018; doi:10.1038/leu.2012.90 Keywords: microRNA; hematopoiesis; hematological malignancies; acute myeloid leukemia; acute lymphoblastic leukemia MicroRNAs (miRNAs) are 21–23-nucleotide non-coding RNAs that nucleotides with the seed region of miR-125b (ebv-miR-BART21-5p, have crucial roles in fundamental biological processes by ebv-miR-BART8 and rlcv-miR-rL1-25). In humans, as in most of the regulating the levels of multiple proteins. They are transcribed genomes, there are two paralogs (hsa-miR-125b-1 on chromosome as primary miRNAs and processed in the nucleus by the RNase III 11 and hsa-miR-125b-2 on chromosome 21), coding for the same endonuclease DROSHA to liberate 70-nucleotide stem loops, the mature sequence. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Specific Aim # 2A to Determine If Mir-122 Down-Regulates OCLN In
NOVEL ROLES OF MICRORNAS IN HEPATITIS C by Hossein Sendi A dissertation submitted to the faculty of The University of North Carolina at Charlotte in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology Charlotte 2013 Approved by: ______________________________ Dr. Mark G. Clemens ______________________________ Dr. Herbert L. Bonkovsky ______________________________ Dr. Laura W. Schrum _____________________________ Dr. Valery Grdzelishvili ____________________________ Dr. Kent E. Curran ii ©2013 Hossein Sendi ALL RIGHTS RESERVED iii ABSTRACT HOSSEIN SENDI. Novel roles of microRNAs in hepatitis C. (Under the direction of MARK CLEMENS and HERBERT BONKOVSKY) Approximately, 170 million people are infected by hepatitis C virus (HCV) worldwide, and of these, nearly 85% will develop chronic hepatitis C (CHC). Despite finding new anti-viral treatment that increase response rate from 45 % to 65-70 %, investigations continue to find more effective treatments for hepatitis C because of side effects and limitations of current treatment. It is known that miR-122 enhances HCV replication by binding to two closely spaced target sites in the 5’-UTR of the viral genome, which leads to an increase in abundance of HCV RNA. We found that miR-122 down- regulates Occludin (OCLN), one of the key HCV receptors, by directly targeting 3’-UTR of OCLN mRNA. We also found that interaction of miR-122 with 3’-UTR of OCLN mRNA eventually results in a decrease in HCV entry. In accordance with our in vitro study, we found an inverse correlation between pre-treatment levels of miR-122 and HCV RNA levels in patients with CHC. This is a new finding of our study which is consonant with our hypothesis that miR-122 may play an antiviral role in uninfected hepatocytes and early stages of HCV infection. -
A Catalogue of Stress Granules' Components
Catarina Rodrigues Nunes A Catalogue of Stress Granules’ Components: Implications for Neurodegeneration UNIVERSIDADE DO ALGARVE Departamento de Ciências Biomédicas e Medicina 2019 Catarina Rodrigues Nunes A Catalogue of Stress Granules’ Components: Implications for Neurodegeneration Master in Oncobiology – Molecular Mechanisms of Cancer This work was done under the supervision of: Clévio Nóbrega, Ph.D UNIVERSIDADE DO ALGARVE Departamento de Ciências Biomédicas e Medicina 2019 i ii A catalogue of Stress Granules’ Components: Implications for neurodegeneration Declaração de autoria de trabalho Declaro ser a autora deste trabalho, que é original e inédito. Autores e trabalhos consultados estão devidamente citados no texto e constam na listagem de referências incluída. I declare that I am the author of this work, that is original and unpublished. Authors and works consulted are properly cited in the text and included in the list of references. _______________________________ (Catarina Nunes) iii Copyright © 2019 Catarina Nunes A Universidade do Algarve reserva para si o direito, em conformidade com o disposto no Código do Direito de Autor e dos Direitos Conexos, de arquivar, reproduzir e publicar a obra, independentemente do meio utilizado, bem como de a divulgar através de repositórios científicos e de admitir a sua cópia e distribuição para fins meramente educacionais ou de investigação e não comerciais, conquanto seja dado o devido crédito ao autor e editor respetivos. iv Part of the results of this thesis were published in Nunes,C.; Mestre,I.; Marcelo,A. et al. MSGP: the first database of the protein components of the mammalian stress granules. Database (2019) Vol. 2019. (In annex A). v vi ACKNOWLEDGEMENTS A realização desta tese marca o final de uma etapa académica muito especial e que jamais irei esquecer. -
Novel Targets of Apparently Idiopathic Male Infertility
International Journal of Molecular Sciences Review Molecular Biology of Spermatogenesis: Novel Targets of Apparently Idiopathic Male Infertility Rossella Cannarella * , Rosita A. Condorelli , Laura M. Mongioì, Sandro La Vignera * and Aldo E. Calogero Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; [email protected] (R.A.C.); [email protected] (L.M.M.); [email protected] (A.E.C.) * Correspondence: [email protected] (R.C.); [email protected] (S.L.V.) Received: 8 February 2020; Accepted: 2 March 2020; Published: 3 March 2020 Abstract: Male infertility affects half of infertile couples and, currently, a relevant percentage of cases of male infertility is considered as idiopathic. Although the male contribution to human fertilization has traditionally been restricted to sperm DNA, current evidence suggest that a relevant number of sperm transcripts and proteins are involved in acrosome reactions, sperm-oocyte fusion and, once released into the oocyte, embryo growth and development. The aim of this review is to provide updated and comprehensive insight into the molecular biology of spermatogenesis, including evidence on spermatogenetic failure and underlining the role of the sperm-carried molecular factors involved in oocyte fertilization and embryo growth. This represents the first step in the identification of new possible diagnostic and, possibly, therapeutic markers in the field of apparently idiopathic male infertility. Keywords: spermatogenetic failure; embryo growth; male infertility; spermatogenesis; recurrent pregnancy loss; sperm proteome; DNA fragmentation; sperm transcriptome 1. Introduction Infertility is a widespread condition in industrialized countries, affecting up to 15% of couples of childbearing age [1]. It is defined as the inability to achieve conception after 1–2 years of unprotected sexual intercourse [2]. -
Interferon-Inducible Antiviral Effectors
REVIEWS Interferon-inducible antiviral effectors Anthony J. Sadler and Bryan R. G. Williams Abstract | Since the discovery of interferons (IFNs), considerable progress has been made in describing the nature of the cytokines themselves, the signalling components that direct the cell response and their antiviral activities. Gene targeting studies have distinguished four main effector pathways of the IFN-mediated antiviral response: the Mx GTPase pathway, the 2′,5′-oligoadenylate-synthetase-directed ribonuclease L pathway, the protein kinase R pathway and the ISG15 ubiquitin-like pathway. As discussed in this Review, these effector pathways individually block viral transcription, degrade viral RNA, inhibit translation and modify protein function to control all steps of viral replication. Ongoing research continues to expose additional activities for these effector proteins and has revealed unanticipated functions of the antiviral response. Pattern-recognition Interferon (IFN) was discovered more than 50 years ago in components of the IFNR signalling pathway (STAT1 receptors as an agent that inhibited the replication of influenza (signal transducer and activator of transcription 1), TYK2 (PRRs). Host receptors that can virus1. The IFN family of cytokines is now recognized as (tyrosine kinase 2) or UNC93B) die of viral disease, with sense pathogen-associated a key component of the innate immune response and the the defect in IFNAR (rather than IFNGR) signalling molecular patterns and initiate 6–9 signalling cascades that lead to first line of defence against viral infection. Accordingly, having the more significant role . an innate immune response. IFNs are currently used therapeutically, with the most The binding of type I IFNs to the IFNAR initiates a These can be membrane bound noteworthy example being the treatment of hepatitis C signalling cascade, which leads to the induction of more (such as Toll-like receptors) or virus (HCV) infection, and they are also used against than 300 IFN-stimulated genes (ISGs)10. -
Mutations in DCHS1 Cause Mitral Valve Prolapse Ronen Durst, Kimberly Sauls, David S
Mutations in DCHS1 cause mitral valve prolapse Ronen Durst, Kimberly Sauls, David S. Peal, Annemarieke Devlaming, Katelynn Toomer, Maire Leyne, Monica Salani, Michael E. Talkowski, Harrison Brand, Maëlle Perrocheau, et al. To cite this version: Ronen Durst, Kimberly Sauls, David S. Peal, Annemarieke Devlaming, Katelynn Toomer, et al.. Mutations in DCHS1 cause mitral valve prolapse. Nature, Nature Publishing Group, 2015, Equipe 3, 525 (7567), pp.109–113. 10.1038/nature14670. hal-01830584 HAL Id: hal-01830584 https://hal.archives-ouvertes.fr/hal-01830584 Submitted on 12 Jul 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. HHS Public Access Author manuscript Author Manuscript Author ManuscriptNature. Author ManuscriptAuthor manuscript; Author Manuscript available in PMC 2016 March 03. Published in final edited form as: Nature. 2015 September 3; 525(7567): 109–113. doi:10.1038/nature14670. Mutations in DCHS1 Cause Mitral Valve Prolapse Ronen Durst1,2,*, Kimberly Sauls5,*, David S Peal3,*, Annemarieke deVlaming5, Katelynn Toomer5, Maire Leyne1, Monica Salani1, Michael E. Talkowski1, Harrison Brand1, Maëlle Perrocheau9, Charles Simpson1, Christopher Jett1, Matthew R. Stone1, Florie Charles1, Colby Chiang1, Stacey N. Lynch3, Nabila Bouatia-Naji9,10, Francesca N. Delling7, Lisa A. -
125B Occurs Through Evolving Mirna–Target Gene Pairs
Conserved Regulation of p53 Network Dosage by MicroRNA– 125b Occurs through Evolving miRNA–Target Gene Pairs The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Le, Minh T. N. et al. “Conserved Regulation of P53 Network Dosage by MicroRNA–125b Occurs Through Evolving miRNA–Target Gene Pairs.” Ed. Michael T. McManus. PLoS Genetics 7.9 (2011): e1002242. Web. 10 Feb. 2012. As Published http://dx.doi.org/10.1371/journal.pgen.1002242 Publisher Public Library of Science Version Final published version Citable link http://hdl.handle.net/1721.1/69088 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/2.5/ Conserved Regulation of p53 Network Dosage by MicroRNA–125b Occurs through Evolving miRNA–Target Gene Pairs Minh T. N. Le1,2,3., Ng Shyh-Chang1,4., Swea Ling Khaw1,5, Lingzi Chin1, Cathleen Teh6, Junliang Tay1, Elizabeth O’Day2, Vladimir Korzh5, Henry Yang7, Ashish Lal2,8, Judy Lieberman2, Harvey F. Lodish3,9,10*, Bing Lim1,3,11* 1 Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore, 2 Immune Disease Institute and Program in Cellular and Molecular Medicine, Children’s Hospital Boston, Harvard Medical School, Boston, Massachusetts, United States of America, 3 Computation and Systems Biology, Singapore–MIT Alliance, Singapore, Singapore, 4 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America, 5 NUS Graduate -
Detecting Differential Copy Number Variation Between Groups of Samples
Downloaded from genome.cshlp.org on October 7, 2021 - Published by Cold Spring Harbor Laboratory Press Method Detecting differential copy number variation between groups of samples Craig B. Lowe,1,2,5 Nicelio Sanchez-Luege,1,5 Timothy R. Howes,1 Shannon D. Brady,1 Rhea R. Daugherty,1,3 Felicity C. Jones,1,3,6 Michael A. Bell,4 and David M. Kingsley1,2 1Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA; 2Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA; 3Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; 4Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA We present a method to detect copy number variants (CNVs) that are differentially present between two groups of sequenced samples. We use a finite-state transducer where the emitted read depth is conditioned on the mappability and GC-content of all reads that occur at a given base position. In this model, the read depth within a region is a mixture of binomials, which in simulations matches the read depth more closely than the often-used negative binomial distribution. The method analyzes all samples simultaneously, preserving uncertainty as to the breakpoints and magnitude of CNVs present in an individual when it identifies CNVs differentially present between the two groups. We apply this method to identify CNVs that are recurrently associated with postglacial adaptation of marine threespine stickleback (Gasterosteus aculeatus) to freshwater. We identify 6664 regions of the stickleback genome, totaling 1.7 Mbp, which show consistent copy number differences between marine and freshwater populations. -
Missense Mutation in the Second RNA Binding Domain Reveals a Role for Prkra (PACT/RAX) During Skull Development Benjamin K
Missense mutation in the second RNA binding domain reveals a role for Prkra (PACT/RAX) during skull development Benjamin K. Dickerman, Christine L. White, Claire Chevalier, Valerie Nalesso, Cyril Charles, Sophie Fouchécourt, Florian Jean Louis Guillou, Laurent Viriot, Ganes C. Sen, Yann Hérault To cite this version: Benjamin K. Dickerman, Christine L. White, Claire Chevalier, Valerie Nalesso, Cyril Charles, et al.. Missense mutation in the second RNA binding domain reveals a role for Prkra (PACT/RAX) during skull development. PLoS ONE, Public Library of Science, 2011, 6 (12), pp.e28537. 10.1371/jour- nal.pone.0028537. hal-01129622 HAL Id: hal-01129622 https://hal.archives-ouvertes.fr/hal-01129622 Submitted on 29 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Missense Mutation in the Second RNA Binding Domain Reveals a Role for Prkra (PACT/RAX) during Skull Development Benjamin K. Dickerman1,2, Christine L. White1, Claire Chevalier3, Vale´rie Nalesso3, Cyril Charles4, Sophie Fouche´court5, Florian Guillou5, Laurent Viriot4, Ganes C. Sen1,2*, -
Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
Research Article: New Research Development Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth Jeremy S. Toma,1 Konstantina Karamboulas,1,ª Matthew J. Carr,1,2,ª Adelaida Kolaj,1,3 Scott A. Yuzwa,1 Neemat Mahmud,1,3 Mekayla A. Storer,1 David R. Kaplan,1,2,4 and Freda D. Miller1,2,3,4 https://doi.org/10.1523/ENEURO.0066-20.2020 1Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada, 2Institute of Medical Sciences University of Toronto, Toronto, Ontario M5G 1A8, Canada, 3Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada, and 4Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada Abstract Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are es- sential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, in- cluding known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesen- chymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons. -
The Human GCOM1 Complex Gene Interacts with the NMDA Receptor and Internexin-Alpha☆
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Gene. Author Manuscript Author manuscript; Manuscript Author available in PMC 2018 June 20. Published in final edited form as: Gene. 2018 March 30; 648: 42–53. doi:10.1016/j.gene.2018.01.029. The human GCOM1 complex gene interacts with the NMDA receptor and internexin-alpha☆ Raymond S. Roginskia,b,*, Chi W. Laua,1, Phillip P. Santoiemmab,2, Sara J. Weaverc,3, Peicheng Dud, Patricia Soteropoulose, and Jay Yangc aDepartment of Anesthesiology, CMC VA Medical Center, Philadelphia, PA 19104, United States bDepartment of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States cDepartment of Anesthesia, University of Wisconsin at Madison, Madison, WI 53706, United States dBioinformatics, Rutgers-New Jersey Medical School, Newark, NJ 07103, United States eDepartment of Genetics, Rutgers-New Jersey Medical School, Newark, NJ 07103, United States Abstract The known functions of the human GCOM1 complex hub gene include transcription elongation and the intercalated disk of cardiac myocytes. However, in all likelihood, the gene's most interesting, and thus far least understood, roles will be found in the central nervous system. To investigate the functions of the GCOM1 gene in the CNS, we have cloned human and rat brain cDNAs encoding novel, 105 kDa GCOM1 combined (Gcom) proteins, designated Gcom15, and identified a new group of GCOM1 interacting genes, termed Gints, from yeast two-hybrid (Y2H) screens. We showed that Gcom15 interacts with the NR1 subunit of the NMDA receptor by co- expression in heterologous cells, in which we observed bi-directional co-immunoprecipitation of human Gcom15 and murine NR1.