The Phosphoinositide 5-Phosphatase Inpp5k: from Gene Structure to in Vivo Functions
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Analyses of Allele-Specific Gene Expression in Highly Divergent
ARTICLES Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance James J Crowley1,10, Vasyl Zhabotynsky1,10, Wei Sun1,2,10, Shunping Huang3, Isa Kemal Pakatci3, Yunjung Kim1, Jeremy R Wang3, Andrew P Morgan1,4,5, John D Calaway1,4,5, David L Aylor1,9, Zaining Yun1, Timothy A Bell1,4,5, Ryan J Buus1,4,5, Mark E Calaway1,4,5, John P Didion1,4,5, Terry J Gooch1,4,5, Stephanie D Hansen1,4,5, Nashiya N Robinson1,4,5, Ginger D Shaw1,4,5, Jason S Spence1, Corey R Quackenbush1, Cordelia J Barrick1, Randal J Nonneman1, Kyungsu Kim2, James Xenakis2, Yuying Xie1, William Valdar1,4, Alan B Lenarcic1, Wei Wang3,9, Catherine E Welsh3, Chen-Ping Fu3, Zhaojun Zhang3, James Holt3, Zhishan Guo3, David W Threadgill6, Lisa M Tarantino7, Darla R Miller1,4,5, Fei Zou2,11, Leonard McMillan3,11, Patrick F Sullivan1,5,7,8,11 & Fernando Pardo-Manuel de Villena1,4,5,11 Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. Effects from these variants influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. -
Functional Annotation of Exon Skipping Event in Human Pora Kim1,*,†, Mengyuan Yang1,†,Keyiya2, Weiling Zhao1 and Xiaobo Zhou1,3,4,*
D896–D907 Nucleic Acids Research, 2020, Vol. 48, Database issue Published online 23 October 2019 doi: 10.1093/nar/gkz917 ExonSkipDB: functional annotation of exon skipping event in human Pora Kim1,*,†, Mengyuan Yang1,†,KeYiya2, Weiling Zhao1 and Xiaobo Zhou1,3,4,* 1School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, 2College of Electronics and Information Engineering, Tongji University, Shanghai, China, 3McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA and 4School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA Received August 13, 2019; Revised September 21, 2019; Editorial Decision October 03, 2019; Accepted October 03, 2019 ABSTRACT been used as therapeutic targets (3–8). For example, MET has lost the binding site of E3 ubiquitin ligase CBL through Exon skipping (ES) is reported to be the most com- exon 14 skipping event (9), resulting in an enhanced expres- mon alternative splicing event due to loss of func- sion level of MET. MET amplification drives the prolifera- tional domains/sites or shifting of the open read- tion of tumor cells. Multiple tyrosine kinase inhibitors, such ing frame (ORF), leading to a variety of human dis- as crizotinib, cabozantinib and capmatinib, have been used eases and considered therapeutic targets. To date, to treat patients with MET exon 14 skipping (10). Another systematic and intensive annotations of ES events example is the dystrophin gene (DMD) in Duchenne mus- based on the skipped exon units in cancer and cular dystrophy (DMD), a progressive neuromuscular dis- normal tissues are not available. -
Identification of the Binding Partners for Hspb2 and Cryab Reveals
Brigham Young University BYU ScholarsArchive Theses and Dissertations 2013-12-12 Identification of the Binding arP tners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non- Redundant Roles for Small Heat Shock Proteins Kelsey Murphey Langston Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Langston, Kelsey Murphey, "Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins" (2013). Theses and Dissertations. 3822. https://scholarsarchive.byu.edu/etd/3822 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Julianne H. Grose, Chair William R. McCleary Brian Poole Department of Microbiology and Molecular Biology Brigham Young University December 2013 Copyright © 2013 Kelsey Langston All Rights Reserved ABSTRACT Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactors and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston Department of Microbiology and Molecular Biology, BYU Master of Science Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity. -
A Database Integrating Genomic Indel Polymorphisms That Distinguish Mouse Strains Keiko Akagi1,2, Robert M
D600–D606 Nucleic Acids Research, 2010, Vol. 38, Database issue Published online 20 November 2009 doi:10.1093/nar/gkp1046 MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains Keiko Akagi1,2, Robert M. Stephens3, Jingfeng Li2,4, Evgenji Evdokimov5, Michael R. Kuehn5, Natalia Volfovsky3 and David E. Symer2,4,6,7,8,9,* 1Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, 2Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, 3Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, 4Basic Research Laboratory, 5Laboratory of Protein Dynamics and Signaling, 6Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, 7Human Cancer Genetics Program, 8Departments of Internal Medicine and 9Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA Received August 5, 2009; Revised October 23, 2009; Accepted October 27, 2009 ABSTRACT wide-ranging functional differences. This extensive phenotypic variation has helped to make the mouse a MouseIndelDB is an integrated database resource premier model organism, mimicking many aspects of containing thousands of previously unreported human diversity and diseases. Understanding the mouse genomic indel (insertion and deletion) genomic differences that -
Cooperative Gene Regulation by Microrna Pairs and Their
Published online 29 May 2014 Nucleic Acids Research, 2014, Vol. 42, No. 12 7539–7552 doi: 10.1093/nar/gku465 Cooperative gene regulation by microRNA pairs and their identification using a computational workflow Ulf Schmitz1,*, Xin Lai2, Felix Winter1, Olaf Wolkenhauer1,3, Julio Vera2 and Shailendra K. Gupta1,4 Downloaded from 1Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany, 2Laboratory of Systems Tumor Immunology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Germany, 3Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa and 4Department of Bioinformatics, CSIR-Indian Institute of Toxicology Research, 226001 Lucknow, Uttar Pradesh, India http://nar.oxfordjournals.org/ Received December 22, 2013; Revised April 18, 2014; Accepted May 10, 2014 ABSTRACT fine-tuned through a cellular context-dependent regulation by multiple miRNAs, where miRNAs can either induce MicroRNAs (miRNAs) are an integral part of gene reg- translational repression or target mRNA degradation (4). ulation at the post-transcriptional level. Recently, it Thereby, the miRNA-target regulation machinery can real- at Universitaet Erlangen-Nuernberg, Wirtschafts- und Sozialwissenschaftliche Z on August 3, 2016 has been shown that pairs of miRNAs can repress the ize elaborate gene control functions, including noise buffer- translation of a target mRNA in a cooperative man- ing or homeostasis, and can ultimately mediate distinct tar- ner, which leads to an enhanced effectiveness and get expression patterns appropriate to the demand of differ- specificity in target repression. However, it remains ent biological processes (3,5,6). However, deregulated miR- unclear which miRNA pairs can synergize and which NAs have also been associated with the pathogenesis and genes are target of cooperative miRNA regulation. -
Rev7 Dimerization Is Important for Assembly and Function of the Rev1/Pol# Translesion Synthesis Complex
Rev7 dimerization is important for assembly and function of the Rev1/Pol# translesion synthesis complex The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Rizzo, Alessandro A. et al. “Rev7 Dimerization Is Important for Assembly and Function of the Rev1/Polζ Translesion Synthesis Complex.” Proceedings of the National Academy of Sciences 115, 35 (August 2018): E8191–E8200 © 2018 National Academy of Sciences As Published http://dx.doi.org/10.1073/pnas.1801149115 Publisher National Academy of Sciences (U.S.) Version Final published version Citable link http://hdl.handle.net/1721.1/120569 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. Rev7 dimerization is important for assembly and function of the Rev1/Polζ translesion synthesis complex Alessandro A. Rizzoa, Faye-Marie Vasselb, Nimrat Chatterjeeb, Sanjay D’Souzab, Yunfeng Lia, Bing Haoa, Michael T. Hemannb,c, Graham C. Walkerb, and Dmitry M. Korzhneva,1 aDepartment of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030; bDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and cThe David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 Edited by Gerhard Wagner, Harvard Medical School, Boston, MA, and approved July 18, 2018 (received for review January 20, 2018) The translesion synthesis (TLS) polymerases Polζ and Rev1 form a Besides TLS, Polζ participates in the repair of DNA in- complex that enables replication of damaged DNA. -
INPP5A Monoclonal Antibody (M05), Clone 3D8
INPP5A monoclonal antibody (M05), clone 3D8 Catalog # : H00003632-M05 規格 : [ 100 ug ] List All Specification Application Image Product Mouse monoclonal antibody raised against a partial recombinant Western Blot (Recombinant protein) Description: INPP5A. Immunoprecipitation Immunogen: INPP5A (NP_005530, 288 a.a. ~ 387 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Sequence: YFNQEVFRDNNGTALLEFDKELSVFKDRLYELDISFPPSYPYSEDARQG EQYMNTRCPAWCDRILMSPSAKELVLRVSVCCPSPGHRGMWSAGSGL AQPW enlarge Host: Mouse Sandwich ELISA (Recombinant Reactivity: Human protein) Isotype: IgG2a Kappa Quality Control Antibody Reactive Against Recombinant Protein. Testing: enlarge ELISA Western Blot detection against Immunogen (36.74 KDa) . Storage Buffer: In 1x PBS, pH 7.4 Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. Instruction: MSDS: Download Datasheet: Download Applications Western Blot (Recombinant protein) Protocol Download Immunoprecipitation Page 1 of 3 2016/5/21 Immunoprecipitation of INPP5A transfected lysate using anti-INPP5A monoclonal antibody and Protein A Magnetic Bead (U0007), and immunoblotted with INPP5A MaxPab rabbit polyclonal antibody. Protocol Download Sandwich ELISA (Recombinant protein) Detection limit for recombinant GST tagged INPP5A is 0.1 ng/ml as a capture antibody. Protocol Download ELISA Gene Information Entrez GeneID: 3632 GeneBank NM_005539 Accession#: Protein NP_005530 Accession#: Gene Name: INPP5A Gene Alias: 5PTASE,DKFZp434A1721,MGC116947,MGC116949 Gene inositol polyphosphate-5-phosphatase, 40kDa Description: Omim ID: 600106 Gene Ontology: Hyperlink Gene Summary: The protein encoded by this gene is a membrane-associated type I inositol 1,4,5-trisphosphate (InsP3) 5-phosphatase. InsP3 5- phosphatases hydrolyze Ins(1,4,5)P3, which mobilizes intracellular calcium and acts as a second messenger mediating cell responses to various stimulation. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
Identification of Holocarboxylase Synthetase Chromatin Binding Sites in Human Mammary Cell Lines Using the Damid Technology
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Biological Systems Engineering--Dissertations, Theses, and Student Research Biological Systems Engineering 12-2010 IDENTIFICATION OF HOLOCARBOXYLASE SYNTHETASE CHROMATIN BINDING SITES IN HUMAN MAMMARY CELL LINES USING THE DAMID TECHNOLOGY Dipika Singh University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/biosysengdiss Part of the Biological Engineering Commons Singh, Dipika, "IDENTIFICATION OF HOLOCARBOXYLASE SYNTHETASE CHROMATIN BINDING SITES IN HUMAN MAMMARY CELL LINES USING THE DAMID TECHNOLOGY" (2010). Biological Systems Engineering--Dissertations, Theses, and Student Research. 11. https://digitalcommons.unl.edu/biosysengdiss/11 This Article is brought to you for free and open access by the Biological Systems Engineering at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Biological Systems Engineering--Dissertations, Theses, and Student Research by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. IDENTIFICATION OF HOLOCARBOXYLASE SYNTHETASE CHROMATIN BINDING SITES IN HUMAN MAMMARY CELL LINES USING THE DAMID TECHNOLOGY by Dipika Singh A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science Major: Agricultural and Biological Systems Engineering Under the Supervision of Professors Angela K. Pannier and Janos Zempleni Lincoln, Nebraska December, 2010 Identification of holocarboxylase synthetase chromatin binding sites in human mammary cell lines using the DamID technology Dipika Singh, M.S. University of Nebraska, 2010 Advisers: Angela Pannier and Janos Zempleni Holocarboxylase synthetase (HCS) is a chromatin protein that is essential for mediating the covalent binding of biotin to histones. -
Allele-Specific Demethylation at an Imprinted Mammalian Promoter Andrew J
Published online 16 October 2007 Nucleic Acids Research, 2007, Vol. 35, No. 20 7031–7039 doi:10.1093/nar/gkm742 Allele-specific demethylation at an imprinted mammalian promoter Andrew J. Wood1,De´ borah Bourc’his2, Timothy H. Bestor3 and Rebecca J. Oakey1,* 1Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, London, SE1 9RT, UK, 2INSERM U741, Institut Jacques Monod, 2 Place Jussieu, 75251 Paris, CEDEX 05, France and 3Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, NY10032, USA Received July 4, 2007; Revised August 24, 2007; Accepted September 6, 2007 ABSTRACT Mutations in members of the de novo methyltransferase gene family lead to disruptions in imprinted gene A screen for imprinted genes on mouse expression and to retrotransposon animation (3,4), Chromosome 7 recently identified Inpp5f_v2, suggesting that the two processes are controlled by a a paternally expressed retrogene lying within an common mechanism (5). Dnmt3l encodes a regulatory intron of Inpp5f. Here, we identify a novel paternally protein that stimulates de novo methylation by Dnmt3a expressed variant of the Inpp5f gene (Inpp5f_v3) that and Dnmt3b, but lacks the catalytic motifs necessary for shows a number of unusual features. Inpp5f_v3 methyltransferase activity. Male mice lacking functional initiates from a CpG-rich repeat region adjoining copies of the Dnmt3l gene are sterile due to meiotic arrest, two B1 elements, despite previous reports that which is associated with the upregulation of endogenous SINEs are generally excluded from imprinted pro- retrotransposons (3). Females carrying null mutations in moters. Accordingly, we find that the Inpp5f_v3 the Dnmt3l gene fail to establish imprinted methylation promoter acquires methylation around the time of marks during oogenesis, but show no obvious effects on implantation, when many repeat families undergo de retrotransposon activity (6). -
Identification of Conserved Genes Triggering Puberty in European Sea
Blázquez et al. BMC Genomics (2017) 18:441 DOI 10.1186/s12864-017-3823-2 RESEARCHARTICLE Open Access Identification of conserved genes triggering puberty in European sea bass males (Dicentrarchus labrax) by microarray expression profiling Mercedes Blázquez1,2* , Paula Medina1,2,3, Berta Crespo1,4, Ana Gómez1 and Silvia Zanuy1* Abstract Background: Spermatogenesisisacomplexprocesscharacterized by the activation and/or repression of a number of genes in a spatio-temporal manner. Pubertal development in males starts with the onset of the first spermatogenesis and implies the division of primary spermatogonia and their subsequent entry into meiosis. This study is aimed at the characterization of genes involved in the onset of puberty in European sea bass, and constitutes the first transcriptomic approach focused on meiosis in this species. Results: European sea bass testes collected at the onset of puberty (first successful reproduction) were grouped in stage I (resting stage), and stage II (proliferative stage). Transition from stage I to stage II was marked by an increase of 11ketotestosterone (11KT), the main fish androgen, whereas the transcriptomic study resulted in 315 genes differentially expressed between the two stages. The onset of puberty induced 1) an up-regulation of genes involved in cell proliferation, cell cycle and meiosis progression, 2) changes in genes related with reproduction and growth, and 3) a down-regulation of genes included in the retinoic acid (RA) signalling pathway. The analysis of GO-terms and biological pathways showed that cell cycle, cell division, cellular metabolic processes, and reproduction were affected, consistent with the early events that occur during the onset of puberty. -
Genetic Variant in 3' Untranslated Region of the Mouse Pycard Gene
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.26.437184; this version posted March 26, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 2 3 Title: 4 Genetic Variant in 3’ Untranslated Region of the Mouse Pycard Gene Regulates Inflammasome 5 Activity 6 Running Title: 7 3’UTR SNP in Pycard regulates inflammasome activity 8 Authors: 9 Brian Ritchey1*, Qimin Hai1*, Juying Han1, John Barnard2, Jonathan D. Smith1,3 10 1Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 11 Cleveland, OH 44195 12 2Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 13 44195 14 3Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western 15 Reserve University, Cleveland, OH 44195 16 *, These authors contributed equally to this study. 17 Address correspondence to Jonathan D. Smith: email [email protected]; ORCID ID 0000-0002-0415-386X; 18 mailing address: Cleveland Clinic, Box NC-10, 9500 Euclid Avenue, Cleveland, OH 44195, USA. 19 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.26.437184; this version posted March 26, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 20 Abstract 21 Quantitative trait locus mapping for interleukin-1 release after inflammasome priming and activation 22 was performed on bone marrow-derived macrophages (BMDM) from an AKRxDBA/2 strain intercross.