Dramatically Reduced Spliceosome in Cyanidioschyzon Merolae
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Reconstituting Cell Dynamics with Synthetic Biology
REVIEW CELL BIOLOGY Toward total synthesis of cell function: Reconstituting cell dynamics with synthetic biology Allen K. Kim,1,2,3 Robert DeRose,1,2* Tasuku Ueno,4† Benjamin Lin,3,5,6† Toru Komatsu,4,7† Hideki Nakamura,1,2 Takanari Inoue1,2,3,7* Biological phenomena, such as cellular differentiation and phagocytosis, are fundamental processes that enable cells to fulfill important physiological roles in multicellular organisms. In the field of synthetic biology, the study of these behaviors relies on the use of a broad range of molecular tools that enable the real-time manipulation and measurement of key components in the underlying signaling pathways. This Review will focus on a subset of synthetic biology tools known as bottom-up techniques, which use technologies such as optogenetics and chemically induced dimerization to reconstitute cellular behavior Downloaded from in cells. These techniques have been crucial not only in revealing causal relationships within signaling networks but also in identifying the minimal signaling components that are necessary for a given cellular function. We discuss studies that used these systems in a broad range of cellular and molecular phenomena, including the time-dependent modulation of protein activity in cellular proliferation and dif- ferentiation, the reconstitution of phagocytosis, the reconstitution of chemotaxis, and the regulation of actin reorganization. Finally, we discuss the potential contribution of synthetic biology to medicine. http://stke.sciencemag.org/ Introduction lation of biomolecules with subcellular resolution. One of the ultimate One of the prevailing aspirations of synthetic biology is the intelligent de- goals of synthetic biology is the recapitulation of these behaviors in a sign of biological systems to perform a specific function, which is achieved cell-free system, in which all of the components are introduced in a through the assembly of modular components consisting of genes and pro- controlled manner. -
Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases
cells Review Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases Paulina Prorok 1 , Inga R. Grin 2,3, Bakhyt T. Matkarimov 4, Alexander A. Ishchenko 5 , Jacques Laval 5, Dmitry O. Zharkov 2,3,* and Murat Saparbaev 5,* 1 Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany; [email protected] 2 SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; [email protected] 3 Center for Advanced Biomedical Research, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia 4 National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; [email protected] 5 Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif, France; [email protected] (A.A.I.); [email protected] (J.L.) * Correspondence: [email protected] (D.O.Z.); [email protected] (M.S.); Tel.: +7-(383)-3635187 (D.O.Z.); +33-(1)-42115404 (M.S.) Abstract: It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the Citation: Prorok, P.; Grin, I.R.; major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field Matkarimov, B.T.; Ishchenko, A.A.; and alkylating metabolic radicals added to these threats. -
Alterations of RNA Splicing Patterns in Esophagus Squamous Cell Carcinoma
Ding et al. Cell Biosci (2021) 11:36 https://doi.org/10.1186/s13578-021-00546-z Cell & Bioscience RESEARCH Open Access Alterations of RNA splicing patterns in esophagus squamous cell carcinoma Jiyu Ding1,2, Chunquan Li3, Yinwei Cheng1,2, Zepeng Du4, Qiuyu Wang3, Zhidong Tang3, Chao Song3, Qiaoxi Xia1,2, Wenjing Bai1,2, Ling Lin1,2, Wei Liu1,2, Liyan Xu1,5, Enmin Li1,2* and Bingli Wu1,2* Abstract Alternative splicing (AS) is an important biological process for regulating the expression of various isoforms from a single gene and thus to promote proteome diversity. In this study, RNA-seq data from 15 pairs of matched esopha- geal squamous cell carcinoma (ESCC) and normal tissue samples as well as two cell lines were analyzed. AS events with signifcant diferences were identifed between ESCC and matched normal tissues, which were re-annotated to fnd protein coding genes or non-coding RNAs. A total of 45,439 AS events were found. Of these, 6019 (13.25%) signifcant diferentially AS events were identifed. Exon skipping (SE) events occupied the largest proportion of abnormal splicing events. Fifteen diferential splicing events with the same trends of ΔΨ values in ESCC tissues, as well in the two cell lines were found. Four pathways and 20 biological processes related to pro-metastasis cell junction and migration were signifcantly enriched for the diferentially spliced genes. The upregulated splicing factor SF3B4, which regulates 92 gene splicing events, could be a potential prognostic factor of ESCC. Diferentially spliced genes, includ- ing HNRNPC, VCL, ZNF207, KIAA1217, TPM1 and CALD1 are shown with a sashimi plot. -
SF3B3) and Sin3a Associated Protein 130 (SAP130
cells Communication Ambiguity about Splicing Factor 3b Subunit 3 (SF3B3) and Sin3A Associated Protein 130 (SAP130) Paula I. Metselaar 1,* , Celine Hos 1, Olaf Welting 1, Jos A. Bosch 2,3, Aletta D. Kraneveld 4 , Wouter J. de Jonge 1 and Anje A. Te Velde 1 1 Tytgat Institute for Liver and Intestinal Research, AGEM, Amsterdam UMC, University of Amsterdam, 1105BK Amsterdam, The Netherlands; [email protected] (C.H.); [email protected] (O.W.); [email protected] (W.J.d.J.); [email protected] (A.A.T.V.) 2 Department of Psychology, University of Amsterdam, 1018WS Amsterdam, The Netherlands; [email protected] 3 Department of Medical Psychology, Amsterdam UMC, University of Amsterdam, 1001NK Amsterdam, The Netherlands 4 Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584CG Utrecht, The Netherlands; [email protected] * Correspondence: [email protected] Abstract: In 2020, three articles were published on a protein that can activate the immune system by binding to macrophage-inducible C-type lectin receptor (Mincle). In the articles, the protein was referred to as ‘SAP130, a subunit of the histone deacetylase complex.’ However, the Mincle ligand the authors aimed to investigate is splicing factor 3b subunit 3 (SF3B3). This splicing factor is unrelated to SAP130 (Sin3A associated protein 130, a subunit of the histone deacetylase-dependent Sin3A corepressor complex). The conclusions in the three articles were formulated for SF3B3, Citation: Metselaar, P.I.; Hos, C.; while the researchers used qPCR primers and antibodies against SAP130. -
Responses of Bats to White-Nose Syndrome and Implications for Conservation
University of New Hampshire University of New Hampshire Scholars' Repository Doctoral Dissertations Student Scholarship Spring 2020 Responses of Bats to White-Nose Syndrome and Implications for Conservation Meghan Stark University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/dissertation Recommended Citation Stark, Meghan, "Responses of Bats to White-Nose Syndrome and Implications for Conservation" (2020). Doctoral Dissertations. 2518. https://scholars.unh.edu/dissertation/2518 This Dissertation is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. RESPONSES OF BATS TO WHITE-NOSE SYNDROME AND IMPLICATIONS FOR CONSERVATION BY MEGHAN A. STARK B.S., University of Alabama at Birmingham, 2013 DISSERTATION Submitted to the University of New Hampshire in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy In Genetics May 2020 i This dissertation was examined and approved in partial fulfillment of the requirements for the degree of Ph.D. in Genetics by: Dissertation Director, Matthew MacManes, Assoc. Prof. UNH MCBS Jeffrey T. Foster, Associate Professor, NAU PMI W. Kelley Thomas, Professor, UNH MCBS Rebecca Rowe, Associate Professor, UNH NREN Thomas Lee, Associate Professor Emeritus, UNH NREN On April 6, 2020 Approval signatures are on file with the University of New Hampshire Graduate School. ii DEDICATION I dedicate this work to all of the strong women in my life: Myra Michele Ange Heather Michelle Coons Kaitlyn Danielle Cagle Brindlee Michelle Coons Patricia Gail Miller Sarah Jean Lane “Here’s to strong women. -
Urabe VK, Et Al. Influences on U2 Snrna Structure U2
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.05.451154; this version posted July 6, 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-NC-ND 4.0 International license. Urabe VK, et al. Influences on U2 snRNA structure U2 snRNA structure is influenced by SF3A and SF3B proteins but not by SF3B inhibitors Veronica K. Urabe1, Meredith Stevers1, Arun K. Ghosh3 and Melissa S. Jurica1,2 * 1Department of Molecular Cell and Developmental Biology and 2Center for Molecular Biology of RNA, University of California, Santa Cruz, California, United States of America 3Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana United States of America *Corresponding author E-mail: [email protected] (MSJ) bioRxiv preprint doi: https://doi.org/10.1101/2021.07.05.451154; this version posted July 6, 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-NC-ND 4.0 International license. Urabe VK, et al. Influences on U2 snRNA structure Abstract U2 snRNP is an essential component of the spliceosome. It is responsible for branch point recognition in the spliceosome A-complex via base-pairing of U2 snRNA with an intron to form the branch helix. Small molecule inhibitors target the SF3B component of the U2 snRNP and interfere with A-complex formation during spliceosome assembly. -
SF3B2 Monoclonal Antibody (M01J), Clone 5D2
SF3B2 monoclonal antibody (M01J), clone 5D2 Catalog # : H00010992-M01J 規格 : [ 100 ug ] List All Specification Application Image Product Mouse monoclonal antibody raised against a partial recombinant Western Blot (Cell lysate) Description: SF3B2. Immunogen: SF3B2 (NP_006833, 592 a.a. ~ 645 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Sequence: YEGKEFETRLKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYG PPPSY enlarge Western Blot (Cell lysate) Host: Mouse Reactivity: Human, Mouse, Rat Preparation Cell Culture Production Method: (CX Grade Antibody List) enlarge Isotype: IgG2a Kappa Western Blot (Recombinant protein) Quality Control Antibody Reactive Against Recombinant Protein. Immunofluorescence Testing: enlarge Immunohistochemistry (Formalin/PFA-fixed paraffin- embedded sections) Western Blot detection against Immunogen (31.68 KDa) . Storage Buffer: In 1x PBS, pH 7.4 Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. enlarge Instruction: Sandwich ELISA (Recombinant protein) MSDS: Download Interspecies Mouse (98); Rat (98) Antigen Sequence: Datasheet: Download enlarge ELISA Applications Western Blot (Cell lysate) Page 1 of 3 2021/6/15 SF3B2 monoclonal antibody (M01J), clone 5D2. Western Blot analysis of SF3B2 expression in Hela S3 NE. Protocol Download Western Blot (Cell lysate) SF3B2 monoclonal antibody (M01J), clone 5D2. Western Blot analysis of SF3B2 expression in Jurkat. Protocol Download Western Blot (Recombinant protein) Protocol Download Immunofluorescence enlarge this image Immunofluorescence of monoclonal antibody to SF3B2 on HeLa cell . [antibody concentration 10 ug/ml] Immunohistochemistry (Formalin/PFA-fixed paraffin-embedded sections) enlarge this image Page 2 of 3 2021/6/15 Immunoperoxidase of monoclonal antibody to SF3B2 on formalin-fixed paraffin-embedded human kidney. [antibody concentration 6 ug/ml] Protocol Download Sandwich ELISA (Recombinant protein) Detection limit for recombinant GST tagged SF3B2 is 0.1 ng/ml as a capture antibody. -
Genome-Wide Association Study of Copy Number Variations (Cnvs) with Opioid Dependence
Neuropsychopharmacology (2015) 40, 1016–1026 & 2015 American College of Neuropsychopharmacology. All rights reserved 0893-133X/15 www.neuropsychopharmacology.org Genome-Wide Association Study of Copy Number Variations (CNVs) with Opioid Dependence Dawei Li*,1,2,3,4, Hongyu Zhao5,6, Henry R Kranzler7, Ming D Li8, Kevin P Jensen1, Tetyana Zayats1, Lindsay A Farrer9 and Joel Gelernter1,6,10 1 2 Department of Psychiatry, School of Medicine, Yale University, New Haven, CT, USA; Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA; 3Department of Computer Science, University of Vermont, Burlington, VT, USA; 4Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, VT, USA; 5Department of Biostatistics, Yale School of Public Health, New Haven, 6 7 CT, USA; Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA; Department of Psychiatry, University of 8 Pennsylvania School of Medicine and VISN 4 MIRECC, Philadelphia VAMC, Philadelphia, PA, USA; Department of Psychiatry and 9 Neurobehavioral Sciences, University of Virginia, Charlottesville, VA, USA; Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Genetics and Genomics, Biostatistics, and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, MA, USA; 10VA Connecticut Healthcare Center, Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA Single-nucleotide polymorphisms that have been associated with opioid dependence (OD) altogether account for only a small proportion of the known heritability. Most of the genetic risk factors are unknown. Some of the ‘missing heritability’ might be explained by copy number variations (CNVs) in the human genome. We used Illumina HumanOmni1 arrays to genotype 5152 African-American and European-American OD cases and screened controls and implemented combined CNV calling methods. -
Coupling of Spliceosome Complexity to Intron Diversity
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.19.436190; this version posted March 20, 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-NC-ND 4.0 International license. Coupling of spliceosome complexity to intron diversity Jade Sales-Lee1, Daniela S. Perry1, Bradley A. Bowser2, Jolene K. Diedrich3, Beiduo Rao1, Irene Beusch1, John R. Yates III3, Scott W. Roy4,6, and Hiten D. Madhani1,6,7 1Dept. of Biochemistry and Biophysics University of California – San Francisco San Francisco, CA 94158 2Dept. of Molecular and Cellular Biology University of California - Merced Merced, CA 95343 3Department of Molecular Medicine The Scripps Research Institute, La Jolla, CA 92037 4Dept. of Biology San Francisco State University San Francisco, CA 94132 5Chan-Zuckerberg Biohub San Francisco, CA 94158 6Corresponding authors: [email protected], [email protected] 7Lead Contact 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.19.436190; this version posted March 20, 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-NC-ND 4.0 International license. SUMMARY We determined that over 40 spliceosomal proteins are conserved between many fungal species and humans but were lost during the evolution of S. cerevisiae, an intron-poor yeast with unusually rigid splicing signals. We analyzed null mutations in a subset of these factors, most of which had not been investigated previously, in the intron-rich yeast Cryptococcus neoformans. -
SF3B4 Gene Splicing Factor 3B Subunit 4
SF3B4 gene splicing factor 3b subunit 4 Normal Function The SF3B4 gene provides instructions for making the SAP49 protein, which is part of a complex called a spliceosome. Spliceosomes help process messenger RNA (mRNA), which is a chemical cousin of DNA that serves as a genetic blueprint for making proteins. The spliceosomes recognize and then remove regions from mRNA molecules that are not used in the blueprint (which are called introns). The SAP49 protein may also be involved in a chemical signaling pathway known as the bone morphogenic protein (BMP) pathway. This signaling pathway regulates various cellular processes and is involved in the growth of cells. The SAP49 protein is particularly important for the maturation of cells that build bones and cartilage ( osteoblasts and chondrocytes). Health Conditions Related to Genetic Changes Nager syndrome More than 30 mutations in the SF3B4 gene have been found to cause Nager syndrome, which is primarily characterized by abnormalities of the face, hands, and arms, such as underdeveloped cheek bones (malar hypoplasia), a small lower jaw (micrognathia), and malformed or absent thumbs. The condition can also affect development of other parts of the body. More than half of people with this condition have a mutation in the SF3B4 gene. These mutations prevent the production of SAP49 protein or lead to production of a nonfunctional protein. It is unclear how a shortage of functional SAP49 protein leads to the development problems in Nager syndrome. Researchers suspect that problems with spliceosome formation may impair mRNA processing and alter the activity of genes involved in development of several parts of the body. -
SF3B2-Mediated RNA Splicing Drives Human Prostate Cancer Progression
Published OnlineFirst August 20, 2019; DOI: 10.1158/0008-5472.CAN-18-3965 Cancer Molecular Cell Biology Research SF3B2-Mediated RNA Splicing Drives Human Prostate Cancer Progression Norihiko Kawamura1,2, Keisuke Nimura1, Kotaro Saga1, Airi Ishibashi1, Koji Kitamura1,3, Hiromichi Nagano1, Yusuke Yoshikawa4, Kyoso Ishida1,5, Norio Nonomura2, Mitsuhiro Arisawa4, Jun Luo6, and Yasufumi Kaneda1 Abstract Androgen receptor splice variant-7 (AR-V7) is a General RNA splicing SF3B2 complex-mediated alternative RNA splicing constitutively active AR variant implicated in U2 castration-resistant prostate cancers. Here, we show U2 snRNA that the RNA splicing factor SF3B2, identified by 3’ 3’ in silico and CRISPR/Cas9 analyses, is a critical 5’ 3’ splice site 5’ SF3B7 AR-V7 5’ A U2AF2 AGA Exon ? determinant of expression and is correlated SF3B6(p14) SF3B4 SF3B1 SF3B4 SF3B1 with aggressive cancer phenotypes. Transcriptome SF3B5 SF3B2 SF3B3 SF3B2 SF3B3 and PAR-CLIP analyses revealed that SF3B2 con- SF3A3 SF3B2 complex SF3A3 SF3A1 SF3A1 SF3b complex trols the splicing of target genes, including AR, to AR pre-mRNA drive aggressive phenotypes. SF3B2-mediated CE3 aggressive phenotypes in vivo were reversed by AR-V7 mRNA AR mRNA AR-V7 knockout. Pladienolide B, an inhibitor of CE3 a splicing modulator of the SF3b complex, sup- Drive malignancy pressed the growth of tumors addicted to high While the SF3b complex is critical for general RNA splicing, SF3B2 promotes inclusion of the target exon through recognizing a specific RNA motif. SF3B2 expression. These findings support the idea © 2019 American Association for Cancer Research that alteration of the splicing pattern by high SF3B2 expression is one mechanism underlying prostate cancer progression and therapeutic resistance. -
Mrna Turnover Philip Mitchell* and David Tollervey†
320 mRNA turnover Philip Mitchell* and David Tollervey† Nuclear RNA-binding proteins can record pre-mRNA are cotransported to the cytoplasm with the mRNP. These processing events in the structure of messenger proteins may preserve a record of the nuclear history of the ribonucleoprotein particles (mRNPs). During initial rounds of pre-mRNA in the cytoplasmic mRNP structure. This infor- translation, the mature mRNP structure is established and is mation can strongly influence the cytoplasmic fate of the monitored by mRNA surveillance systems. Competition for the mRNA and is used by mRNA surveillance systems that act cap structure links translation and subsequent mRNA as a checkpoint of mRNP integrity, particularly in the identi- degradation, which may also involve multiple deadenylases. fication of premature translation termination codons (PTCs). Addresses Cotransport of nuclear mRNA-binding proteins with mRNA Wellcome Trust Centre for Cell Biology, ICMB, University of Edinburgh, from the nucleus to the cytoplasm (nucleocytoplasmic shut- Kings’ Buildings, Edinburgh EH9 3JR, UK tling) was first observed for the heterogeneous nuclear *e-mail: [email protected] ribonucleoprotein (hnRNP) proteins. Some hnRNP proteins †e-mail: [email protected] are stripped from the mRNA at export [1], but hnRNP A1, Current Opinion in Cell Biology 2001, 13:320–325 A2, E, I and K are all exported (see [2]). Although roles for 0955-0674/01/$ — see front matter these hnRNP proteins in transport and translation have been © 2001 Elsevier Science Ltd. All rights reserved. reported [3•,4•], their affects on mRNA stability have been little studied. More is known about hnRNP D/AUF1 and Abbreviations AREs AU-rich sequence elements another nuclear RNA-binding protein, HuR, which act CBC cap-binding complex antagonistically to modulate the stability of a range of DAN deadenylating nuclease mRNAs containing AU-rich sequence elements (AREs) DSEs downstream sequence elements (reviewed in [2]).