Localization of Condensin Subunit XCAP-E in Interphase Nucleus, Nucleoid and Nuclear
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PSF and P54nrb/Nono ^ Multi-Functional Nuclear Proteins
FEBS 26628 FEBS Letters 531 (2002) 109^114 View metadata, citation and similar papers at core.ac.uk brought to you by CORE Minireview provided by Elsevier - Publisher Connector PSF and p54nrb/NonO ^ multi-functional nuclear proteins Yaron Shav-Tal, Dov Ziporià Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel Received 30 May 2002; revised 10 September 2002; accepted 11 September 2002 First published online 7 October 2002 Edited by Takashi Gojobori glutamine-rich N-terminus of PSF might be involved in pro- Abstract Proteins are often referred to in accordance with the activity with which they were ¢rst associated or the organelle in tein^protein interactions [2]. nrb which they were initially identi¢ed. However, a variety of nu- p54 (human) and NonO (mouse) are highly homologous clear factors act in multiple molecular reactions occurring si- to the C-terminus of PSF (Fig. 1) [7,8]. Proteomics have iden- multaneously within the nucleus. This review describes the func- ti¢ed PSF and p54nrb/NonO in the nucleolus [9] and in asso- tions of the nuclear factors PSF (polypyrimidine tract-binding ciation with the nuclear membrane [10]. p54nrb/NonO was protein-associated splicing factor) and p54nrb/NonO. PSF was recently shown to be a component of a novel nuclear domain initially termed a splicing factor due to its association with the termed paraspeckles [11].TheDrosophila homolog of these nrb second step of pre-mRNA splicing while p54 /NonO was proteins is the NONA/BJ6 protein encoded by the no-on-tran- thought to participate in transcriptional regulation. -
Building the Interphase Nucleus: a Study on the Kinetics of 3D Chromosome Formation, Temporal Relation to Active Transcription, and the Role of Nuclear Rnas
University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2020-07-28 Building the Interphase Nucleus: A study on the kinetics of 3D chromosome formation, temporal relation to active transcription, and the role of nuclear RNAs Kristin N. Abramo University of Massachusetts Medical School Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_diss Part of the Bioinformatics Commons, Cell Biology Commons, Computational Biology Commons, Genomics Commons, Laboratory and Basic Science Research Commons, Molecular Biology Commons, Molecular Genetics Commons, and the Systems Biology Commons Repository Citation Abramo KN. (2020). Building the Interphase Nucleus: A study on the kinetics of 3D chromosome formation, temporal relation to active transcription, and the role of nuclear RNAs. GSBS Dissertations and Theses. https://doi.org/10.13028/a9gd-gw44. Retrieved from https://escholarship.umassmed.edu/ gsbs_diss/1099 Creative Commons License This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Dissertations and Theses by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. BUILDING THE INTERPHASE NUCLEUS: A STUDY ON THE KINETICS OF 3D CHROMOSOME FORMATION, TEMPORAL RELATION TO ACTIVE TRANSCRIPTION, AND THE ROLE OF NUCLEAR RNAS A Dissertation Presented By KRISTIN N. ABRAMO Submitted to the Faculty of the University of Massachusetts Graduate School of Biomedical Sciences, Worcester in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSPOPHY July 28, 2020 Program in Systems Biology, Interdisciplinary Graduate Program BUILDING THE INTERPHASE NUCLEUS: A STUDY ON THE KINETICS OF 3D CHROMOSOME FORMATION, TEMPORAL RELATION TO ACTIVE TRANSCRIPTION, AND THE ROLE OF NUCLEAR RNAS A Dissertation Presented By KRISTIN N. -
Nuclear Matrix
Nuclear matrix, nuclear envelope and premature aging syndromes in a translational research perspective Pierre Cau, Claire Navarro, Karim Harhouri, Patrice Roll, Sabine Sigaudy, Elise Kaspi, Sophie Perrin, Annachiara de Sandre-Giovannoli, Nicolas Lévy To cite this version: Pierre Cau, Claire Navarro, Karim Harhouri, Patrice Roll, Sabine Sigaudy, et al.. Nuclear matrix, nuclear envelope and premature aging syndromes in a translational research perspective. Seminars in Cell and Developmental Biology, Elsevier, 2014, 29, pp.125-147. 10.1016/j.semcdb.2014.03.021. hal-01646524 HAL Id: hal-01646524 https://hal-amu.archives-ouvertes.fr/hal-01646524 Submitted on 20 Dec 2017 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. Review Nuclear matrix, nuclear envelope and premature aging syndromes in a translational research perspective Pierre Cau a,b,c,∗, Claire Navarro a,b,1, Karim Harhouri a,b,1, Patrice Roll a,b,c,1,2, Sabine Sigaudy a,b,d,1,3, Elise Kaspi a,b,c,1,2, Sophie Perrin a,b,1, Annachiara De Sandre-Giovannoli a,b,d,1,3, Nicolas Lévy a,b,d,∗∗ a Aix-Marseille -
Nuclear Domains
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Cold Spring Harbor Laboratory Institutional Repository CELL SCIENCE AT A GLANCE 2891 Nuclear domains dynamic structures and, in addition, nuclear pore complex has been shown to rapid protein exchange occurs between have a remarkable substructure, in which David L. Spector many of the domains and the a basket extends into the nucleoplasm. Cold Spring Harbor Laboratory, One Bungtown nucleoplasm (Misteli, 2001). An The peripheral nuclear lamina lies Road, Cold Spring Harbor, NY 11724, USA extensive effort is currently underway by inside the nuclear envelope and is (e-mail: [email protected]) numerous laboratories to determine the composed of lamins A/C and B and is biological function(s) associated with thought to play a role in regulating Journal of Cell Science 114, 2891-2893 (2001) © The Company of Biologists Ltd each domain. The accompanying poster nuclear envelope structure and presents an overview of commonly anchoring interphase chromatin at the The mammalian cell nucleus is a observed nuclear domains. nuclear periphery. Internal patches of membrane-bound organelle that contains lamin protein are also present in the the machinery essential for gene The nucleus is bounded by a nuclear nucleoplasm (Moir et al., 2000). The expression. Although early studies envelope, a double-membrane structure, cartoon depicts much of the nuclear suggested that little organization exists of which the outer membrane is envelope/peripheral lamina as within this compartment, more contiguous with the rough endoplasmic transparent, so that internal structures contemporary studies have identified an reticulum and is often studded with can be more easily observed. -
Association of DNA with Nuclear Matrix in in Vitro Assembled Nuclei
Cell Research (1997), 7, 107-117 Association of DNA with nuclear matrix in in vitro as- sembled nuclei induced by rDNA from Tetrahymena shang- haiensis in Xenopus egg extracts CHEN YING, BO ZHANG, XIU FEN LI, ZHONG HE ZHAI Department of Cell Biology and Genetics, College of Life Sciences, Peking University, Beijing 100871 ABSTRACT The nuclei assembled from exogenous DNA or chro- matin in egg extracts resemble their in vivo counterparts in many aspects. However, the distribution pattern of DNA in these nuclei remains unknown. We introduced rDNA from the macronuclei of Tetrahymena into Xenopus cell- free extracts to examine the association of specific DNA sequences with nuclear matrix (NM) in the nuclei assem- bled in vitro. Our previous works showed the 5'NTS (non- transcription sequences) of the rDNA specifically bind to the NM system in the macronuclei. We show now the rDNA could induce chromatin assembly and nuclear for- mation in Xenopus cell-free system. When we extracted the NM system and compared the binding affinity of differ- ent regions of rDNA with the NM system, we found that the 5'NTS still hold their binding affinity with insoluble structure of the assembled nuclei in the extracts of Xeno- pus eggs. Key words: Nuclear assembly, nuclear matrix, Xeno- pus egg extracts, Tetrahymena rDNA. On the occasion of Professor Lu Ji SHI's (L. C. Sze), eightieth birthday, we present this paper and extend our sincere greetings to Professor SHI. As we mentioned in our paper, in early 1950's, it is Professor SHI who first studied the behavior of exogenous homologous desoxyribose nucleoprotein (chromatin) in amphibian eggs. -
Monoclonal Antibody to SMC2 / CAPE - Purified
OriGene Technologies, Inc. OriGene Technologies GmbH 9620 Medical Center Drive, Ste 200 Schillerstr. 5 Rockville, MD 20850 32052 Herford UNITED STATES GERMANY Phone: +1-888-267-4436 Phone: +49-5221-34606-0 Fax: +1-301-340-8606 Fax: +49-5221-34606-11 [email protected] [email protected] AM05324PU-N Monoclonal Antibody to SMC2 / CAPE - Purified Alternate names: CAP-E, Chromosome-associated protein E, SMC protein 2, SMC-2, SMC2L1, Structural maintenance of chromosomes protein 2, XCAP-E homolog Quantity: 0.1 mg Concentration: 1.0 mg/ml Background: CAP-E and CAP-C (Chromosome Associated Protein-E & C) are also SMC (Structural Maintenance of Chromosome) family members that form a heterodimeric complex required for mitotic chromosome condensation to achieve proper segregation of genetic information during subsequent cell division. hCAP-C/hCAP-E is a component of a multiprotein complex called condensin that interacts with phosphorylation of Histone H3 resulting in the mitotic chromosome condensation. The distribution patterns of the two heterodimeric complexes in interphase nucleus indicate independent behaviour of the two complexes during cell cycle. These results suggest that the two distinct complexes are involved in different aspects of mitotic chromosome organization in human cells. Uniprot ID: O95347 NCBI: NP_001036015.1 GeneID: 10592 Host / Isotype: Mouse / IgG Clone: E1M Immunogen: Hybridoma produced by the fusion of splenocytes from mice immunized with recombinant protein corresponding to amino acids 523-768 of Human CAP-E and Mouse myeloma cells. Genename: SMC2 Format: State: Liquid purified IgG fraction. Buffer System: PBS containing 0.08% Sodium Azide as preservative. Applications: Western Blot: 1-5 µg/ml. -
Supplementary Table S1. Correlation Between the Mutant P53-Interacting Partners and PTTG3P, PTTG1 and PTTG2, Based on Data from Starbase V3.0 Database
Supplementary Table S1. Correlation between the mutant p53-interacting partners and PTTG3P, PTTG1 and PTTG2, based on data from StarBase v3.0 database. PTTG3P PTTG1 PTTG2 Gene ID Coefficient-R p-value Coefficient-R p-value Coefficient-R p-value NF-YA ENSG00000001167 −0.077 8.59e-2 −0.210 2.09e-6 −0.122 6.23e-3 NF-YB ENSG00000120837 0.176 7.12e-5 0.227 2.82e-7 0.094 3.59e-2 NF-YC ENSG00000066136 0.124 5.45e-3 0.124 5.40e-3 0.051 2.51e-1 Sp1 ENSG00000185591 −0.014 7.50e-1 −0.201 5.82e-6 −0.072 1.07e-1 Ets-1 ENSG00000134954 −0.096 3.14e-2 −0.257 4.83e-9 0.034 4.46e-1 VDR ENSG00000111424 −0.091 4.10e-2 −0.216 1.03e-6 0.014 7.48e-1 SREBP-2 ENSG00000198911 −0.064 1.53e-1 −0.147 9.27e-4 −0.073 1.01e-1 TopBP1 ENSG00000163781 0.067 1.36e-1 0.051 2.57e-1 −0.020 6.57e-1 Pin1 ENSG00000127445 0.250 1.40e-8 0.571 9.56e-45 0.187 2.52e-5 MRE11 ENSG00000020922 0.063 1.56e-1 −0.007 8.81e-1 −0.024 5.93e-1 PML ENSG00000140464 0.072 1.05e-1 0.217 9.36e-7 0.166 1.85e-4 p63 ENSG00000073282 −0.120 7.04e-3 −0.283 1.08e-10 −0.198 7.71e-6 p73 ENSG00000078900 0.104 2.03e-2 0.258 4.67e-9 0.097 3.02e-2 Supplementary Table S2. -
Lorena Novoa-Aponte
A Strain: fl/fl ∆hep Strain: fl/fl ∆hep AnalysisAAV: ofLuc the ironLuc chaperonePCBP1-WT PCBP1PCBP1-∆Fe interactome:PCBP1-∆RNA PCBP1 variant intersection of DNA repair and iron traffickingAAV: Luc Luc WT ∆Fe ∆RNA PCBP1 −40 Lorena Novoa-Aponte a*, Sarju J. Patel a, Olga Protchenko a, James Wohlschlegel b, Caroline C. Philpott a −40 PCBP1, IHC PCBP1, GAPDH - a Genetics and Metabolism Section,a NIDDK, NIH, Bethesda, MD, USA. b Department of Biological Chemistry, UCLA, Los Angeles, CA, USA C.C. Philpott, et al. *[email protected] 80 B P = 0.0262 60 40 1. Iron is essential but toxic 2. Increased DNA damage in cells lacking PCBP1 ns H&E ? + 20 C.C. Philpott, et al. Iron is used as an essential cofactor by several enzymes involved in DNA ⦿ Increased TUNEL in cells and tissue livers from mice lacking PCBP1. ? replication and repair. However, unchaperoned iron promotes redox ⦿ PCBP1 binds both, iron and single-stranded nucleicTG, nmol/mg protein 0 acids. stress that may affect DNA stability. Strain: Δhep Δhep Δhep ? ⦿ The iron binding activity of PCBP1 controls suppressionAAV: of DNA damage C WT ∆Fe ∆RNA PCBP1 variant ? Iron storage HEK293 cells Mouse Liver ? A 8 siNT+P1var 100 ? A 8 var siPCBP1 2 ? Mammals use the iron siNT+P1 ns var Fe-S cluster assembly 6 siPCBP1+P1siPCBP1 80 ADI1 TUNEL chaperone PCBP1 to var ? 6 siPCBP1+P1 metalate several iron- 60 = 0.0468 = 0.0354 = 0.0465 cell / mm population P P P population + dependent enzymes + 4 + 4 ? 40 Degradation of HIF1α Fig. 3. Iron chaperone-mediated handling of cytosolic labile iron pool. -
A Yeast Phenomic Model for the Influence of Warburg Metabolism on Genetic Buffering of Doxorubicin Sean M
Santos and Hartman Cancer & Metabolism (2019) 7:9 https://doi.org/10.1186/s40170-019-0201-3 RESEARCH Open Access A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Sean M. Santos and John L. Hartman IV* Abstract Background: The influence of the Warburg phenomenon on chemotherapy response is unknown. Saccharomyces cerevisiae mimics the Warburg effect, repressing respiration in the presence of adequate glucose. Yeast phenomic experiments were conducted to assess potential influences of Warburg metabolism on gene-drug interaction underlying the cellular response to doxorubicin. Homologous genes from yeast phenomic and cancer pharmacogenomics data were analyzed to infer evolutionary conservation of gene-drug interaction and predict therapeutic relevance. Methods: Cell proliferation phenotypes (CPPs) of the yeast gene knockout/knockdown library were measured by quantitative high-throughput cell array phenotyping (Q-HTCP), treating with escalating doxorubicin concentrations under conditions of respiratory or glycolytic metabolism. Doxorubicin-gene interaction was quantified by departure of CPPs observed for the doxorubicin-treated mutant strain from that expected based on an interaction model. Recursive expectation-maximization clustering (REMc) and Gene Ontology (GO)-based analyses of interactions identified functional biological modules that differentially buffer or promote doxorubicin cytotoxicity with respect to Warburg metabolism. Yeast phenomic and cancer pharmacogenomics data were integrated to predict differential gene expression causally influencing doxorubicin anti-tumor efficacy. Results: Yeast compromised for genes functioning in chromatin organization, and several other cellular processes are more resistant to doxorubicin under glycolytic conditions. Thus, the Warburg transition appears to alleviate requirements for cellular functions that buffer doxorubicin cytotoxicity in a respiratory context. -
Gemin4 Is an Essential Gene in Mice, and Its Overexpression in Human Cells Causes Relocalization of the SMN Complex to the Nucleoplasm Ingo D
© 2018. Published by The Company of Biologists Ltd | Biology Open (2018) 7, bio032409. doi:10.1242/bio.032409 RESEARCH ARTICLE Gemin4 is an essential gene in mice, and its overexpression in human cells causes relocalization of the SMN complex to the nucleoplasm Ingo D. Meier1,*,§, Michael P. Walker1,2,‡,§ and A. Gregory Matera¶ ABSTRACT nuclear ribonucleoproteins (snRNPs). Each of these snRNPs Gemin4 is a member of the Survival Motor Neuron (SMN) protein contains a common set of seven RNA binding factors, called Sm complex, which is responsible for the assembly and maturation of Sm- proteins, that forms a heptameric ring around the snRNA, known as class small nuclear ribonucleoproteins (snRNPs). In metazoa, Sm the Sm core. Biogenesis of the Sm core is carried out by another snRNPs are assembled in the cytoplasm and subsequently imported macromolecular assemblage called the Survival Motor Neuron into the nucleus. We previously showed that the SMN complex is (SMN) complex, consisting of at least nine proteins (Gemins 2-8, required for snRNP import in vitro, although it remains unclear which unrip and SMN) (reviewed in Battle et al., 2006a; Matera et al., specific components direct this process. Here, we report that Gemin4 2007; Matera and Wang, 2014). overexpression drives SMN and the other Gemin proteins from the Following RNA polymerase II-mediated transcription in the cytoplasm into the nucleus. Moreover, it disrupts the subnuclear nucleus, pre-snRNAs are exported to the cytoplasm for assembly localization of the Cajal body marker protein, coilin, in a dose- into stable RNP particles (Jarmolowski et al., 1994; Ohno et al., dependent manner. -
Nuclear Matrix Protein Matrin 3 Is a Regulator of ZAP-Mediated Retroviral
Erazo and Goff. Retrovirology (2015) 12:57 DOI 10.1186/s12977-015-0182-4 RESEARCH Open Access Nuclear matrix protein Matrin 3 is a regulator of ZAP‑mediated retroviral restriction Angela Erazo1 and Stephen P Goff1,2* Abstract Background: Matrin 3 is a nuclear matrix protein involved in multiple nuclear processes. In HIV-1 infection, Matrin 3 serves as a Rev cofactor important for the cytoplasmic accumulation of HIV-1 transcripts. ZAP is a potent host restric- tion factor of multiple viruses including retroviruses HIV-1 and MoMuLV. In this study we sought to further character- ize Matrin 3 functions in the regulation of HIV gene expression. Results: Here we describe a function for Matrin 3 as a negative regulator of the ZAP-mediated restriction of retro- viruses. Mass spectrometry analysis of Matrin 3-associated proteins uncovered interactions with proteins of the ZAP degradation complex, DDX17 and EXOSC3. Coimmunoprecipitation studies confirmed Matrin 3 associations with DDX17, EXOSC3 and ZAP, in a largely RNA-dependent manner, indicating that RNA is mediating the Matrin 3 interac- tions with these components of the ZAP degradation complex. Silencing Matrin 3 expression caused a remarkably enhanced ZAP-driven inhibition of HIV-1 and MoMuLV luciferase reporter viruses. This effect was shared with addi- tional nuclear matrix proteins. ZAP targets multiply-spliced HIV-1 transcripts, but in the context of Matrin 3 suppres- sion, this ZAP restriction was broadened to unspliced and multiply-spliced RNAs. Conclusions: Here we reveal an unprecedented role for a nuclear matrix protein, Matrin 3, in the regulation of ZAP’s antiretroviral activity. -
Direct Interaction Between Hnrnp-M and CDC5L/PLRG1 Proteins Affects Alternative Splice Site Choice
Direct interaction between hnRNP-M and CDC5L/PLRG1 proteins affects alternative splice site choice David Llères, Marco Denegri, Marco Biggiogera, Paul Ajuh, Angus Lamond To cite this version: David Llères, Marco Denegri, Marco Biggiogera, Paul Ajuh, Angus Lamond. Direct interaction be- tween hnRNP-M and CDC5L/PLRG1 proteins affects alternative splice site choice. EMBO Reports, EMBO Press, 2010, 11 (6), pp.445 - 451. 10.1038/embor.2010.64. hal-03027049 HAL Id: hal-03027049 https://hal.archives-ouvertes.fr/hal-03027049 Submitted on 26 Nov 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. scientificscientificreport report Direct interaction between hnRNP-M and CDC5L/ PLRG1 proteins affects alternative splice site choice David Lle`res1*, Marco Denegri1*w,MarcoBiggiogera2,PaulAjuh1z & Angus I. Lamond1+ 1Wellcome Trust Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, UK, and 2LaboratoriodiBiologiaCellulareandCentrodiStudioperl’IstochimicadelCNR,DipartimentodiBiologiaAnimale, Universita’ di Pavia, Pavia, Italy Heterogeneous nuclear ribonucleoprotein-M (hnRNP-M) is an and affect the fate of heterogeneous nuclear RNAs by influencing their abundant nuclear protein that binds to pre-mRNA and is a structure and/or by facilitating or hindering the interaction of their component of the spliceosome complex.