Chapter One: Introduction
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Histone Isoform H2A1H Promotes Attainment of Distinct Physiological
Bhattacharya et al. Epigenetics & Chromatin (2017) 10:48 DOI 10.1186/s13072-017-0155-z Epigenetics & Chromatin RESEARCH Open Access Histone isoform H2A1H promotes attainment of distinct physiological states by altering chromatin dynamics Saikat Bhattacharya1,4,6, Divya Reddy1,4, Vinod Jani5†, Nikhil Gadewal3†, Sanket Shah1,4, Raja Reddy2,4, Kakoli Bose2,4, Uddhavesh Sonavane5, Rajendra Joshi5 and Sanjay Gupta1,4* Abstract Background: The distinct functional efects of the replication-dependent histone H2A isoforms have been dem- onstrated; however, the mechanistic basis of the non-redundancy remains unclear. Here, we have investigated the specifc functional contribution of the histone H2A isoform H2A1H, which difers from another isoform H2A2A3 in the identity of only three amino acids. Results: H2A1H exhibits varied expression levels in diferent normal tissues and human cancer cell lines (H2A1C in humans). It also promotes cell proliferation in a context-dependent manner when exogenously overexpressed. To uncover the molecular basis of the non-redundancy, equilibrium unfolding of recombinant H2A1H-H2B dimer was performed. We found that the M51L alteration at the H2A–H2B dimer interface decreases the temperature of melting of H2A1H-H2B by ~ 3 °C as compared to the H2A2A3-H2B dimer. This diference in the dimer stability is also refected in the chromatin dynamics as H2A1H-containing nucleosomes are more stable owing to M51L and K99R substitu- tions. Molecular dynamic simulations suggest that these substitutions increase the number of hydrogen bonds and hydrophobic interactions of H2A1H, enabling it to form more stable nucleosomes. Conclusion: We show that the M51L and K99R substitutions, besides altering the stability of histone–histone and histone–DNA complexes, have the most prominent efect on cell proliferation, suggesting that the nucleosome sta- bility is intimately linked with the physiological efects observed. -
Gene Symbol Gene Description ACVR1B Activin a Receptor, Type IB
Table S1. Kinase clones included in human kinase cDNA library for yeast two-hybrid screening Gene Symbol Gene Description ACVR1B activin A receptor, type IB ADCK2 aarF domain containing kinase 2 ADCK4 aarF domain containing kinase 4 AGK multiple substrate lipid kinase;MULK AK1 adenylate kinase 1 AK3 adenylate kinase 3 like 1 AK3L1 adenylate kinase 3 ALDH18A1 aldehyde dehydrogenase 18 family, member A1;ALDH18A1 ALK anaplastic lymphoma kinase (Ki-1) ALPK1 alpha-kinase 1 ALPK2 alpha-kinase 2 AMHR2 anti-Mullerian hormone receptor, type II ARAF v-raf murine sarcoma 3611 viral oncogene homolog 1 ARSG arylsulfatase G;ARSG AURKB aurora kinase B AURKC aurora kinase C BCKDK branched chain alpha-ketoacid dehydrogenase kinase BMPR1A bone morphogenetic protein receptor, type IA BMPR2 bone morphogenetic protein receptor, type II (serine/threonine kinase) BRAF v-raf murine sarcoma viral oncogene homolog B1 BRD3 bromodomain containing 3 BRD4 bromodomain containing 4 BTK Bruton agammaglobulinemia tyrosine kinase BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) C9orf98 chromosome 9 open reading frame 98;C9orf98 CABC1 chaperone, ABC1 activity of bc1 complex like (S. pombe) CALM1 calmodulin 1 (phosphorylase kinase, delta) CALM2 calmodulin 2 (phosphorylase kinase, delta) CALM3 calmodulin 3 (phosphorylase kinase, delta) CAMK1 calcium/calmodulin-dependent protein kinase I CAMK2A calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha CAMK2B calcium/calmodulin-dependent -
Download The
BIOCHEMICAL CHARACTERIZATION AND REGULATION OF TRANSCRIPTION OF POLYCOMB GROUP RING FINGER 5 by Christopher Larson Cochrane B.Sc., The University of British Columbia, 2004 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Experimental Medicine) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) August 2013 © Christopher Larson Cochrane, 2013 Abstract The Polycomb Group (PcG) is a highly conserved group of genes which serve to repress transcription via specific modifications of histones in chromatin. The PcG has well-established roles in development and is involved, by mutation or dysregulation, in many human diseases including cancer. This study identifies the gene PCGF5, which is a paralogue of the oncogene Bmi1, as a transcriptional target of Notch signalling in T cell acute lymphoblastic leukemia (T-ALL). Evidence suggests that this regulation is direct and that the Notch transactivation complex binds DNA at several regions near the PCGF5 gene. PCGF5 is found to be expressed at a higher level in T-ALL than other hematopoietic malignancies. PCGF5 is found to associate with the PcG proteins RING1A and RING1B and its overexpression results in increased ubiquitylation of histone H2A, suggesting it shares functional similarity to Bmi1. Despite their similarities, Bmi1 and PCGF5 have a different spectrum of binding partners and are targeted to different locations in the genome. Overexpression of PCGF5 does not significantly alter hematopoietic development in vivo; however, enforced expression of PCGF5 in bone marrow progenitors results in the generation of fewer colonies in a myeloid colony forming assay. This study suggests that PCGF5 may have as yet unappreciated roles in PcG biology and merits further study into its effects on development and hematopoietic neoplasia. -
Environmental Influences on Endothelial Gene Expression
ENDOTHELIAL CELL GENE EXPRESSION John Matthew Jeff Herbert Supervisors: Prof. Roy Bicknell and Dr. Victoria Heath PhD thesis University of Birmingham August 2012 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Tumour angiogenesis is a vital process in the pathology of tumour development and metastasis. Targeting markers of tumour endothelium provide a means of targeted destruction of a tumours oxygen and nutrient supply via destruction of tumour vasculature, which in turn ultimately leads to beneficial consequences to patients. Although current anti -angiogenic and vascular targeting strategies help patients, more potently in combination with chemo therapy, there is still a need for more tumour endothelial marker discoveries as current treatments have cardiovascular and other side effects. For the first time, the analyses of in-vivo biotinylation of an embryonic system is performed to obtain putative vascular targets. Also for the first time, deep sequencing is applied to freshly isolated tumour and normal endothelial cells from lung, colon and bladder tissues for the identification of pan-vascular-targets. Integration of the proteomic, deep sequencing, public cDNA libraries and microarrays, delivers 5,892 putative vascular targets to the science community. -
Repertoire of Morphable Proteins in an Organism
Repertoire of morphable proteins in an organism Keisuke Izumi, Eitaro Saho, Ayuka Kutomi, Fumiaki Tomoike and Tetsuji Okada Department of Life Science, Gakushuin University, Tokyo, Japan ABSTRACT All living organisms have evolved to contain a set of proteins with variable physical and chemical properties. Efforts in the field of structural biology have contributed to uncovering the shape and the variability of each component. However, quantification of the variability has been performed mostly by multiple pair-wise comparisons. A set of experimental coordinates for a given protein can be used to define the “morphness/unmorphness”. To understand the evolved repertoire in an organism, here we show the results of global analysis of more than a thousand Escherichia coli proteins, by the recently introduced method, distance scoring analysis (DSA). By collecting a new index “UnMorphness Factor” (UMF), proposed in this study and determined from DSA for each of the proteins, the lowest and the highest boundaries of the experimentally observable structural variation are comprehensibly defined. The distribution plot of UMFs obtained for E. coli represents the first view of a substantial fraction of non-redundant proteome set of an organism, demonstrating how rigid and flexible components are balanced. The present analysis extends to evaluate the growing data from single particle cryo-electron microscopy, providing valuable information on effective interpretation to structural changes of proteins and the supramolecular complexes. Subjects Biochemistry, Bioinformatics, Biophysics, Molecular Biology Keywords Protein, Structure, Crystallography, cryo-EM, E. coli, Human, PDB, Coordinates Submitted 21 October 2019 Accepted 20 January 2020 INTRODUCTION Published 11 February 2020 Self-replicating (living) species are defined by the presence of a genome that is used to Corresponding author Tetsuji Okada, produce a set of proteins and RNAs. -
The Landscape of Somatic Mutations in Epigenetic Regulators Across 1,000 Paediatric Cancer Genomes
ARTICLE Received 24 Sep 2013 | Accepted 12 Mar 2014 | Published 8 Apr 2014 DOI: 10.1038/ncomms4630 The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes Robert Huether1,*, Li Dong2,*, Xiang Chen1, Gang Wu1, Matthew Parker1, Lei Wei1, Jing Ma2, Michael N. Edmonson1, Erin K. Hedlund1, Michael C. Rusch1, Sheila A. Shurtleff2, Heather L. Mulder3, Kristy Boggs3, Bhavin Vadordaria3, Jinjun Cheng2, Donald Yergeau3, Guangchun Song2, Jared Becksfort1, Gordon Lemmon1, Catherine Weber2, Zhongling Cai2, Jinjun Dang2, Michael Walsh4, Amanda L. Gedman2, Zachary Faber2, John Easton3, Tanja Gruber2,4, Richard W. Kriwacki5, Janet F. Partridge6, Li Ding7,8,9, Richard K. Wilson7,8,9, Elaine R. Mardis7,8,9, Charles G. Mullighan2, Richard J. Gilbertson10, Suzanne J. Baker10, Gerard Zambetti6, David W. Ellison2, Jinghui Zhang1 & James R. Downing2 Studies of paediatric cancers have shown a high frequency of mutation across epigenetic regulators. Here we sequence 633 genes, encoding the majority of known epigenetic regulatory proteins, in over 1,000 paediatric tumours to define the landscape of somatic mutations in epigenetic regulators in paediatric cancer. Our results demonstrate a marked variation in the frequency of gene mutations across 21 different paediatric cancer subtypes, with the highest frequency of mutations detected in high-grade gliomas, T-lineage acute lymphoblastic leukaemia and medulloblastoma, and a paucity of mutations in low-grade glioma and retinoblastoma. The most frequently mutated genes are H3F3A, PHF6, ATRX, KDM6A, SMARCA4, ASXL2, CREBBP, EZH2, MLL2, USP7, ASXL1, NSD2, SETD2, SMC1A and ZMYM3. We identify novel loss-of-function mutations in the ubiquitin-specific processing protease 7 (USP7) in paediatric leukaemia, which result in decreased deubiquitination activity. -
Specification in Embryonic Stem Cells Through Activation and Repression
Article Polycomb Regulates Mesoderm Cell Fate- Specification in Embryonic Stem Cells through Activation and Repression Mechanisms Graphical Abstract Authors Lluis Morey, Alexandra Santanach, Enrique Blanco, ..., Elphe` ge P. Nora, Benoit G. Bruneau, Luciano Di Croce Correspondence [email protected] (L.M.), [email protected] (L.D.C.) In Brief Morey et al. reveal that Mel18, a Polycomb-complex-associated protein, is an essential epigenetic regulator of cardiac differentiation. During directed differentiation of embryonic stem cells, Morey et al. find that Mel18-PRC1 complexes exchange subunits in a stage- specific manner and instruct sequential gene activation and repression programs to specify mesoderm fate, prevent alternate lineage commitment, and promote cardiac differentiation. Highlights Accession Numbers d Mel18 is required for PRC1 stability and maintenance of gene GSE67868 repression in ESCs d Mel18 is essential for ESC differentiation into early cardiac- mesoderm precursors d Different Mel18-PRC1 complexes are assembled during cardiac differentiation d Distinctive PRC1 complexes bind to highly active and repressed genes in MES cells Morey et al., 2015, Cell Stem Cell 17, 300–315 September 3, 2015 ª2015 Elsevier Inc. http://dx.doi.org/10.1016/j.stem.2015.08.009 Cell Stem Cell Article Polycomb Regulates Mesoderm Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms Lluis Morey,1,2,6,* Alexandra Santanach,1,2 Enrique Blanco,1,2 Luigi Aloia,1,2 Elphe` ge P. Nora,3,4 Benoit G. Bruneau,3,4 -
FGFR1 Fusion and Amplification in a Solid Variant of Alveolar Rhabdomyosarcoma
Modern Pathology (2011) 24, 1327–1335 & 2011 USCAP, Inc. All rights reserved 0893-3952/11 $32.00 1327 FOXO1–FGFR1 fusion and amplification in a solid variant of alveolar rhabdomyosarcoma Jinglan Liu1,2, Miguel A Guzman1,2, Donna Pezanowski1, Dilipkumar Patel1, John Hauptman1, Matthew Keisling3, Steve J Hou2,3, Peter R Papenhausen4, Judy M Pascasio1,2, Hope H Punnett1,5, Gregory E Halligan2,6 and Jean-Pierre de Chadare´vian1,2 1Department of Pathology and Laboratory Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA; 2Drexel University College of Medicine, Philadelphia, PA, USA; 3Department of Pathology and Laboratory Medicine, Hahnneman University Hospital, Philadelphia, PA, USA; 4Laboratory Corporation of America, The Research Triangle Park, NC, USA; 5Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA, USA and 6Department of Pediatrics, Section of Oncology, St Christopher’s Hospital for Children, Philadelphia, PA, USA Rhabdomyosarcoma is the most common pediatric soft tissue malignancy. Two major subtypes, alveolar rhabdomyosarcoma and embryonal rhabdomyosarcoma, constitute 20 and 60% of all cases, respectively. Approximately 80% of alveolar rhabdomyosarcoma carry two signature chromosomal translocations, t(2;13)(q35;q14) resulting in PAX3–FOXO1 fusion, and t(1;13)(p36;q14) resulting in PAX7–FOXO1 fusion. Whether the remaining cases are truly negative for gene fusion has been questioned. We are reporting the case of a 9-month-old girl with a metastatic neck mass diagnosed histologically as solid variant alveolar rhabdomyosarcoma. Chromosome analysis showed a t(8;13;9)(p11.2;q14;9q32) three-way translocation as the sole clonal aberration. Fluorescent in situ hybridization (FISH) demonstrated a rearrangement at the FOXO1 locus and an amplification of its centromeric region. -
Tsrna Signatures in Cancer
tsRNA signatures in cancer Veronica Balattia, Giovanni Nigitaa,1, Dario Venezianoa,1, Alessandra Druscoa, Gary S. Steinb,c, Terri L. Messierb,c, Nicholas H. Farinab,c, Jane B. Lianb,c, Luisa Tomaselloa, Chang-gong Liud, Alexey Palamarchuka, Jonathan R. Harte, Catherine Belle, Mariantonia Carosif, Edoardo Pescarmonaf, Letizia Perracchiof, Maria Diodorof, Andrea Russof, Anna Antenuccif, Paolo Viscaf, Antonio Ciardig, Curtis C. Harrish, Peter K. Vogte, Yuri Pekarskya,2, and Carlo M. Crocea,2 aDepartment of Cancer Biology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210; bDepartment of Biochemistry, University of Vermont College of Medicine, Burlington, VT 05405; cUniversity of Vermont Cancer Center, College of Medicine, Burlington, VT 05405; dMD Anderson Cancer Center, Houston, TX 77030; eDepartment of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037; fIstituto di Ricovero e Cura a Carattere Scientifico, Regina Elena National Cancer Institute, 00144 Rome, Italy; gUniversita’ Di Roma La Sapienza, 00185 Rome, Italy; and hLaboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 Contributed by Carlo M. Croce, June 13, 2017 (sent for review April 26, 2017; reviewed by Riccardo Dalla-Favera and Philip N. Tsichlis) Small, noncoding RNAs are short untranslated RNA molecules, some these molecules, which we defined as single-stranded small of which have been associated with cancer development. Recently RNAs, 16–48 nt long, ending with a stretch of four Ts (4). When we showed that a class of small RNAs generated during the matu- tsRNAs accumulate in the nucleus, they can be exported, sug- ration process of tRNAs (tRNA-derived small RNAs, hereafter gesting that tsRNAs could regulate gene expression at different “tsRNAs”) is dysregulated in cancer. -
M2139: Molecular Analysis for Gliomas
Molecular Analysis for Gliomas Policy Number: AHS – M2139 – Molecular Analysis Prior Policy Name and Number, as applicable: for Gliomas • AHS – M2139 – Analysis of MGMT Promoter Methylation for Malignant Gliomas Initial Presentation Date: 06/16/2021 Revision Date: N/A I. Policy Description Glioma refers to tumors resulting from metaplastic transformation of glial tissue of the nervous system. Tumors have historically been classified by the retained histologic features of the three types of glial cells: astrocytes, oligodendrocytes, and ependymal cells. Tumors of each type can vary widely in aggressiveness, response to treatment, and prognosis (Louis, Schiff, & Batchelor, 2020). Molecular genetic features were added to histopathologic appearance in the current WHO classification to yield more biologically homogeneous and narrowly defined diagnostic entities for greater diagnostic accuracy, improved patient management, more accurate determinations of prognosis, and better treatment response (Louis et al., 2016). II. Related Policies Policy Number Policy Title AHS-M2109 Molecular Panel Testing of Cancers for Diagnosis, Prognosis, and Identification of Targeted Therapy III. Indications and/or Limitations of Coverage Application of coverage criteria is dependent upon an individual’s benefit coverage at the time of the request 1. MGMT promoter methylation testing IS MEDICALLY NECESSARY for prognosis of malignant gliomas. 2. IDH1 and IDH2 testing IS MEDICALLY NECESSARY for prognosis of malignant gliomas. M2139 Molecular Analysis for Gliomas Page 1 of 15 3. Testing for the co-deletion of 1p and 19q by either fluorescence in situ hybridization (FISH) or polymerase chain reaction (PCR) for the characterization of gliomas and/or to guide treatment decisions IS MEDICALLY NECESSARY. 4. ATRX mutation testing via EITHER immunohistochemistry OR gene sequencing IS MEDICALLY NECESSARY for the prognosis of malignant gliomas. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
Snf2h-Mediated Chromatin Organization and Histone H1 Dynamics Govern Cerebellar Morphogenesis and Neural Maturation
ARTICLE Received 12 Feb 2014 | Accepted 15 May 2014 | Published 20 Jun 2014 DOI: 10.1038/ncomms5181 OPEN Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation Matı´as Alvarez-Saavedra1,2, Yves De Repentigny1, Pamela S. Lagali1, Edupuganti V.S. Raghu Ram3, Keqin Yan1, Emile Hashem1,2, Danton Ivanochko1,4, Michael S. Huh1, Doo Yang4,5, Alan J. Mears6, Matthew A.M. Todd1,4, Chelsea P. Corcoran1, Erin A. Bassett4, Nicholas J.A. Tokarew4, Juraj Kokavec7, Romit Majumder8, Ilya Ioshikhes4,5, Valerie A. Wallace4,6, Rashmi Kothary1,2, Eran Meshorer3, Tomas Stopka7, Arthur I. Skoultchi8 & David J. Picketts1,2,4 Chromatin compaction mediates progenitor to post-mitotic cell transitions and modulates gene expression programs, yet the mechanisms are poorly defined. Snf2h and Snf2l are ATP-dependent chromatin remodelling proteins that assemble, reposition and space nucleosomes, and are robustly expressed in the brain. Here we show that mice conditionally inactivated for Snf2h in neural progenitors have reduced levels of histone H1 and H2A variants that compromise chromatin fluidity and transcriptional programs within the developing cerebellum. Disorganized chromatin limits Purkinje and granule neuron progenitor expansion, resulting in abnormal post-natal foliation, while deregulated transcriptional programs contribute to altered neural maturation, motor dysfunction and death. However, mice survive to young adulthood, in part from Snf2l compensation that restores Engrailed-1 expression. Similarly, Purkinje-specific Snf2h ablation affects chromatin ultrastructure and dendritic arborization, but alters cognitive skills rather than motor control. Our studies reveal that Snf2h controls chromatin organization and histone H1 dynamics for the establishment of gene expression programs underlying cerebellar morphogenesis and neural maturation.