DOCSLIB.ORG

Notchless Interacts with Multiple Signaling Pathways During Mouse Peri-Implantation Development Chiao-Ling Lo Purdue University

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Purdue University Purdue e-Pubs Open Access Dissertations Theses and Dissertations Fall 2013 Notchless Interacts with Multiple Signaling Pathways during Mouse Peri-Implantation Development Chiao-Ling Lo Purdue University Follow this and additional works at: https://docs.lib.purdue.edu/open_access_dissertations Part of the Animal Sciences Commons, and the Genetics Commons Recommended Citation Lo, Chiao-Ling, "Notchless Interacts with Multiple Signaling Pathways during Mouse Peri-Implantation Development" (2013). Open Access Dissertations. 105. https://docs.lib.purdue.edu/open_access_dissertations/105 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. Graduate School ETD Form 9 (Revised 12/07) PURDUE UNIVERSITY GRADUATE SCHOOL Thesis/Dissertation Acceptance This is to certify that the thesis/dissertation prepared By Chiao-Ling Lo Entitled Notchless Interacts with Multiple Signaling Pathways during Mouse Peri-Implantation Development Doctor of Philosophy For the degree of Is approved by the final examining committee: Amy C. Lossie Chair Ann L. Kirchmaier Shihuan Kuang Yuk Fai Leung To the best of my knowledge and as understood by the student in the Research Integrity and Copyright Disclaimer (Graduate School Form 20), this thesis/dissertation adheres to the provisions of Purdue University’s “Policy on Integrity in Research” and the use of copyrighted material. Approved by Major Professor(s): ____________________________________Amy C. Lossie ____________________________________ Approved by: Christine A. Hrycyna 11/20/2013 Head of the Graduate Program Date i NOTCHLESS INTERACTS WITH MULTIPLE SIGNALING PATHWAYS DURING MOUSE PERI-IMPLANTATION DEVELOPMENT A Dissertation Submitted to the Faculty of Purdue University by Chiao-Ling Lo In Partial Fulfillment of the Requirements for the Degree i of Doctor of Philosophy December 2013 Purdue University West Lafayette, Indiana ii ACKNOWLEDGEMENTS I would like to thank my major advisor Dr. Amy Lossie, for her mentoring and all the support, financially and emotionally, throughout the course of my PhD. I could not have completed my thesis without her. Thanks to my committee members, Dr. Ann Kirchmaier, Dr. Shihuan Kuang, and Dr. Yuk Fai Leung for their advice and critical review. I also want to thank Dr. William Muir for teaching me NGS data analysis, and Dr. Joseph Garner for his sophisticated statistical analysis on our projects. I appreciate the help from all my former and present labmates: Jon, Giovana, Katherine, Missy, Jeremy, Feichen, Xiao, Jennifer and Muyi. Moreover, I want to thank my parents, my brothers and all of my friends and colleagues in Taiwan and Purdue for their encouragement and care. They let me know that I am loved and I am not alone. Last but not least, I thank the mice that were sacrificed for this project; truly, without them, I could not have accomplished this research. ii iii TABLE OF CONTENTS Page LIST OF TABLES ................................................................................................. vi LIST OF FIGURES ............................................................................................... vii ABSTRACT ......................................................................................................... viii CHAPTER 1. INTRODUCTION ............................................................................. 1 1.1 Signaling During Peri-implantation Developmet………………………. ...... 1 1.2 NOTCH Signaling…………………………………………………………. ..... 5 1.3 Wnt Signaling…………………………………………………………….. ..... 10 1.4 Ribosomal Biogenesis……………………………………………………… . 11 1.5 Generation and Phenotype of l11Jus1 and l11Jus4……………………… 14 1.6 NOTCHLESS in the ribosomal biogenesis pathway……………………... 16 1.7 P53 Regulation……………………………………………………………….. 17 1.8 Objective……………………………………………………………………… 20 CHAPTER 2. IDENTIFICATION OF 129S6/SVEVTAC-SPECIFIC iii POLYMORPHISMS ON MOUSE CHROMOSOME 11 ....................................... 22 2.1 Introduction………………………..………………………..………………… 22 2.2 Methods………………………..………………………..…………………… . 25 2.3 Results…………………………………..…………………………………… . 28 2.4 Discussion………………………………………………………………… ..... 46 CHAPTER 3. ENU MUTAGENESIS REVEALS THAT NOTCHLESS HOMOLOG 1 (DROSOPHILA) AFFECTS CDKN1A AND SEVERAL MEMBERS OF THE WNT PATHWAY DURING MURINE PRE-IMPLANTATION DEVELOPMENT ... 50 3.1 Introduction………………………..………………………..………………… 50 3.2 Methods………………………..………………………..…………………… . 54 iv Page 3.2.1 Mouse Strains, Meiotic Mapping and Generation of Mutants ........... 54 3.2.2 Embryo Analysis ............................................................................... 55 3.2.3 Histology ........................................................................................... 56 3.2.4 Candidate Gene interrogation .......................................................... 56 3.2.5 Notch Pathway Expression of l11Jus1 mutants at E3.5 ................... 56 3.2.6 PCR Array Data Analysis for Gene Expression ............................... 60 3.2.7 Caspase 3 Detection ........................................................................ 60 3.2.8 Quantitative RT-PCR by Taqman ..................................................... 61 3.2.9 Statistical Methods ........................................................................... 62 3.3 Results………………………..………………………..……………………... 63 3.3.1 Phenotypic Analysis of l11Jus1 and l11Jus4 ................................... 63 3.3.2 Positional Cloning of l11Jus1 and l11Jus4 ....................................... 66 3.3.3 The Nle1 locus ................................................................................. 68 3.3.4 Expression Analysis of the Notch Pathway in Mutant Embryos ....... 70 3.3.5 Confirmation of Cdkn1a in Different Stages in Pre-Implantation ...... 73 3.3.6 Apoptosis Occurs at E4.5 in Nle1 Mutants ....................................... 74 3.3.7 qRT-PCR Analysis of Trp53 in Mutant Embryos .............................. 76 3.4 Discussion………………………..………………………..………………… . 77 CHAPTER 4. NLE1 MISSENSE MUTATIONS TIGGER TRP53 ACTIVATION iv AND DISRUPTION IN RIBOSOMAL BIOGENESIS DURING MURINE PRE- IMPLANTATION DEVELOPMENT ...................................................................... 81 4.1 Introduction………………………..………………………..………………… 81 4.2 Methods………………………..………………………..…………………… . 86 4.2.1 Immunofluorescence ........................................................................ 86 4.2.2 Quantitative RT-PCR ........................................................................ 87 4.2.3 Sample Preparation for rRNASeq .................................................... 88 4.2.4 Data analysis .................................................................................... 89 4.3 Results………………………..………………………..……………………... 91 4.3.1 TRP53 is Activated in Mutant Embryos ............................................ 91 v Page 4.3.2 Altered Gene Expression in Cell Cycle and Apoptosis Pathways .... 93 4.3.3 rRNA processing is disrupted in the Nle1 mutants ........................... 97 4.4 Discussion………………………..………………………..……………… .. 102 CHAPTER 5. DISCUSSION .............................................................................. 105 5.1 NLE1 and Its Potential Biological Function in Ribosomal Biogenesis .. 105 5.2 The rRNASeq study………………………..………………………………. 110 5.3 Mutations in NLE1 Affect Wnt Signaling…………………………………. 112 5.4 Altered Nucleolar Structure and p53 Activation in the Mutant………….114 5.5 Model for Signaling Regulation in Nle1 Mutants…………………………116 LIST OF REFERENCES ................................... ……….………. ………………. 119 VITA ……….………. ……………………………………….……….……………...141 v vi LIST OF TABLES Table ................................................................................................................ Page Table 1.1 Mutant lethality / phenotypes of the NOTCH signaling in mice ............. 9 Table 2.1 Primers used for this study .................................................................. 26 Table 2.2 Polymorphisms in the Nle1 locus ........................................................ 31 Table 2.3 Mettl16 polymorphisms ....................................................................... 34 Table 2.4 Psmd11 polymorphisms ...................................................................... 36 Table 2.5 Evi2a polymorphisms .......................................................................... 36 Table 2.6 Cct6b polymorphisms .......................................................................... 37 Table 2.7 Rffl polymorphisms………………………………………………………...39 Table 2.8 Ap2b1 polymorphisms……………………………..………………….…….41 Table 2.9 Summary of polymorphism analysis …………………………………….44 Table 3.1 Primers used for this study .................................................................. 59 Table 3.2 Time of death for Nle1 mutants ........................................................... 65 Table 3.3 X2 analysis of selected timed matings ................................................. 66 vi Table 3.4 Logistic multiple regression analysis of caspase 3 detection .............. 76 Table 4.1 Primers used for this study .................................................................. 87 Table 4.2 Logistic multiple regression analysis of active TRP53 detection ......... 93 Table 4.3 Average coverage of each rRNA subunits .......................................... 98 vii LIST OF FIGURES Figure .............................................................................................................
Recommended publications
  • Updates on the Role of Molecular Alterations and NOTCH Signalling in the Development of Neuroendocrine Neoplasms

    Updates on the Role of Molecular Alterations and NOTCH Signalling in the Development of Neuroendocrine Neoplasms

    Journal of Clinical Medicine Review Updates on the Role of Molecular Alterations and NOTCH Signalling in the Development of Neuroendocrine Neoplasms 1,2, 1, 3, 4 Claudia von Arx y , Monica Capozzi y, Elena López-Jiménez y, Alessandro Ottaiano , Fabiana Tatangelo 5 , Annabella Di Mauro 5, Guglielmo Nasti 4, Maria Lina Tornesello 6,* and Salvatore Tafuto 1,* On behalf of ENETs (European NeuroEndocrine Tumor Society) Center of Excellence of Naples, Italy 1 Department of Abdominal Oncology, Istituto Nazionale Tumori, IRCCS Fondazione “G. Pascale”, 80131 Naples, Italy 2 Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK 3 Cancer Cell Metabolism Group. Centre for Haematology, Immunology and Inflammation Department, Imperial College London, London W12 0HS, UK 4 SSD Innovative Therapies for Abdominal Metastases—Department of Abdominal Oncology, Istituto Nazionale Tumori, IRCCS—Fondazione “G. Pascale”, 80131 Naples, Italy 5 Department of Pathology, Istituto Nazionale Tumori, IRCCS—Fondazione “G. Pascale”, 80131 Naples, Italy 6 Unit of Molecular Biology and Viral Oncology, Department of Research, Istituto Nazionale Tumori IRCCS Fondazione Pascale, 80131 Naples, Italy * Correspondence: [email protected] (M.L.T.); [email protected] (S.T.) These authors contributed to this paper equally. y Received: 10 July 2019; Accepted: 20 August 2019; Published: 22 August 2019 Abstract: Neuroendocrine neoplasms (NENs) comprise a heterogeneous group of rare malignancies, mainly originating from hormone-secreting cells, which are widespread in human tissues. The identification of mutations in ATRX/DAXX genes in sporadic NENs, as well as the high burden of mutations scattered throughout the multiple endocrine neoplasia type 1 (MEN-1) gene in both sporadic and inherited syndromes, provided new insights into the molecular biology of tumour development.
  • In Silico Analysis of Regulatory Elements of the Vitamin D Receptor

    In Silico Analysis of Regulatory Elements of the Vitamin D Receptor

    Open Access Baghdad Science Journal P-ISSN: 2078-8665 2020, 17(2):463-470 E-ISSN: 2411-7986 DOI: http://dx.doi.org/10.21123/bsj.2020.17.2.0463 In Silico Analysis of Regulatory Elements of the Vitamin D Receptor Shirin Farivar 1 Roya Amirinejad 2 Bahar Naghavi gargari 3 Seyedeh Batool Hassani 4 Zeinab Shirvani-Farsani 1* Received 26/2/2019, Accepted 5/1/2020, Published 1/6/2020 This work is licensed under a Creative Commons Attribution 4.0 International License. Abstract Vitamin D receptor (VDR) is a nuclear transcription factor that controls gene expression. Its impaired expression was found to be related to different diseases. VDR also acts as a regulator of different pathways including differentiation, inflammation, calcium and phosphate absorption, etc. but there is no sufficient knowledge about the regulation of the gene itself. Therefore, a better understanding of the genetic and epigenetic factors regulating the VDR may facilitate the improvement of strategies for the prevention and treatment of diseases associated with dysregulation of VDR. In the present investigation, a set of databases and methods were used to identify putative functional elements in the VDR locus. Histone modifications, CpG Islands, epigenetic marks at VDR locus were indicated. In addition, repeated sequences, enhancers, insulators, transcription factor binding sites and targets of the VDR gene, as well as protein- protein interactions with bioinformatics tools, were reported. Some of these genetic elements had overlapped with CpG Islands. These results revealed important new insight into the molecular mechanisms of the VDR gene regulation in human cells and tissues. Key words: CpG Islands, Epigenetics, In silico analysis, Regulation elements, VDR Introduction: Vitamin D is a steroid hormone that multiple sclerosis (10), Rheumatoid Arthritis and balances calcium and phosphate levels and is Systemic Lupus Erythematosus (11), cardiovascular crucial for bone structure.
  • Analysis of Gene Expression Data for Gene Ontology

    Analysis of Gene Expression Data for Gene Ontology

    ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins.
  • UNIVERSITY of CALIFORNIA, SAN DIEGO Functional Analysis of Sall4

    UNIVERSITY of CALIFORNIA, SAN DIEGO Functional Analysis of Sall4

    UNIVERSITY OF CALIFORNIA, SAN DIEGO Functional analysis of Sall4 in modulating embryonic stem cell fate A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Molecular Pathology by Pei Jen A. Lee Committee in charge: Professor Steven Briggs, Chair Professor Geoff Rosenfeld, Co-Chair Professor Alexander Hoffmann Professor Randall Johnson Professor Mark Mercola 2009 Copyright Pei Jen A. Lee, 2009 All rights reserved. The dissertation of Pei Jen A. Lee is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ Co-Chair ______________________________________________________________ Chair University of California, San Diego 2009 iii Dedicated to my parents, my brother ,and my husband for their love and support iv Table of Contents Signature Page……………………………………………………………………….…iii Dedication…...…………………………………………………………………………..iv Table of Contents……………………………………………………………………….v List of Figures…………………………………………………………………………...vi List of Tables………………………………………………….………………………...ix Curriculum vitae…………………………………………………………………………x Acknowledgement………………………………………………….……….……..…...xi Abstract………………………………………………………………..…………….....xiii Chapter 1 Introduction ..…………………………………………………………………………….1 Chapter 2 Materials and Methods……………………………………………………………..…12
  • Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

    Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

    Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle Slim Ben-Jemaa, Gabriele Senczuk, Elena Ciani, Roberta Ciampolini, Gennaro Catillo, Mekki Boussaha, Fabio Pilla, Baldassare Portolano, Salvatore Mastrangelo To cite this version: Slim Ben-Jemaa, Gabriele Senczuk, Elena Ciani, Roberta Ciampolini, Gennaro Catillo, et al.. Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle. Frontiers in Genetics, Frontiers, 2021, 10.3389/fgene.2021.675569. hal-03210766 HAL Id: hal-03210766 https://hal.inrae.fr/hal-03210766 Submitted on 28 Apr 2021 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. Distributed under a Creative Commons Attribution| 4.0 International License ORIGINAL RESEARCH published: 28 April 2021 doi: 10.3389/fgene.2021.675569 Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle Slim Ben-Jemaa 1, Gabriele Senczuk 2, Elena Ciani 3, Roberta
  • Open Dogan Phdthesis Final.Pdf

    Open Dogan Phdthesis Final.Pdf

    The Pennsylvania State University The Graduate School Eberly College of Science ELUCIDATING BIOLOGICAL FUNCTION OF GENOMIC DNA WITH ROBUST SIGNALS OF BIOCHEMICAL ACTIVITY: INTEGRATIVE GENOME-WIDE STUDIES OF ENHANCERS A Dissertation in Biochemistry, Microbiology and Molecular Biology by Nergiz Dogan © 2014 Nergiz Dogan Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2014 ii The dissertation of Nergiz Dogan was reviewed and approved* by the following: Ross C. Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee David S. Gilmour Professor of Molecular and Cell Biology Anton Nekrutenko Professor of Biochemistry and Molecular Biology Robert F. Paulson Professor of Veterinary and Biomedical Sciences Philip Reno Assistant Professor of Antropology Scott B. Selleck Professor and Head of the Department of Biochemistry and Molecular Biology *Signatures are on file in the Graduate School iii ABSTRACT Genome-wide measurements of epigenetic features such as histone modifications, occupancy by transcription factors and coactivators provide the opportunity to understand more globally how genes are regulated. While much effort is being put into integrating the marks from various combinations of features, the contribution of each feature to accuracy of enhancer prediction is not known. We began with predictions of 4,915 candidate erythroid enhancers based on genomic occupancy by TAL1, a key hematopoietic transcription factor that is strongly associated with gene induction in erythroid cells. Seventy of these DNA segments occupied by TAL1 (TAL1 OSs) were tested by transient transfections of cultured hematopoietic cells, and 56% of these were active as enhancers. Sixty-six TAL1 OSs were evaluated in transgenic mouse embryos, and 65% of these were active enhancers in various tissues.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
  • GIGANTUS1 (GTS1), a Member of Transducin/WD40 Protein

    GIGANTUS1 (GTS1), a Member of Transducin/WD40 Protein

    Gachomo et al. BMC Plant Biology 2014, 14:37 http://www.biomedcentral.com/1471-2229/14/37 RESEARCH ARTICLE Open Access GIGANTUS1 (GTS1), a member of Transducin/WD40 protein superfamily, controls seed germination, growth and biomass accumulation through ribosome-biogenesis protein interactions in Arabidopsis thaliana Emma W Gachomo1,2†, Jose C Jimenez-Lopez3,4†, Lyla Jno Baptiste1 and Simeon O Kotchoni1,2* Abstract Background: WD40 domains have been found in a plethora of eukaryotic proteins, acting as scaffolding molecules assisting proper activity of other proteins, and are involved in multi-cellular processes. They comprise several stretches of 44-60 amino acid residues often terminating with a WD di-peptide. They act as a site of protein-protein interactions or multi-interacting platforms, driving the assembly of protein complexes or as mediators of transient interplay among other proteins. In Arabidopsis, members of WD40 protein superfamily are known as key regulators of plant-specific events, biologically playing important roles in development and also during stress signaling. Results: Using reverse genetic and protein modeling approaches, we characterize GIGANTUS1 (GTS1), a new member of WD40 repeat protein in Arabidopsis thaliana and provide evidence of its role in controlling plant growth development. GTS1 is highly expressed during embryo development and negatively regulates seed germination, biomass yield and growth improvement in plants. Structural modeling analysis suggests that GTS1 folds into a β-propeller with seven pseudo symmetrically arranged blades around a central axis. Molecular docking analysis shows that GTS1 physically interacts with two ribosomal protein partners, a component of ribosome Nop16, and a ribosome-biogenesis factor L19e through β-propeller blade 4 to regulate cell growth development.
  • Sequence Composition and Evolution of Mammalian B Chromosomes

    Sequence Composition and Evolution of Mammalian B Chromosomes

    G C A T T A C G G C A T genes Review Sequence Composition and Evolution of Mammalian B Chromosomes Nikolay B. Rubtsov 1,2,* and Yury M. Borisov 3 1 The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev Ave. 10, Novosibirsk 630090, Russia 2 Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia 3 Severtzov Institute of Ecology and Evolution, Russia Academy of Sciences, Leninsky Pr. 33, Moscow 119071, Russia; [email protected] * Correspondence: [email protected]; Tel.: +7-913-941-5682 Received: 28 August 2018; Accepted: 1 October 2018; Published: 10 October 2018 Abstract: B chromosomes (Bs) revealed more than a hundred years ago remain to be some of the most mysterious elements of the eukaryotic genome. Their origin and evolution, DNA composition, transcriptional activity, impact on adaptiveness, behavior in meiosis, and transfer to the next generation require intensive investigations using modern methods. Over the past years, new experimental techniques have been applied and helped us gain a deeper insight into the nature of Bs. Here, we consider mammalian Bs, taking into account data on their DNA sequencing, transcriptional activity, positions in nuclei of somatic and meiotic cells, and impact on genome functioning. Comparative cytogenetics of Bs suggests the existence of different mechanisms of their formation and evolution. Due to the long and complicated evolvement of Bs, the similarity of their morphology could be explained by the similar mechanisms involved in their development while the difference between Bs even of the same origin could appear due to their positioning at different stages of their evolution.
  • Insights Into Regulation of Human RAD51 Nucleoprotein Filament Activity During

    Insights Into Regulation of Human RAD51 Nucleoprotein Filament Activity During

    Insights into Regulation of Human RAD51 Nucleoprotein Filament Activity During Homologous Recombination Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Ravindra Bandara Amunugama, B.S. Biophysics Graduate Program The Ohio State University 2011 Dissertation Committee: Richard Fishel PhD, Advisor Jeffrey Parvin MD PhD Charles Bell PhD Michael Poirier PhD Copyright by Ravindra Bandara Amunugama 2011 ABSTRACT Homologous recombination (HR) is a mechanistically conserved pathway that occurs during meiosis and following the formation of DNA double strand breaks (DSBs) induced by exogenous stresses such as ionization radiation. HR is also involved in restoring replication when replication forks have stalled or collapsed. Defective recombination machinery leads to chromosomal instability and predisposition to tumorigenesis. However, unregulated HR repair system also leads to similar outcomes. Fortunately, eukaryotes have evolved elegant HR repair machinery with multiple mediators and regulatory inputs that largely ensures an appropriate outcome. A fundamental step in HR is the homology search and strand exchange catalyzed by the RAD51 recombinase. This process requires the formation of a nucleoprotein filament (NPF) on single-strand DNA (ssDNA). In Chapter 2 of this dissertation I describe work on identification of two residues of human RAD51 (HsRAD51) subunit interface, F129 in the Walker A box and H294 of the L2 ssDNA binding region that are essential residues for salt-induced recombinase activity. Mutation of F129 or H294 leads to loss or reduced DNA induced ATPase activity and formation of a non-functional NPF that eliminates recombinase activity. DNA binding studies indicate that these residues may be essential for sensing the ATP nucleotide for a functional NPF formation.
  • Noelia Díaz Blanco

    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.
  • Large-Scale Functional Prediction of Individual M6a RNA Methylation Sites from an RNA Co-Methylation Network

    Large-Scale Functional Prediction of Individual M6a RNA Methylation Sites from an RNA Co-Methylation Network

    Wu et al. BMC Bioinformatics (2019) 20:223 https://doi.org/10.1186/s12859-019-2840-3 RESEARCHARTICLE Open Access m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co- methylation network Xiangyu Wu1,2, Zhen Wei1,2, Kunqi Chen1,2, Qing Zhang1,4, Jionglong Su5, Hui Liu6, Lin Zhang6* and Jia Meng1,3* Abstract Background: Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methylation, especially N6-methyladenosine, has become one of the most researched topics in epigenetics. Results: To date, the study of epitranscriptome layer gene regulation is mostly focused on the function of mediator proteins of RNA methylation, i.e., the readers, writers and erasers. There is limited investigation of the functional relevance of individual m6A RNA methylation site. To address this, we annotated human m6A sites in large-scale based on the guilt-by-association principle from an RNA co-methylation network. It is constructed based on public human MeRIP-Seq datasets profiling the m6A epitranscriptome under 32 independent experimental conditions. By systematically examining the network characteristics obtained from the RNA methylation profiles, a total of 339,158 putative gene ontology functions associated with 1446 human m6A sites were identified. These are biological functions that may be regulated at epitranscriptome layer via reversible m6A RNA methylation. The results were further validated on a soft benchmark by comparing to a random predictor. Conclusions: An online web server m6Acomet was constructed to support direct query for the predicted biological functions of m6A sites as well as the sites exhibiting co-methylated patterns at the epitranscriptome layer.