The Prognosis Analysis of RFWD2 Inhibiting the Expression of ETV1 in Colorectal Cancer
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A Systems-Genetics Analyses of Complex Phenotypes
A systems-genetics analyses of complex phenotypes A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2015 David Ashbrook Table of contents Table of contents Table of contents ............................................................................................... 1 Tables and figures ........................................................................................... 10 General abstract ............................................................................................... 14 Declaration ....................................................................................................... 15 Copyright statement ........................................................................................ 15 Acknowledgements.......................................................................................... 16 Chapter 1: General introduction ...................................................................... 17 1.1 Overview................................................................................................... 18 1.2 Linkage, association and gene annotations .............................................. 20 1.3 ‘Big data’ and ‘omics’ ................................................................................ 22 1.4 Systems-genetics ..................................................................................... 24 1.5 Recombinant inbred (RI) lines and the BXD .............................................. 25 Figure 1.1: -
NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer
Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-7-2018 Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer Jairo Ramos [email protected] Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Clinical Epidemiology Commons Recommended Citation Ramos, Jairo, "Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer" (2018). FIU Electronic Theses and Dissertations. 3872. https://digitalcommons.fiu.edu/etd/3872 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida DECIPHER MECHANISMS BY WHICH NUCLEAR RESPIRATORY FACTOR ONE (NRF1) COORDINATES CHANGES IN THE TRANSCRIPTIONAL AND CHROMATIN LANDSCAPE AFFECTING DEVELOPMENT AND PROGRESSION OF INVASIVE BREAST CANCER A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in PUBLIC HEALTH by Jairo Ramos 2018 To: Dean Tomás R. Guilarte Robert Stempel College of Public Health and Social Work This dissertation, Written by Jairo Ramos, and entitled Decipher Mechanisms by Which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer, having been approved in respect to style and intellectual content, is referred to you for judgment. -
A Study of Alterations in DNA Epigenetic Modifications (5Mc and 5Hmc) and Gene Expression Influenced by Simulated Microgravity I
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital Repository @ Iowa State University Genome Informatics Facility Publications Genome Informatics Facility 1-28-2016 A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells Basudev Chowdhury Purdue University Arun S. Seetharam Iowa State University, [email protected] Zhiping Wang Indiana University School of Medicine Yunlong Liu Indiana University School of Medicine Amy C. Lossie Purdue University See next page for additional authors Follow this and additional works at: https://lib.dr.iastate.edu/genomeinformatics_pubs Part of the Bioinformatics Commons, Genetics Commons, and the Genomics Commons Recommended Citation Chowdhury, Basudev; Seetharam, Arun S.; Wang, Zhiping; Liu, Yunlong; Lossie, Amy C.; Thimmapuram, Jyothi; and Irudayaraj, Joseph, "A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells" (2016). Genome Informatics Facility Publications. 4. https://lib.dr.iastate.edu/genomeinformatics_pubs/4 This Article is brought to you for free and open access by the Genome Informatics Facility at Iowa State University Digital Repository. It has been accepted for inclusion in Genome Informatics Facility Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells Abstract Cells alter their gene expression in response to exposure to various environmental changes. Epigenetic mechanisms such as DNA methylation are believed to regulate the alterations in gene expression patterns. -
DMC1 Protein-Protein Interactions Are Directly Linked to Meiosis Homeostasis and Fertility
Open Access Austin Cell Biology Research Article DMC1 Protein-Protein Interactions are Directly Linked to Meiosis Homeostasis and Fertility Silva KSF* Biological Sciences Institute, Federal University of Goiás, Abstract Brazil Infertility is a disorder of the reproductive system. Couples are infertile *Corresponding author: Kleber Santiago Freitas e when they are unable to conceive children by a functional pregnancy after one Silva, Biological Sciences Institute, Federal University of year of regular and unprotected sexual intercourse. About 15% of couples in Goiás, Brazil the reproductive age around the world cannot conceive children and around 30% of all cases of infertility are idiopathic, with unknown underlying causes. Received: September 10, 2018; Accepted: October 23, Protein-protein interactions have not yet been extensively explored regarding 2018; Published: October 30, 2018 those underlying causes of infertility and one can assume that PPIs could be directly related to some of the idiopathic cases of infertility. Meiosis is a cell division process governed by a multitude of proteins and multiprotein complexes that regulate DNA double strand breaks, homologous recombination, synapsis [1], mismatch repair, chromosome maintenance and synaptonemal complex. PPI studies have been used in a variety of ways in other to shed some light on unknown molecular biologic processes that take place in the microenvironment of cells and may lead to diseases. PPI approaches have been used to identify the dynamic of biological systems and diseases onset, progression, diagnosis and treatment. Here, we present bioinformatics and in silico analysis of DMC1 and interacting protein partners that play important roles in meiosis homeostasis and consequently in human fertility. -
Agricultural University of Athens
ΓΕΩΠΟΝΙΚΟ ΠΑΝΕΠΙΣΤΗΜΙΟ ΑΘΗΝΩΝ ΣΧΟΛΗ ΕΠΙΣΤΗΜΩΝ ΤΩΝ ΖΩΩΝ ΤΜΗΜΑ ΕΠΙΣΤΗΜΗΣ ΖΩΙΚΗΣ ΠΑΡΑΓΩΓΗΣ ΕΡΓΑΣΤΗΡΙΟ ΓΕΝΙΚΗΣ ΚΑΙ ΕΙΔΙΚΗΣ ΖΩΟΤΕΧΝΙΑΣ ΔΙΔΑΚΤΟΡΙΚΗ ΔΙΑΤΡΙΒΗ Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων ΕΙΡΗΝΗ Κ. ΤΑΡΣΑΝΗ ΕΠΙΒΛΕΠΩΝ ΚΑΘΗΓΗΤΗΣ: ΑΝΤΩΝΙΟΣ ΚΟΜΙΝΑΚΗΣ ΑΘΗΝΑ 2020 ΔΙΔΑΚΤΟΡΙΚΗ ΔΙΑΤΡΙΒΗ Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων Genome-wide association analysis and gene network analysis for (re)production traits in commercial broilers ΕΙΡΗΝΗ Κ. ΤΑΡΣΑΝΗ ΕΠΙΒΛΕΠΩΝ ΚΑΘΗΓΗΤΗΣ: ΑΝΤΩΝΙΟΣ ΚΟΜΙΝΑΚΗΣ Τριμελής Επιτροπή: Aντώνιος Κομινάκης (Αν. Καθ. ΓΠΑ) Ανδρέας Κράνης (Eρευν. B, Παν. Εδιμβούργου) Αριάδνη Χάγερ (Επ. Καθ. ΓΠΑ) Επταμελής εξεταστική επιτροπή: Aντώνιος Κομινάκης (Αν. Καθ. ΓΠΑ) Ανδρέας Κράνης (Eρευν. B, Παν. Εδιμβούργου) Αριάδνη Χάγερ (Επ. Καθ. ΓΠΑ) Πηνελόπη Μπεμπέλη (Καθ. ΓΠΑ) Δημήτριος Βλαχάκης (Επ. Καθ. ΓΠΑ) Ευάγγελος Ζωίδης (Επ.Καθ. ΓΠΑ) Γεώργιος Θεοδώρου (Επ.Καθ. ΓΠΑ) 2 Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων Περίληψη Σκοπός της παρούσας διδακτορικής διατριβής ήταν ο εντοπισμός γενετικών δεικτών και υποψηφίων γονιδίων που εμπλέκονται στο γενετικό έλεγχο δύο τυπικών πολυγονιδιακών ιδιοτήτων σε κρεοπαραγωγικά ορνίθια. Μία ιδιότητα σχετίζεται με την ανάπτυξη (σωματικό βάρος στις 35 ημέρες, ΣΒ) και η άλλη με την αναπαραγωγική -
Promoterless Transposon Mutagenesis Drives Solid Cancers Via Tumor Suppressor Inactivation
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.17.254565; this version posted August 17, 2020. 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. 1 Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation 2 Aziz Aiderus1, Ana M. Contreras-Sandoval1, Amanda L. Meshey1, Justin Y. Newberg1,2, Jerrold M. Ward3, 3 Deborah Swing4, Neal G. Copeland2,3,4, Nancy A. Jenkins2,3,4, Karen M. Mann1,2,3,4,5,6,7, and Michael B. 4 Mann1,2,3,4,6,7,8,9 5 1Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA 6 2Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA 7 3Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 8 Singapore, Republic of Singapore 9 4Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, 10 Maryland, USA 11 5Departments of Gastrointestinal Oncology & Malignant Hematology, Moffitt Cancer Center & Research 12 Institute, Tampa, FL, USA 13 6Cancer Biology and Evolution Program, Moffitt Cancer Center & Research Institute, Tampa, FL, USA 14 7Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, 15 USA. 16 8Donald A. Adam Melanoma and Skin Cancer Research Center of Excellence, Moffitt Cancer Center, Tampa, 17 FL, USA 18 9Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA 19 These authors contributed equally: Aziz Aiderus, Ana M. -
Enrichment of in Vivo Transcription Data from Dietary Intervention
Hulst et al. Genes & Nutrition (2017) 12:11 DOI 10.1186/s12263-017-0559-1 RESEARCH Open Access Enrichment of in vivo transcription data from dietary intervention studies with in vitro data provides improved insight into gene regulation mechanisms in the intestinal mucosa Marcel Hulst1,3* , Alfons Jansman2, Ilonka Wijers1, Arjan Hoekman1, Stéphanie Vastenhouw3, Marinus van Krimpen2, Mari Smits1,3 and Dirkjan Schokker1 Abstract Background: Gene expression profiles of intestinal mucosa of chickens and pigs fed over long-term periods (days/ weeks) with a diet rich in rye and a diet supplemented with zinc, respectively, or of chickens after a one-day amoxicillin treatment of chickens, were recorded recently. Such dietary interventions are frequently used to modulate animal performance or therapeutically for monogastric livestock. In this study, changes in gene expression induced by these three interventions in cultured “Intestinal Porcine Epithelial Cells” (IPEC-J2) recorded after a short-term period of 2 and 6 hours, were compared to the in vivo gene expression profiles in order to evaluate the capability of this in vitro bioassay in predicting in vivo responses. Methods: Lists of response genes were analysed with bioinformatics programs to identify common biological pathways induced in vivo as well as in vitro. Furthermore, overlapping genes and pathways were evaluated for possible involvement in the biological processes induced in vivo by datamining and consulting literature. Results: For all three interventions, only a limited number of identical genes and a few common biological processes/ pathways were found to be affected by the respective interventions. However, several enterocyte-specific regulatory and secreted effector proteins that responded in vitro could be related to processes regulated in vivo, i.e. -
Analyzing the Mirna-Gene Networks to Mine the Important Mirnas Under Skin of Human and Mouse
Hindawi Publishing Corporation BioMed Research International Volume 2016, Article ID 5469371, 9 pages http://dx.doi.org/10.1155/2016/5469371 Research Article Analyzing the miRNA-Gene Networks to Mine the Important miRNAs under Skin of Human and Mouse Jianghong Wu,1,2,3,4,5 Husile Gong,1,2 Yongsheng Bai,5,6 and Wenguang Zhang1 1 College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China 2Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China 3Inner Mongolia Prataculture Research Center, Chinese Academy of Science, Hohhot 010031, China 4State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 5Department of Biology, Indiana State University, Terre Haute, IN 47809, USA 6The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN 47809, USA Correspondence should be addressed to Yongsheng Bai; [email protected] and Wenguang Zhang; [email protected] Received 11 April 2016; Revised 15 July 2016; Accepted 27 July 2016 Academic Editor: Nicola Cirillo Copyright © 2016 Jianghong Wu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Genetic networks provide new mechanistic insights into the diversity of species morphology. In this study, we have integrated the MGI, GEO, and miRNA database to analyze the genetic regulatory networks under morphology difference of integument of humans and mice. We found that the gene expression network in the skin is highly divergent between human and mouse. -
Epigenomic Strategies at the Interface of Genetic and Environmental Risk Factors for Autism
Journal of Human Genetics (2013) 58, 396–401 & 2013 The Japan Society of Human Genetics All rights reserved 1434-5161/13 www.nature.com/jhg REVIEW Epigenomic strategies at the interface of genetic and environmental risk factors for autism Janine M LaSalle Autism spectrum disorders (ASD) have been increasing in prevalence over the last two decades, primarily because of increased awareness and diagnosis. However, autism is clearly a complex human genetic disorder that involves interactions between genes and environment. Epigenetic mechanisms, such as DNA methylation, act at the interface of genetic and environmental risk and protective factors. Advancements in genome-wide sequencing has broadened the view of the human methylome and revealed the organization of the human genome into large-scale methylation domains that footprint over neurologically important genes involved in embryonic development. Future integrative epigenomic analyses of genetic risk factors with environmental exposures and methylome analyses are expected to be important for understanding the complex etiology of ASD. Journal of Human Genetics (2013) 58, 396–401; doi:10.1038/jhg.2013.49; published online 16 May 2013 Keywords: autism spectrum disorders; DNA methylation; epidemiology; epigenetics; genetics; genomics INTRODUCTION However, in more recent twin studies, the estimates of dizygotic Autism spectrum disorder (ASD) is collectively used to refer to the twin concordance have been increasing and monozygotic twin heterogeneous collection of neurodevelopmental disorders -
A High Density of Human Communication-Associated
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Publication Server of Greifswald University Original Article Cytogenet Genome Res 2012;136:97–106 Accepted: November 7, 2011 DOI: 10.1159/000335465 by M. Schmid Published online: January 19, 2012 A High Density of Human Communication- Associated Genes in Chromosome 7q31-q36: Differential Expression in Human and Non-Human Primate Cortices a b c f f d E. Schneider L.R. Jensen R. Farcas I. Kondova R.E. Bontrop B. Navarro e b a E. Fuchs A.W. Kuss T. Haaf a b Institute of Human Genetics, Julius Maximilians University, Würzburg , Interfaculty Institute for Genetics and c Functional Genomics, Ernst Moritz Arndt University, Greifswald , Institute for Cardiovascular Regeneration, d Goethe University, Frankfurt/Main , Institute of Legal Medicine, University Medical Center, Mainz , and e f German Primate Center, Göttingen , Germany; Biomedical Primate Research Center, Rijswijk , The Netherlands Key Words chromosomes X and 7, in particular chromosome 7q31-q36. -Baboon ؒ Chimpanzee ؒ Chromosome 7q31-q36 ؒ Compared to the rest of the genome, we found a high num Communication abilities ؒ Cortex ؒ Gene expression ؒ ber of COAG to be differentially expressed in the cortices of ,Language evolution ؒ Marmoset ؒ T cell receptor beta locus humans and non-human primates (chimpanzee, baboon and/or marmoset). The role of X-linked genes for the devel- opment of human-specific cognitive abilities is well known. Abstract We now propose that chromosome 7q31-q36 also repre- The human brain is distinguished by its remarkable size, high sents a hot spot for the evolution of human-specific commu- energy consumption, and cognitive abilities compared to all nication abilities. -
Constitutive Photomorphogensis Protein1 (COP1) Mediated P53 Pathway and Its Oncogenic Role
Biomedical Research and Therapy 2014, 1(5): 142-151 ISSN 2198-4093 www.bmrat.org REVIEW Constitutive Photomorphogensis Protein1 (COP1) mediated p53 pathway and its oncogenic role Md. Golam Rabbani1, Sk. Amir Hossain1,2,*, Khandker Khaldun Islam1 and Sarder Nasir Uddin1 1Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh. 2Department of Biological Sciences, King Abdulaziz University, Saudi Arabia. *Corresponding author: [email protected] Received: 24 November 2014 / Accepted: 02 December 2014 / Published online: 09 December 2014 © The Author(s) 2014. This article is published with open access by BioMedPress (BMP), Laboratory of Stem Cell Research and Application. Abstract– We have reviewed the COP1 mediated tumor suppressor protein p53 pathway and its oncogenic role. COP1 is a negative regulator of p53 and acts as a pivotal controller of p53-Akt death-live switch (Protein kinase B). In presence of p53, COP1 is overexpressed in breast, ovarian, gastric cancers, even without MDM2 (Mouse double minute-2) amplification. Following DNA damage, COP1 is phosphorylated instantly by ATM (Ataxia telangiectasia mutated) and degraded by 14-3-3σ following nuclear export and enhancing ubiquitination. In ATM lacking cell, oth- er kinases, i.e. ATR (ataxia telangiectasia and Rad3-related protein), Jun kinases and DNA-PK (DNA-dependent pro- tein kinase) cause COP1 & CSN3 (COP9 signalosome complex subunit-3) phosphorylation and initiate COP1’s down regulation. Although, it has been previously found that co-knockout of MDM2 and COP1 enhance p53’s half-life by eight fold, the reason is still unknown. Additionally, while interacting with p53, COP1 upregulate MDM2’s E3 ubiq- uitin ligase, Akt, CSN6 (COP9 signalosome 6) activity and inhibit 14-3-3σ’s negative regulation on MDM2 and COP1 itself. -
Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens
biology Article Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens Alexandra S. Abdelmanova 1, Arsen V. Dotsev 1 , Michael N. Romanov 2,3,* , Olga I. Stanishevskaya 4, Elena A. Gladyr 1 , Andrey N. Rodionov 1, Anastasia N. Vetokh 1 , Natalia A. Volkova 1 , Elena S. Fedorova 4, Igor V. Gusev 1, Darren K. Griffin 2 , Gottfried Brem 5 and Natalia A. Zinovieva 1,* 1 L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; [email protected] (A.S.A.); [email protected] (A.V.D.); [email protected] (E.A.G.); [email protected] (A.N.R.); [email protected] (A.N.V.); [email protected] (N.A.V.); [email protected] (I.V.G.) 2 School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; D.K.Griffi[email protected] 3 K.I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 23 Akademika Skryabina St., 109472 Moscow, Russia 4 Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; [email protected] (O.I.S.); [email protected] (E.S.F.) 5 Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria; [email protected] * Correspondence: [email protected] (M.N.R.); [email protected] (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.) Citation: Abdelmanova, A.S.; Dotsev, A.V.; Romanov, M.N.; Stanishevskaya, Simple Summary: The search for genomic regions of putative selective signaling is instrumental in O.I.; Gladyr, E.A.; Rodionov, A.N.; obtaining information about selection history in various species and populations.