DOCSLIB.ORG

Defining the Regulation and Function of SAFB1 and SAFB2 in Human Breast Cancer Cells

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Defining the Regulation and Function of SAFB1 and SAFB2 in Human Breast Cancer Cells Defining the regulation and function of SAFB1 and SAFB2 in human breast cancer cells Elaine Hong Institute of Cellular Medicine Newcastle University A thesis submitted for the degree of Doctor of Philosophy July 2013 Abstract Scaffold attachment factor B1 (SAFB1) and SAFB2 are oestrogen receptor (ER) corepressors that bind and modulate ER activity through chromatin remodelling or interaction with the basal transcription machinery. However, little is known about the fundamental characteristics and function of SAFB1 and SAFB2 proteins in breast cancer. In this study, an investigation of the characteristics and function(s) of SAFB1 and SAFB2 was undertaken; their expression profile was first assessed in ER-positive (MCF-7) and ER-negative (MDA-MB-231) breast cancer cell lines. Results show that SAFB1 and SAFB2 are themselves regulated by an active metabolite of oestrogen, 17β-oestradiol, in both ER positive and ER negative breast cancer cells. Using a combined approach of RNA interference and gene expression profile studies, 12 novel targets closely linked to tumour progression were identified for SAFB1 and SAFB2. Expression levels of the following genes, CDKN2A, CLU, ESR1, IGFBP2, IL2RA, ITGB4, KIT, KLK5, MT3, NGFR and SPRR1B increased while IL-6 expression and secretion decreased when cells were depleted of SAFB proteins. This observation supports their primary role as transcriptional repressors with SAFB2 playing a prominent role in transcriptional regulation in MDA-MB-231 cells. This study has also established a novel link between SAFB proteins and ITGB4 and IL-6 expression. Both SAFB proteins have an internal RNA-recognition motif but little is known about the RNA-binding properties of SAFB1 or SAFB2. To investigate this, the concluding part of the project utilised crosslinking and immunoprecipitation (CLIP) coupled with high-throughput sequencing. This experimental approach enabled a transcriptome-wide mapping of SAFB1 protein-RNA interactions in breast cancer cells. SAFB1 crosslink sites are significantly enriched in ncRNAs, particularly within snRNAs. A putative RNA-binding motif for SAFB1 that contains adenine-rich sequences, highly similar to the RNA-binding motifs for SR proteins was also identified. In summary, this study has defined the characteristics of SAFB1 and SAFB2 in both ER positive and ER negative breast cancer cell lines. It has also identified transcriptional targets and the RNA-binding ability of SAFB1 and SAFB2 in human breast cancer cells. i Acknowledgements I would like to extend my thanks to my supervisor, Dr Alison Tyson-Capper for her constant support, patience, enthusiasm and motivation throughout my research. Also to my second supervisor, Prof David Elliott for his help and guidance especially in the CLIP work. I have benefited immensely from the strengths of this supervisory team and am truly grateful for the both of you. I would also like to thank my PhD progress assessors, Prof Simi Ali and Prof Zofia Chrzanowska-Lightowlers for helping me progress from an average scientist to a critical thinker. The annual progress assessments have continuously challenged me to question my work, thus sharpening my critical thinking skills and giving me a clear objective to every experiment attempted. My thanks also go to my fellow labmates: Dr David Cork, Dr Hannah Gautrey, Dr Rachel Eyre, Helen Lawrence, Andrew Best; and lab technician: Liz Shiells and Caroline Dalgiesh for all their support, advice and practical help in the lab. You have made my time in the lab a pleasant one and I'm thankful to have worked alongside each of you. My sincere appreciation goes to all the close friends I've made throughout this journey in Newcastle: Stephanie Chin for being the best friend/housemate I could ever ask for. Thank you for those nights where you stayed up to accompany this mad scientist! You have been most supportive at my toughest times, you're such a gem! Cynthia Wong, Karen Chan and Lihyun Wong for being the friends I could trust and rely on when all else seem to fail. Thank you for bringing fun into my life and putting smiles on my face. All of you have been an integral part of my life here and our friendship is always precious to me. My very special thanks go to my beloved family: Daddy and Mummy for always believing in me even though I've always doubted myself. Thank you for the continuous love, patience and grace that you've showered upon my entire life. Emily Hong for taking over my responsibility in the family while I'm away. Thank you for stepping up to the challenge and doing it so well. Adeline Hong for being here beside me and cheering me on at the final sprint of this journey. Thank you for your love and great support at my most crucial time. Above all else, I would like to thank my Saviour and my Lord, Jesus Christ for being my constant and firm foundation in this temporal and fading world. Thank You for Your mercy, faithfulness and immeasurable love that has led me to discover the greater purpose of my existence. This life is no longer my own, I've been redeemed and transformed to pursue Your kingdom first. Let my life sing Your glory and praises. I am eternally grateful for everything You've done in and through me. ii Table of contents Abstract.............................................................................................................................i Acknowledgements .......................................................................................................... ii Table of contents ............................................................................................................ iii Abbreviations ................................................................................................................. ix List of Figures ................................................................................................................. xi List of Tables ................................................................................................................ xiv Chapter 1 : Introduction ................................................................................................ 1 1.1 The mammary gland ......................................................................................... 1 1.1.1 Normal development of the mammary gland .............................................. 1 1.1.2 Anatomy of the breast .................................................................................. 2 1.2 Breast cancer..................................................................................................... 3 1.2.1 Epidemiology ............................................................................................... 3 1.2.2 Risk factors .................................................................................................. 4 1.2.3 Breast screening ........................................................................................... 6 1.2.4 Pathology ..................................................................................................... 7 1.2.4.1 Types of breast cancer ............................................................................. 7 1.2.4.2 Breast cancer grading and staging........................................................... 9 1.2.4.3 Tumour characteristics .......................................................................... 10 1.2.5 Breast cancer treatment .............................................................................. 11 1.2.5.1 Surgery .................................................................................................. 11 1.2.5.2 Radiation therapy .................................................................................. 12 1.2.5.3 Chemotherapy ....................................................................................... 12 1.2.5.4 Endocrine therapy ................................................................................. 13 1.2.5.5 Targeted therapy.................................................................................... 14 iii 1.3 Oestrogen and breast cancer ........................................................................... 14 1.3.1 Oestrogen receptors (ER) ........................................................................... 15 1.3.2 Genomic action of oestrogen ..................................................................... 17 1.3.3 Non-genomic action of oestrogen .............................................................. 18 1.3.4 Anti-oestrogen action in breast cancer ....................................................... 21 1.3.5 Anti-oestrogen resistance in breast cancer ................................................. 22 1.3.6 ER coregulators and breast cancer ............................................................. 24 1.4 Scaffold attachment factor B1 (SAFB1) and SAFB2 ..................................... 27 1.4.1 SAFB family, gene and protein ................................................................. 27 1.4.2 SAFB function ........................................................................................... 29 1.4.2.1 Chromatin organisation ......................................................................... 29 1.4.2.2 Transcriptional regulation ..................................................................... 29 1.4.2.3 RNA metabolism ................................................................................... 31 1.4.3 SAFB mechanism of transcriptional regulation ......................................... 32 1.4.4 SAFB and breast cancer
Load more

Recommended publications
  • 1 Supporting Information for a Microrna Network Regulates
    Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia.
    [Show full text]
  • Host Cell Factors Necessary for Influenza a Infection: Meta-Analysis of Genome Wide Studies
    Host Cell Factors Necessary for Influenza A Infection: Meta-Analysis of Genome Wide Studies Juliana S. Capitanio and Richard W. Wozniak Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta Abstract: The Influenza A virus belongs to the Orthomyxoviridae family. Influenza virus infection occurs yearly in all countries of the world. It usually kills between 250,000 and 500,000 people and causes severe illness in millions more. Over the last century alone we have seen 3 global influenza pandemics. The great human and financial cost of this disease has made it the second most studied virus today, behind HIV. Recently, several genome-wide RNA interference studies have focused on identifying host molecules that participate in Influen- za infection. We used nine of these studies for this meta-analysis. Even though the overlap among genes identified in multiple screens was small, network analysis indicates that similar protein complexes and biological functions of the host were present. As a result, several host gene complexes important for the Influenza virus life cycle were identified. The biological function and the relevance of each identified protein complex in the Influenza virus life cycle is further detailed in this paper. Background and PA bound to the viral genome via nucleoprotein (NP). The viral core is enveloped by a lipid membrane derived from Influenza virus the host cell. The viral protein M1 underlies the membrane and anchors NEP/NS2. Hemagglutinin (HA), neuraminidase Viruses are the simplest life form on earth. They parasite host (NA), and M2 proteins are inserted into the envelope, facing organisms and subvert the host cellular machinery for differ- the viral exterior.
    [Show full text]
  • The Increasing Diversity of Functions Attributed to the SAFB Family of RNA-/DNA-Binding Proteins
    Biochemical Journal (2016) 473 4271–4288 DOI: 10.1042/BCJ20160649 Review Article The increasing diversity of functions attributed to the SAFB family of RNA-/DNA-binding proteins Michael Norman1, Caroline Rivers1, Youn-Bok Lee2, Jalilah Idris1 and James Uney1 1Regenerative Medicine Laboratories, School of Clinical Sciences, Cellular and Molecular Medicine, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K. and 2Maurice Wohl Clinical Neuroscience Institute, Kings College, 125 Coldharbour Lane, Camberwell, London SE5 9NU, U.K. Correspondence: Michael Norman ([email protected]) RNA-binding proteins play a central role in cellular metabolism by orchestrating the complex interactions of coding, structural and regulatory RNA species. The SAFB (scaf- fold attachment factor B) proteins (SAFB1, SAFB2 and SAFB-like transcriptional modula- tor, SLTM), which are highly conserved evolutionarily, were first identified on the basis of their ability to bind scaffold attachment region DNA elements, but attention has subse- quently shifted to their RNA-binding and protein–protein interactions. Initial studies identi- fied the involvement of these proteins in the cellular stress response and other aspects of gene regulation. More recently, the multifunctional capabilities of SAFB proteins have shown that they play crucial roles in DNA repair, processing of mRNA and regulatory RNA, as well as in interaction with chromatin-modifying complexes. With the advent of new techniques for identifying RNA-binding sites, enumeration of individual RNA targets has now begun. This review aims to summarise what is currently known about the func- tions of SAFB proteins. Introduction In this review, we discuss three scaffold attachment factor B (SAFB) proteins [SAFB1, SAFB2 and SAFB-like transcriptional modulator, SLTM] that bind both DNA and RNA.
    [Show full text]
  • Inhibitory G-Protein Modulation of CNS Excitability by Jason Howard
    Inhibitory G-protein Modulation of CNS Excitability by Jason Howard Kehrl A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Pharmacology) in the University of Michigan 2014 Doctoral Committee: Professor Richard R. Neubig, Michigan State University, Co-Chair Professor Lori L. Isom, Co-Chair Professor Helen A. Baghdoyan Assistant Professor Asim A. Beg Research Associate Professor Geoffrey G. Murphy © Jason Howard Kehrl 2014 DEDICATION For Bud, Gagi, and Judy ii ACKNOWLEDGEMENTS This work would not have been possible without tremendous help from so many people. Scientifically my mentor, Rick, as he prefers to be called, was always available for collaborative discussions. He also provided me a great level of scientific freedom in pursuing what I found interesting, affording me the opportunity to learn more than I would have in most any other environment. Beyond what I’ve learned about the subject of pharmacology, what he has instilled in me is a sharp eye in the analysis of data-driven arguments, a great problem-solving toolset, and the ability to lead a team. This is what I will always value, no matter where I go in life. To my undergrads I am also exceedingly grateful. There are so many of you that I dare not name you individually for risk of putting some rank-order to the amount of fun and joy you each brought to my thesis work. I hope you each grew and learned from the experience as much as I learned from my attempts at mentoring each of you. This thesis is in no small part due to all the contributions you made.
    [Show full text]
  • Human Proteins That Interact with RNA/DNA Hybrids
    Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Resource Human proteins that interact with RNA/DNA hybrids Isabel X. Wang,1,2 Christopher Grunseich,3 Jennifer Fox,1,2 Joshua Burdick,1,2 Zhengwei Zhu,2,4 Niema Ravazian,1 Markus Hafner,5 and Vivian G. Cheung1,2,4 1Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA; 2Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA; 3Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland 20892, USA; 4Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109, USA; 5Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland 20892, USA RNA/DNA hybrids form when RNA hybridizes with its template DNA generating a three-stranded structure known as the R-loop. Knowledge of how they form and resolve, as well as their functional roles, is limited. Here, by pull-down assays followed by mass spectrometry, we identified 803 proteins that bind to RNA/DNA hybrids. Because these proteins were identified using in vitro assays, we confirmed that they bind to R-loops in vivo. They include proteins that are involved in a variety of functions, including most steps of RNA processing. The proteins are enriched for K homology (KH) and helicase domains. Among them, more than 300 proteins preferred binding to hybrids than double-stranded DNA. These proteins serve as starting points for mechanistic studies to elucidate what RNA/DNA hybrids regulate and how they are regulated.
    [Show full text]
  • Interplay of RNA-Binding Proteins and Micrornas in Neurodegenerative Diseases
    International Journal of Molecular Sciences Review Interplay of RNA-Binding Proteins and microRNAs in Neurodegenerative Diseases Chisato Kinoshita 1,* , Noriko Kubota 1,2 and Koji Aoyama 1,* 1 Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; [email protected] 2 Teikyo University Support Center for Women Physicians and Researchers, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan * Correspondence: [email protected] (C.K.); [email protected] (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.) Abstract: The number of patients with neurodegenerative diseases (NDs) is increasing, along with the growing number of older adults. This escalation threatens to create a medical and social crisis. NDs include a large spectrum of heterogeneous and multifactorial pathologies, such as amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and multiple system atrophy, and the formation of inclusion bodies resulting from protein misfolding and aggregation is a hallmark of these disorders. The proteinaceous components of the pathological inclusions include several RNA-binding proteins (RBPs), which play important roles in splicing, stability, transcription and translation. In addition, RBPs were shown to play a critical role in regulating miRNA biogenesis and metabolism. The dysfunction of both RBPs and miRNAs is Citation: Kinoshita, C.; Kubota, N.; often observed in several NDs. Thus, the data about the interplay among RBPs and miRNAs and Aoyama, K. Interplay of RNA-Binding Proteins and their cooperation in brain functions would be important to know for better understanding NDs and microRNAs in Neurodegenerative the development of effective therapeutics.
    [Show full text]
  • De Novo Duplication on Chromosome 19 Observed in Nuclear Family Displaying Neurodevelopmental Disorders
    Downloaded from molecularcasestudies.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press Title: De novo duplication on chromosome 19 observed in nuclear family displaying neurodevelopmental disorders Running Title: De novo CNV on chromosome 19 Authors: Sjaarda CP1,2*, Kaiser B1,2, McNaughton AJM1,2, Hudson ML1,2, Harris-Lowe L1,3, Lou K1,2, Guerin A4, Ayub M2, Liu X1,2 Affiliations: 1 Queen's Genomics Lab at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario, Canada 2 Department of Psychiatry, Queen’s University, Kingston, Ontario, Canada 3 School of Applied Science and Computing, St. Lawrence College, Kingston, Ontario, Canada 4 Division of Medical Genetics, Department of Pediatrics, Queen's University, Kingston, Ontario, Canada. * Author for correspondence Calvin P. Sjaarda, PhD Tel: (613) 548-4419 x 1200 [email protected] 1 Downloaded from molecularcasestudies.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Pleiotropy and variable expressivity have been cited to explain the seemingly distinct neurodevelopmental disorders due to a common genetic etiology within the same family. Here we present a family with a de novo 1 Mb duplication involving 18 genes on chromosome 19. Within the family there are multiple cases of neurodevelopmental disorders including: Autism Spectrum Disorder, Attention Deficit/Hyperactivity Disorder, Intellectual Disability, and psychiatric disease in individuals carrying this Copy Number Variant (CNV). Quantitative PCR confirmed the CNV was de novo in the mother and inherited by both sons. Whole exome sequencing did not uncover further genetic risk factors segregating within the family. Transcriptome analysis of peripheral blood demonstrated a ~1.5-fold increase in RNA transcript abundance in 12 of the 15 detected genes within the CNV region for individuals carrying the CNV compared with their non-carrier relatives.
    [Show full text]
  • Enrichment of Mutations in Chromatin Regulators in People with Rett Syndrome Lacking Mutations in MECP2
    HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Genet Med Manuscript Author . Author manuscript; Manuscript Author available in PMC 2016 November 14. Enrichment of mutations in chromatin regulators in people with Rett Syndrome lacking mutations in MECP2 Samin A. Sajan, PhD1,2,#, Shalini N. Jhangiani, MS3, Donna M. Muzny, MS3, Richard A. Gibbs, PhD3,4, James R. Lupski, MD, PhD3,4,5, Daniel G. Glaze, MD1, Walter E. Kaufmann, MD6, Steven A. Skinner, MD7, Fran Anese7, Michael J. Friez, PhD7, Lane Jane, RN8, Alan K. Percy, MD8, and Jeffrey L. Neul, MD, PhD1,2,4,# 1Section of Child Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA 2Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA 3Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA 4Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA 5Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA 6Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA 7Greenwood Genetic Center, Greenwood, South Carolina, USA 8Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA Abstract Purpose—Rett Syndrome (RTT) is a neurodevelopmental disorder caused primarily by de novo mutations (DNMs) in MECP2 and sometimes in CDKL5 and FOXG1. However, some RTT cases lack mutations in these genes. Methods—Twenty-two RTT cases without apparent MECP2, CDKL5, and FOXG1 mutations were subjected to both whole exome sequencing and single nucleotide polymorphism array-based copy number variant (CNV) analyses. Results—Three cases had MECP2 mutations initially missed by clinical testing.
    [Show full text]
  • The Neurodegenerative Diseases ALS and SMA Are Linked at The
    Nucleic Acids Research, 2019 1 doi: 10.1093/nar/gky1093 The neurodegenerative diseases ALS and SMA are linked at the molecular level via the ASC-1 complex Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gky1093/5162471 by [email protected] on 06 November 2018 Binkai Chi, Jeremy D. O’Connell, Alexander D. Iocolano, Jordan A. Coady, Yong Yu, Jaya Gangopadhyay, Steven P. Gygi and Robin Reed* Department of Cell Biology, Harvard Medical School, 240 Longwood Ave. Boston MA 02115, USA Received July 17, 2018; Revised October 16, 2018; Editorial Decision October 18, 2018; Accepted October 19, 2018 ABSTRACT Fused in Sarcoma (FUS) and TAR DNA Binding Protein (TARDBP) (9–13). FUS is one of the three members of Understanding the molecular pathways disrupted in the structurally related FET (FUS, EWSR1 and TAF15) motor neuron diseases is urgently needed. Here, we family of RNA/DNA binding proteins (14). In addition to employed CRISPR knockout (KO) to investigate the the RNA/DNA binding domains, the FET proteins also functions of four ALS-causative RNA/DNA binding contain low-complexity domains, and these domains are proteins (FUS, EWSR1, TAF15 and MATR3) within the thought to be involved in ALS pathogenesis (5,15). In light RNAP II/U1 snRNP machinery. We found that each of of the discovery that mutations in FUS are ALS-causative, these structurally related proteins has distinct roles several groups carried out studies to determine whether the with FUS KO resulting in loss of U1 snRNP and the other two members of the FET family, TATA-Box Bind- SMN complex, EWSR1 KO causing dissociation of ing Protein Associated Factor 15 (TAF15) and EWS RNA the tRNA ligase complex, and TAF15 KO resulting in Binding Protein 1 (EWSR1), have a role in ALS.
    [Show full text]
  • Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Fall 2010 Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress Renuka Nayak University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Computational Biology Commons, and the Genomics Commons Recommended Citation Nayak, Renuka, "Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress" (2010). Publicly Accessible Penn Dissertations. 1559. https://repository.upenn.edu/edissertations/1559 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1559 For more information, please contact [email protected]. Coexpression Networks Based on Natural Variation in Human Gene Expression at Baseline and Under Stress Abstract Genes interact in networks to orchestrate cellular processes. Here, we used coexpression networks based on natural variation in gene expression to study the functions and interactions of human genes. We asked how these networks change in response to stress. First, we studied human coexpression networks at baseline. We constructed networks by identifying correlations in expression levels of 8.9 million gene pairs in immortalized B cells from 295 individuals comprising three independent samples. The resulting networks allowed us to infer interactions between biological processes. We used the network to predict the functions of poorly-characterized human genes, and provided some experimental support. Examining genes implicated in disease, we found that IFIH1, a diabetes susceptibility gene, interacts with YES1, which affects glucose transport. Genes predisposing to the same diseases are clustered non-randomly in the network, suggesting that the network may be used to identify candidate genes that influence disease susceptibility.
    [Show full text]
  • Novel Neuroprotective Loci Modulating Ischemic Stroke Volume in Wild-Derived Inbred Mouse Strains
    | INVESTIGATION Novel Neuroprotective Loci Modulating Ischemic Stroke Volume in Wild-Derived Inbred Mouse Strains Han Kyu Lee,* Samuel J. Widmayer,† Min-Nung Huang,‡ David L. Aylor,† and Douglas A. Marchuk*,1 *Department of Molecular Genetics and Microbiology and ‡Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, and †Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695 ORCID IDs: 0000-0002-0876-7404 (H.K.L.); 0000-0002-1200-4768 (S.J.W.); 0000-0002-7589-3734 (M.-N.H.); 0000-0001-6065-4039 (D.L.A.); 0000-0002-3110-6671 (D.A.M.) ABSTRACT To identify genes involved in cerebral infarction, we have employed a forward genetic approach in inbred mouse strains, using quantitative trait loci (QTL) mapping for cerebral infarct volume after middle cerebral artery occlusion. We had previously observed that infarct volume is inversely correlated with cerebral collateral vessel density in most strains. In this study, we expanded the pool of allelic variation among classical inbred mouse strains by utilizing the eight founder strains of the Collaborative Cross and found a wild-derived strain, WSB/EiJ, that breaks this general rule that collateral vessel density inversely correlates with infarct volume. WSB/ EiJ and another wild-derived strain, CAST/EiJ, show the highest collateral vessel densities of any inbred strain, but infarct volume of WSB/EiJ mice is 8.7-fold larger than that of CAST/EiJ mice. QTL mapping between these strains identified four new neuroprotective loci modulating cerebral infarct volume while not affecting collateral vessel phenotypes. To identify causative variants in genes, we surveyed nonsynonymous coding SNPs between CAST/EiJ and WSB/EiJ and found 96 genes harboring coding SNPs predicted to be damaging and mapping within one of the four intervals.
    [Show full text]
  • The RNA-Mediated Estrogen Receptor Α Interactome of Hormone-Dependent Human Breast Cancer Cell Nuclei
    www.nature.com/scientificdata OPEN The RNA-mediated estrogen DATA DesCRIPTOR receptor α interactome of hormone-dependent human Received: 13 February 2019 Accepted: 25 July 2019 breast cancer cell nuclei Published: xx xx xxxx Giovanni Nassa 1, Giorgio Giurato1,2, Annamaria Salvati1, Valerio Gigantino1, Giovanni Pecoraro1, Jessica Lamberti1, Francesca Rizzo1, Tuula A. Nyman3, Roberta Tarallo 1 & Alessandro Weisz1 Estrogen Receptor alpha (ERα) is a ligand-inducible transcription factor that mediates estrogen signaling in hormone-responsive cells, where it controls key cellular functions by assembling in gene-regulatory multiprotein complexes. For this reason, interaction proteomics has been shown to represent a useful tool to investigate the molecular mechanisms underlying ERα action in target cells. RNAs have emerged as bridging molecules, involved in both assembly and activity of transcription regulatory protein complexes. By applying Tandem Afnity Purifcation (TAP) coupled to mass spectrometry (MS) before and after RNase digestion in vitro, we generated a dataset of nuclear ERα molecular partners whose association with the receptor involves RNAs. These data provide a useful resource to elucidate the combined role of nuclear RNAs and the proteins identifed here in ERα signaling to the genome in breast cancer and other cell types. Background & Summary Te Estrogen Receptor alpha (ERα), a ligand-inducible transcription factor encoded by the ESR1 gene, is a key mediator of the estrogen signaling in hormone-responsive breast cancer (BC)1. Tis receptor subtype exerts a direct control on gene transcription machinery by binding chromatin cistromes2, where it assembles in large functional multiprotein complexes. Tese complexes comprise several molecular partners endowed with diferent functions, including co-regulators3–5 and epigenetic modulators6–8 that drive gene expression changes underlying BC development and progression9.
    [Show full text]