TGF-Β1 Signaling Targets Metastasis-Associated Protein 1, a New Effector in Epithelial Cells
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RNA-Binding Protein Hnrnpll Regulates Mrna Splicing and Stability During B-Cell to Plasma-Cell Differentiation
RNA-binding protein hnRNPLL regulates mRNA splicing and stability during B-cell to plasma-cell differentiation Xing Changa,b, Bin Lic, and Anjana Raoa,b,d,e,1 Divisions of aSignaling and Gene Expression and cVaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; bSanford Consortium for Regenerative Medicine, La Jolla, CA 92037; and dDepartment of Pharmacology and eMoores Cancer Center, University of California at San Diego, La Jolla, CA 92093 Contributed by Anjana Rao, December 2, 2014 (sent for review July 20, 2014) Posttranscriptional regulation is a major mechanism to rewire the RBP-binding sites, thus validating the specificity of RBP binding transcriptomes during differentiation. Heterogeneous nuclear to coprecipitating RNAs and mapping RBP-binding sites on the RNA-binding protein LL (hnRNPLL) is specifically induced in terminally validated RNAs at close to single-nucleotide resolution (8). differentiated lymphocytes, including effector T cells and plasma Heterogeneous nuclear RNA-binding proteins (hnRNPs) is cells. To study the molecular functions of hnRNPLL at a genome- the term applied to a collection of unrelated nuclear RBPs. wide level, we identified hnRNPLL RNA targets and binding sites in hnRNPLL was identified through a targeted lentiviral shRNA plasma cells through integrated Photoactivatable-Ribonucleoside- screen for regulators of CD45RA to CD45RO switching during Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP) and memory T-cell development (9) and independently through RNA sequencing. hnRNPLL preferentially recognizes CA dinucleo- two separate screens performed by different groups for exclusion tide-containing sequences in introns and 3′ untranslated regions of CD45 exon 4 in a minigene context (10) and for altered CD44 (UTRs), promotes exon inclusion or exclusion in a context-dependent and CD45R expression on T cells in N-ethyl-N-nitrosourea manner, and stabilizes mRNA when associated with 3′ UTRs. -
Cross-Family Dimerization of Transcription Factors Fos/Jun
Proc. Nati. Acad. Sci. USA Vol. 88, pp. 3720-3724, May 9, 1991 Biochemistry Cross-family dimerization of transcription factors Fos/Jun and ATF/CREB alters DNA binding specificity (gene regulation/oncogenes/leucine zipper/protein dimerization/transcription) TSONWIN HAI*t AND ToM CURRANt of Medical Biochemistry and Ohio State Biotechnology Center, Ohio State University, 1060 Carmack Road, Columbus, OH 43210; and tDepartment*Department of Molecular Oncology and Virology, Roche Institute of Molecular Biology, Roche Research Center, Nutley, NJ 07110 Communicated by Herbert Weissbach, January 31, 1991 ABSTRACT The Fos/Jun and ATF/CREB families of Table 1. Mammalian Fos/Jun and ATF/CREB families transcription factors function in coupling extracellular signals Family Subfamily Gene(s) to alterations in expression of specific target genes. Like many eukaryotic transcription factors, these proteins bind to DNA as Fos/Jun Fos fos, fra-), fra-2, fosB dimers. Dimerization is mediated by a structure known as the Jun c-jun, junB, junD "leucine-zipper" motif. Although Fos/Jun and ATF/CREB ATF/CREB CREB CREB, ATF-I were previously thought to interact preferentially with differ- CRE-BP1 CRE-BPI, ATF-a ent DNA regulatory elements (the AP-1/TRE and ATF/CRE ATF-3 ATF-3* sites, respectively), we rind that members of these two families ATF-4 ATF4* form selective cross-family heterodimers. The resulting het- Alternative names for CRE-BPI are ATF-2 and HB16. ACREB is erodimers display distinguishable DNA binding speclfcities a spliced variant ofCREB, ATF-aA is a spliced variant ofATF-a, and from each other and from their parental homodimers. -
Micrornas in Cardiovascular Disease: from Pathogenesis to Prevention and Treatment
MicroRNAs in cardiovascular disease: from pathogenesis to prevention and treatment Daniel Quiat, Eric N. Olson J Clin Invest. 2013;123(1):11-18. https://doi.org/10.1172/JCI62876. Review Series The management of cardiovascular risk through lifestyle modification and pharmacotherapy is paramount to the prevention of cardiovascular disease. Epidemiological studies have identified obesity, dyslipidemia, diabetes, and hypertension as interrelated factors that negatively affect cardiovascular health. Recently, genetic and pharmacological evidence in model systems has implicated microRNAs as dynamic modifiers of disease pathogenesis. An expanded understanding of the function of microRNAs in gene regulatory networks associated with cardiovascular risk will enable identification of novel genetic mechanisms of disease and inform the development of innovative therapeutic strategies. Find the latest version: https://jci.me/62876/pdf Review series MicroRNAs in cardiovascular disease: from pathogenesis to prevention and treatment Daniel Quiat and Eric N. Olson Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA. The management of cardiovascular risk through lifestyle modification and pharmacotherapy is paramount to the prevention of cardiovascular disease. Epidemiological studies have identified obesity, dyslipidemia, diabetes, and hypertension as interrelated factors that negatively affect cardiovascular health. Recently, genetic and pharmaco- logical evidence in model systems has implicated microRNAs -
Neurobiological Functions of the Period Circadian Clock 2 Gene, Per2
Review Biomol Ther 26(4), 358-367 (2018) Neurobiological Functions of the Period Circadian Clock 2 Gene, Per2 Mikyung Kim, June Bryan de la Peña, Jae Hoon Cheong and Hee Jin Kim* Department of Pharmacy, Uimyung Research Institute for Neuroscience, Sahmyook University, Seoul 01795, Republic of Korea Abstract Most organisms have adapted to a circadian rhythm that follows a roughly 24-hour cycle, which is modulated by both internal (clock-related genes) and external (environment) factors. In such organisms, the central nervous system (CNS) is influenced by the circadian rhythm of individual cells. Furthermore, the period circadian clock 2 (Per2) gene is an important component of the circadian clock, which modulates the circadian rhythm. Per2 is mainly expressed in the suprachiasmatic nucleus (SCN) of the hypothalamus as well as other brain areas, including the midbrain and forebrain. This indicates that Per2 may affect various neurobiological activities such as sleeping, depression, and addiction. In this review, we focus on the neurobiological functions of Per2, which could help to better understand its roles in the CNS. Key Words: Circadian rhythm, Per2 gene, Sleep, Depression, Addiction, Neurotransmitter INTRODUCTION and lives in organisms because it can impart effects from the level of cells to organs including the brain. Thus, it is neces- A circadian rhythm is any physiological process that displays sary to understand clock-related genes that are controlling the a roughly 24 hour cycle in living beings, such as mammals, circadian rhythm endogenously. plants, fungi and cyanobacteria (Albrecht, 2012). In organ- The Period2 (Per2) gene is a member of the Period family isms, most biological functions such as sleeping and feeding of genes consisting of Per1, Per2, and Per3, and is mainly patterns are adapted to the circadian rhythm. -
Conditional Deletion of HIF-1Α Provides New Insight
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.16.426940; this version posted January 16, 2021. 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. Conditional deletion of HIF-1 provides new insight regarding the murine response to gastrointestinal infection with Salmonella Typhimurium Laura Robrahn *, Aline Dupont †, Sandra Jumpertz *, Kaiyi Zhang †, Christian H. Holland ‡ §, Joël Guillaume ¶1, Sabrina Rappold *, Vuk Cerovic ¶, Julio Saez-Rodriguez ‡ §, Mathias W. Hornef † || #, and Thorsten Cramer * ** †† ‡‡ * Department of General, Visceral and Transplantation Surgery, RWTH University Hospital, Pauwelsstraße 30, 52074 Aachen, Germany; † Institute of Medical Microbiology, RWTH University Hospital, Pauwelsstraße 30, 52074 Aachen, Germany; ‡ Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, and Heidelberg University Hospital, Bioquant, Heidelberg, Germany; § Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany; ¶ Institute of Molecular Medicine, RWTH University Hospital, Aachen, Germany; ** ESCAM – European Surgery Center Aachen Maastricht, Germany and The Netherlands; †† Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands; ‡‡ NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, -
Fosb Induction in Nucleus Accumbens by Cocaine Is Regulated by E2f3a
New Research Disorders of the Nervous System Fosb Induction in Nucleus Accumbens by Cocaine Is Regulated by E2F3a Hannah M. Cates,1 Casey K. Lardner,1 Rosemary C. Bagot,1 Rachael L. Neve,2 and Eric J. Nestler1 https://doi.org/10.1523/ENEURO.0325-18.2019 1Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029 and 2Gene Delivery Technology Core, Massachusetts General Hospital, Cambridge, Massachusetts 02139 Abstract The transcription factor ⌬FosB has been proposed as a molecular switch for the transition from casual, volitional drug use into a chronically addicted state, but the upstream regulatory mechanisms governing ⌬FosB expression are incompletely understood. In this study, we find a novel regulatory role for the transcription factor E2F3, recently implicated in transcriptional regulation by cocaine, in controlling ⌬FosB induction in the mouse nucleus accumbens (NAc) following cocaine administration. We find that an E2F consensus sequence 500 bp upstream of the Fosb transcription start site is enriched for E2F3 specifically over other E2F isoforms. We further conclude that ⌬FosB expression is regulated specifically by E2F3a, not E2F3b, that E2f3a expression is specific to D1 receptor-expressing medium spiny neurons, and that E2F3a overexpression in NAc recapitulates the induction of Fosb and ⌬Fosb mRNA expression observed after chronic cocaine exposure. E2F3a knockdown in NAc does not abolish ⌬Fosb induction by cocaine, a result consistent with previously published data showing that singular knockdown of upstream regulators of ⌬FosB is insufficient to block cocaine-induced expression. Finally, to elucidate potential combinatorial epigenetic mechanisms involved in E2F3a’s regulation of Fosb, we explore H3K4me3 enrichment at the Fosb promoter and find that it is not enhanced by E2F3a overexpression, suggesting that it may instead be a pre-existing permissive mark allowing for E2F3a to interact with Fosb. -
BCL6 Repression of EP300 in Human Diffuse Large B Cell Lymphoma Cells Provides a Basis for Rational Combinatorial Therapy Leandro C
Research article BCL6 repression of EP300 in human diffuse large B cell lymphoma cells provides a basis for rational combinatorial therapy Leandro C. Cerchietti,1,2 Katerina Hatzi,1,2 Eloisi Caldas-Lopes,3 Shao Ning Yang,1,2 Maria E. Figueroa,1,2 Ryan D. Morin,4 Martin Hirst,4 Lourdes Mendez,1 Rita Shaknovich,5 Philip A. Cole,6 Kapil Bhalla,7 Randy D. Gascoyne,8 Marco Marra,4 Gabriela Chiosis,3 and Ari Melnick1,2 1Hematology and Oncology Division, and 2Department of Pharmacology, Weill Cornell Medical College, New York, New York, USA. 3Department of Molecular Pharmacology and Chemistry, Sloan-Kettering Institute, New York, New York, USA. 4Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada. 5Department of Pathology, Weill Cornell Medical College, New York, New York, USA. 6Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. 7The University of Kansas Cancer Center, Kansas University Medical Center, Kansas City, Kansas, USA. 8Centre for Lymphoid Cancers and the Departments of Pathology and Experimental Therapeutics, British Columbia Cancer Agency, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada. B cell lymphoma 6 (BCL6), which encodes a transcriptional repressor, is a critical oncogene in diffuse large B cell lymphomas (DLBCLs). Although a retro-inverted BCL6 peptide inhibitor (RI-BPI) was recently shown to potently kill DLBCL cells, the underlying mechanisms remain unclear. Here, we show that RI-BPI induces a particular gene expression signature in human DLBCL cell lines that included genes associated with the actions of histone deacetylase (HDAC) and Hsp90 inhibitors. -
AP-1 in Cell Proliferation and Survival
Oncogene (2001) 20, 2390 ± 2400 ã 2001 Nature Publishing Group All rights reserved 0950 ± 9232/01 $15.00 www.nature.com/onc AP-1 in cell proliferation and survival Eitan Shaulian1 and Michael Karin*,1 1Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, California, CA 92093-0636, USA A plethora of physiological and pathological stimuli extensively discussed previously (Angel and Karin, induce and activate a group of DNA binding proteins 1991; Karin, 1995). that form AP-1 dimers. These proteins include the Jun, The mammalian AP-1 proteins are homodimers and Fos and ATF subgroups of transcription factors. Recent heterodimers composed of basic region-leucine zipper studies using cells and mice de®cient in individual AP-1 (bZIP) proteins that belong to the Jun (c-Jun, JunB proteins have begun to shed light on their physiological and JunD), Fos (c-Fos, FosB, Fra-1 and Fra-2), Jun functions in the control of cell proliferation, neoplastic dimerization partners (JDP1 and JDP2) and the closely transformation and apoptosis. Above all such studies related activating transcription factors (ATF2, LRF1/ have identi®ed some of the target genes that mediate the ATF3 and B-ATF) subfamilies (reviewed by (Angel eects of AP-1 proteins on cell proliferation and death. and Karin, 1991; Aronheim et al., 1997; Karin et al., There is evidence that AP-1 proteins, mostly those that 1997; Liebermann et al., 1998; Wisdom, 1999). In belong to the Jun group, control cell life and death addition, some of the Maf proteins (v-Maf, c-Maf and through their ability to regulate the expression and Nrl) can heterodimerize with c-Jun or c-Fos (Nishiza- function of cell cycle regulators such as Cyclin D1, p53, wa et al., 1989; Swaroop et al., 1992), whereas other p21cip1/waf1, p19ARF and p16. -
Rbpj-Dependent and -Independent Notch2 Signaling Regulates
RBPJ-DEPENDENT AND -INDEPENDENT NOTCH2 SIGNALING REGULATES CILIARY BODY DEVELOPMENT IN THE MOUSE EYE By Yi Zhou B.S., Tsinghua University, 2010 Submitted to the graduate degree program in Anatomy and Cell Biology and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. ________________________________ Ting Xie, Ph.D., Co-Chair ________________________________ William Kinsey, Ph.D., Co-Chair ________________________________ Dale Abrahamson, Ph.D. ________________________________ Peter Smith, Ph.D. ________________________________ Jerry Workman, Ph.D. Date Defended: Jan 6th, 2016 The Dissertation Committee for Yi Zhou certifies that this is the approved version of the following dissertation: RBPJ-DEPENDENT AND -INDEPENDENT NOTCH2 SIGNALING REGULATES CILIARY BODY DEVELOPMENT IN THE MOUSE EYE ________________________________ Ting Xie, Ph.D., Co-Chair ________________________________ William Kinsey, Ph.D., Co-Chair Date Approved: Jan 15th, 2016 ii ABSTRACT The ciliary body (CB) is a two-layered structure in the anterior eye, which is composed of the pigmented outer ciliary epithelium (OCE) and the non-pigmented inner ciliary epithelium (ICE). It is responsible for aqueous humor secretion and lens accommodation. Despite the important roles in maintaining normal eye functions, its development still remains poorly understood. The Notch signaling pathway is an evolutionarily conserved pathway that has diverse functions during tissue development and homeostasis. Canonical Notch signaling is mediated through the recombination signal binding protein for immunoglobulin kappa J region (RBPJ)-dependent transcription activation and repression. In this study, I have demonstrated that Notch2 and RBPJ are important regulators of CB development by conditionally deleting them in the developing CB. -
PDF Hosted at the Radboud Repository of the Radboud University Nijmegen
PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/147462 Please be advised that this information was generated on 2021-10-11 and may be subject to change. Chromatin Regulatory Complexes from an Interaction Proteomics Perspective an Interaction Proteomics from Regulatory Complexes Chromatin Chromatin Regulatory Complexes from an Interaction Proteomics Perspective H. İrem Baymaz H. İrem Baymaz H. İrem Baymaz 2015 Chromatin Regulatory Complexes from an Interaction Proteomics Perspective H. İrem Baymaz printed by: Proefschriftmaken.nl || Uitgeverij BOXPress Copyright © 2015 H. İrem Baymaz Chromatin Regulatory Complexes from an Interaction Proteomics Perspective Chromatine-Regulerende Complexen vanuit een Interactie-Proteomics Perspectief Proefschrift ter verkrijging van de graad van doctor aan de Radboud Universiteit Nijmegen op gezag van de rector magnificus prof. dr. Th.L.M. Engelen, volgens besluit van het college van decanen in het openbaar te verdedigen op donderdag 26 november 2015 om 12.30 uur precies door Hamdiye İrem Baymaz geboren op 8 maart 1986 te Ankara, Turkije Promoter: Prof. dr. M. Vermeulen Manuscriptcommissie: Prof. dr. J.H.L.M. van Bokhoven Prof. dr. H.T.M. Timmers (UMCU) Dr. L.M. Kamminga Anne ve Babama. Table of Contents List of Abbreviations 9 Chapter 1 11 Introduction Chapter 2 45 Identifying nuclear protein-protein interactions using GFP affinity purification -
Estradiol Inhibits ER Stress-Induced Apoptosis Through
Laboratory Investigation (2014) 94, 906–916 & 2014 USCAP, Inc All rights reserved 0023-6837/14 17b-Estradiol inhibits ER stress-induced apoptosis through promotion of TFII-I-dependent Grp78 induction in osteoblasts Yun-Shan Guo1,2,5, Zhen Sun1,5, Jie Ma3,5, Wei Cui4,5, Bo Gao1, Hong-Yang Zhang1, Yue-Hu Han1, Hui-Min Hu1, Long Wang1, Jing Fan1, Liu Yang1, Juan Tang2 and Zhuo-Jing Luo1 Although many studies have suggested that estrogen prevents postmenopausal bone loss partially due to its anti-apoptosis effects in osteoblasts, the underlying mechanism has not been fully elucidated. In the present study, we found that 17b-estradiol (17b-E2), one of the primary estrogens, inhibited endoplasmic reticulum (ER) stress-induced apoptosis in MC3T3-E1 cells and primary osteoblasts. Interestingly, 17b-E2-promoted Grp78 induction, but not CHOP induction in response to ER stress. We further confirmed that Grp78-specific siRNA reversed the inhibition of 17b-E2 on ER stress-induced apoptosis by activating caspase-12 and caspase-3. Moreover, we found that 17b-E2 markedly increased the phosphorylated TFII-I levels and nuclear localization of TFII-I in ER stress conditions. 17b-E2 stimulated Grp78 promoter activity in a dose-dependent manner in the presence of TFII-I and enhanced the binding of TFII-I to the Grp78 promoter. In addition, 17b-E2 notably increased phosphorylated ERK1/2 levels and Ras kinase activity in MC3T3-E1 cells. The ERK1/2 activity-specific inhibitor U0126 remarkably blocked 17b-E2-induced TFII-I phosphorylation and Grp78 expression in response to ER stress. Together, 17b-E2 protected MC3T3-E1 cells against ER stress-induced apoptosis by promoting Ras-ERK1/2-TFII-I signaling pathway-dependent Grp78 induction. -
I3C & Hormone Positive Breast Cancer
ARTICLE IN PRESS Journal of Nutritional Biochemistry xx (2006) xxx–xxx Estrogen receptor a as a target for indole-3-carbinol Thomas T.Y. Wanga,4, Matthew J. Milnerb, John A. Milnerc, Young S. Kimc aPhytonutrients Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA bDepartment of Biology, The Pennsylvania State University, University Park, PA, USA cNutritional Science Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA Received 8 June 2005; received in revised form 14 October 2005; accepted 22 October 2005 Abstract A wealth of preclinical evidence supports the antitumorigenic properties of indole-3-carbinol (I3C), which is a major bioactive food component in cruciferous vegetables. However, the underlying molecular mechanism(s) accounting for these effects remain unresolved. In the present study, estrogen receptor alpha (ER-a) was identified as a potential molecular target for I3C. Treating MCF-7 cells with 100 AM I3C reduced ER-a mRNA expression by approximately 60% compared to controls. This reduction in ER-a transcript levels was confirmed using real-time polymerase chain reaction. The I3C dimer, 3,3V-diindolylmethane (DIM), was considerably more effective in depressing ER-a mRNA in MCF-7 cells than the monomeric unit. The suppressive effects of 5 AM DIM on ER-a mRNA was comparable to that caused by 100 AM I3C. DIM is known to accumulate in the nucleus and is a preferred ligand for aryl hydrocarbon receptor (AhR) to I3C. The addition of other AhR ligands, a-naphthoflavone (a-NF, 10 AM) and luteolin (10 AM), to the culture media resulted in a similar suppression in ER-a mRNA levels to that caused by 5 AM DIM.