Circadian- and Sex-Dependent Increases in Intravenous Cocaine Self-Administration in Npas2 Mutant Mice
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Progesterone Receptor Coregulators As Factors Supporting the Function of the Corpus Luteum in Cows
G C A T T A C G G C A T genes Article Progesterone Receptor Coregulators as Factors Supporting the Function of the Corpus Luteum in Cows Robert Rekawiecki * , Karolina Dobrzyn, Jan Kotwica and Magdalena K. Kowalik Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10, 10–747 Olsztyn, Poland; [email protected] (K.D.); [email protected] (J.K.); [email protected] (M.K.K.) * Correspondence: [email protected]; Tel.: +48-89-539-31-17 Received: 5 July 2020; Accepted: 7 August 2020; Published: 12 August 2020 Abstract: Progesterone receptor (PGR) for its action required connection of the coregulatory proteins, including coactivators and corepressors. The former group exhibits a histone acetyltransferase (HAT) activity, while the latter cooperates with histone deacetylase (HDAC). Regulations of the coregulators mRNA and protein and HAT and HDAC activity can have an indirect effect on the PGR function and thus progesterone (P4) action on target cells. The highest mRNA expression levels for the coactivators—histone acetyltransferase p300 (P300), cAMP response element-binding protein (CREB), and steroid receptor coactivator-1 (SRC-1)—and nuclear receptor corepressor-2 (NCOR-2) were found in the corpus luteum (CL) on days 6 to 16 of the estrous cycle. The CREB protein level was higher on days 2–10, whereas SRC-1 and NCOR-2 were higher on days 2–5. The activity of HAT and HDAC was higher on days 6–10 of the estrous cycle. All of the coregulators were localized in the nuclei of small and large luteal cells. -
Basic Helix-Loop-Helix Transcription Factors DEC1 and DEC2 Regulate the Paclitaxel-Induced Apoptotic Pathway of MCF-7 Human Breast Cancer Cells
INTERNATIONAL JOURNAL OF MoleCular MEDICine 27: 491-495, 2011 Basic helix-loop-helix transcription factors DEC1 and DEC2 regulate the paclitaxel-induced apoptotic pathway of MCF-7 human breast cancer cells YUNYAN WU1,2, FUYUKI SATO1, UJJAL KUMAR BHAWAL3, TAKESHI KAWAMOTO4, KATSUMI FUJIMOTO4, MITSUHIDE NOSHIRO4, SATOKO MOROHASHI1, YUKIO KATO4 and HIROSHI KIJIMA1 1Department of Pathology and Bioscience, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan; 2Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang 110001, P.R. China; 3Department of Oral and Maxillofacial Surgery and High-Tech Research Center, Kanagawa Dental College, Yokosuka 238-8580; 4Department of Dental and Medical Biochemistry, Hiroshima University Graduate School of Biomedical Science, Hiroshima 734-8553, Japan Received November 17, 2010; Accepted January 10, 2011 DOI: 10.3892/ijmm.2011.617 Abstract. Differentiated embryonic chondrocyte gene Introduction (DEC) 1 (BHLHE40/Stra13/Sharp2) and DEC2 (BHLHE41/ Sharp1) are basic helix-loop-helix (bHLH) transcription Paclitaxel is an anti-tumor drug that is used against a wide factors that are associated with the regulation of apoptosis, cell variety of solid tumors (1,2) and affects the expression of proliferation and circadian rhythms, as well as malignancy Bcl-2, Bcl-xL and phosphorylated-c-Jun NH2-terminal kinase in various cancers. However, the roles of DEC1 and DEC2 (JNK), and the activation of caspases and poly (ADP-ribose) expression in breast cancer are poorly understood. In this polymerase PARP (3-6), resulting in the induction of apop- study, we sought to examine the roles of DEC1 and DEC2 tosis by p53-dependent or -independent mechanisms (7-9). -
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. -
TGF-Β1 Signaling Targets Metastasis-Associated Protein 1, a New Effector in Epithelial Cells
Oncogene (2011) 30, 2230–2241 & 2011 Macmillan Publishers Limited All rights reserved 0950-9232/11 www.nature.com/onc ORIGINAL ARTICLE TGF-b1 signaling targets metastasis-associated protein 1, a new effector in epithelial cells SB Pakala1, K Singh1,3, SDN Reddy1, K Ohshiro1, D-Q Li1, L Mishra2 and R Kumar1 1Department of Biochemistry and Molecular Biology and Institute of Coregulator Biology, The George Washington University Medical Center, Washington, DC, USA and 2Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX, USA In spite of a large number of transforming growth factor b1 gene chromatin in response to upstream signals. The (TGF-b1)-regulated genes, the nature of its targets with TGF-b1-signaling is largely mediated by Smad proteins roles in transformation continues to be poorly understood. (Massague et al., 2005) where Smad2 and Smad3 are Here, we discovered that TGF-b1 stimulates transcription phosphorylated by TGF-b1-receptors and associate with of metastasis-associated protein 1 (MTA1), a dual master the common mediator Smad4, which translocates to the coregulator, in epithelial cells, and that MTA1 status is a nucleus to participate in the expression of TGF-b1-target determinant of TGF-b1-induced epithelial-to-mesenchymal genes (Deckers et al., 2006). Previous studies have shown transition (EMT) phenotypes. In addition, we found that that CUTL1, also known as CDP (CCAAT displacement MTA1/polymerase II/activator protein-1 (AP-1) co-activator protein), a target of TGF-b1, is needed for its short-term complex interacts with the FosB-gene chromatin and stimu- effects of TGF-b1 on cell motility involving Smad4- lates its transcription, and FosB in turn, utilizes FosB/histone dependent pathway (Michl et al.,2005). -
Downregulation of Dipeptidyl Peptidase 4 Accelerates Progression to Castration-Resistant Prostate Cancer Joshua W
Published OnlineFirst September 21, 2018; DOI: 10.1158/0008-5472.CAN-18-0687 Cancer Priority Report Research Downregulation of Dipeptidyl Peptidase 4 Accelerates Progression to Castration-Resistant Prostate Cancer Joshua W. Russo1,CeGao2, Swati S. Bhasin2, Olga S. Voznesensky1, Carla Calagua3, Seiji Arai1,4, Peter S. Nelson5, Bruce Montgomery6, Elahe A. Mostaghel5, Eva Corey6, Mary-Ellen Taplin7, Huihui Ye3, Manoj Bhasin2, and Steven P. Balk1 Abstract The standard treatment for metastatic prostate cancer, cleaves dipeptides from multiple growth factors, resulting in androgen deprivation therapy (ADT), is designed to suppress their increased degradation. DPP4 mRNA and protein were androgen receptor (AR) activity. However, men invariably also decreased in clinical CRPC cases, and inhibition of progress to castration-resistant prostate cancer (CRPC), and DPP4 with sitagliptin enhanced the growth of prostate AR reactivation contributes to progression in most cases. To cancer xenografts following castration. Significantly, DPP4 identify mechanisms that may drive CRPC, we examined a inhibitors are frequently used to treat type 2 diabetes as they VCaP prostate cancer xenograft model as tumors progressed increase insulin secretion. Together, these results implicate from initial androgen sensitivity prior to castration to castra- DPP4 as an AR-regulated tumor suppressor gene whose tion resistance and then on to relapse after combined therapy loss enhances growth factor activity and suggest that treat- with further AR-targeted drugs (abiraterone plus enzaluta- ment with DPP4 inhibitors may accelerate emergence of mide). AR activity persisted in castration-resistant and abir- resistance to ADT. aterone/enzalutamide–resistant xenografts and was associated with increased expression of the AR gene and the AR-V7 splice Significance: These findings identify DPP4 as an AR-stim- variant. -
The Title of the Dissertation
UNIVERSITY OF CALIFORNIA SAN DIEGO Novel network-based integrated analyses of multi-omics data reveal new insights into CD8+ T cell differentiation and mouse embryogenesis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Kai Zhang Committee in charge: Professor Wei Wang, Chair Professor Pavel Arkadjevich Pevzner, Co-Chair Professor Vineet Bafna Professor Cornelis Murre Professor Bing Ren 2018 Copyright Kai Zhang, 2018 All rights reserved. The dissertation of Kai Zhang is approved, and it is accept- able in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California San Diego 2018 iii EPIGRAPH The only true wisdom is in knowing you know nothing. —Socrates iv TABLE OF CONTENTS Signature Page ....................................... iii Epigraph ........................................... iv Table of Contents ...................................... v List of Figures ........................................ viii List of Tables ........................................ ix Acknowledgements ..................................... x Vita ............................................. xi Abstract of the Dissertation ................................. xii Chapter 1 General introduction ............................ 1 1.1 The applications of graph theory in bioinformatics ......... 1 1.2 Leveraging graphs to conduct integrated analyses .......... 4 1.3 References .............................. 6 Chapter 2 Systematic -
UNIVERSITY of CALIFORNIA Los Angeles
UNIVERSITY OF CALIFORNIA Los Angeles Circadian Gene Networks In Bone Regeneration A thesis submitted in partial satisfaction of the requirements for the degree Master of Science in Oral Biology by Nathaniel Raphael Hassan 2012 ABSTRACT OF THESIS Circadian Gene Networks In Bone Regeneration By Nathaniel Raphael Hassan Master of Science in Oral Biology University of California, Los Angeles, 2012 Professor Ichiro Nishimura, Chair BACKGROUND: Previous studies suggested that vitamin D played a significant role in bone regeneration, facilitating the establishment of implant osseointegration. A whole genome microarray study further suggested that the vitamin D axis might involve circadian rhythm gene expression in the bone peripheral tissue. OBJECTIVES: To identify key gene networks involved with vitamin D receptor in the bone regeneration process and to explore any correlation with circadian rhythm gene expression in bone marrow mesenchymal stromal/stem cells (BMSC). METHODS: The available whole gene microarray data was analyzed using the weighted gene correlation network analysis (WGCNA) R package and Cytoscape software. Any gene expression correlation was examined for vitamin D receptor (VDR) as well as circadian rhythm ii genes. Separately, Per 1 luciferase transgenic Wistar rats were then applied for in vitro evaluation on BMSC circadian rhythm. Per1::luc BMSCs were seeded on 35mm dishes and forskolin-synchronized luminescence was recorded across different media conditions. The recording media included growth medium containing F12 (10% Fetal Bovine Serum, 1% Pen- Strep and antibiotic) supplemented with or without 1 nM 1,25D. Luminescence was also recorded in F12 growth medium containing bone differentiation factors (beta glycerophosphate, Ascorbic acid and Dexamethasone) supplemented with 0, 1 or 10 nM 1,25D. -
Engineering Zinc-Finger Protein and CRISPR/Cas9 Constructs to Model the Epigenetic and Transcriptional Phenomena That Underlie Cocaine-Related Behaviors
Engineering zinc-finger protein and CRISPR/Cas9 constructs to model the epigenetic and transcriptional phenomena that underlie cocaine-related behaviors Hamilton PJ, Heller EA, Ortiz Torres I, Burek DD, Lombroso SI, Pirpinias ST, Neve RL, Nestler EJ Multiple studies have implicated genome-wide epigenetic remodeling events in brain reward regions following drug exposure. However, only recently has it become possible to target a given type of epigenetic remodeling to a single gene of interest, in order to probe the causal relationship between such regulation and neuropsychiatric disease (Heller et al., Nat Neurosci, 2014). Our group has successfully utilized synthetic zinc- finger proteins (ZFPs), fused to either the transcriptional repressor, G9a, that promotes histone methylation or the transcriptional activator, p65, that promotes histone acetylation, to determine the behavioral effects of targeted in vivo epigenetic reprogramming in a locus-specific and cell-type specific manner. Given the success of our ZFP approaches, we have broadened our technical repertoire to include the more novel and flexible CRISPR/Cas9 technology. We designed guide RNAs to target nuclease-dead Cas9 (dCas9) fused to effector domains to the fosB gene locus, a locus heavily implicated in the pathogenesis of drug abuse. We observe that dCas9 fused to the transcriptional activator, VP64, or the transcriptional repressor, KRAB, and targeted to specific sites in the fosB promoter is sufficient to regulate FosB and ΔFosB mRNA levels, in both cultured cells and in the nucleus accumbens (NAc) of mice receiving viral delivery of CRISPR constructs. Next, we designed a fusion construct linking the dCas9 moiety to a pseudo-phosphorylated isoform of the transcription factor CREB (dCas9 CREB(S133D)). -
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. -
NPAS2 As a Transcriptional Regulator of Non-Rapid Eye Movement Sleep: Genotype and Sex Interactions
NPAS2 as a transcriptional regulator of non-rapid eye movement sleep: Genotype and sex interactions Paul Franken*†‡, Carol A. Dudley§, Sandi Jo Estill§, Monique Barakat*, Ryan Thomason¶, Bruce F. O’Hara¶, and Steven L. McKnight‡§ §Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390; *Department of Biological Sciences, Stanford University, Stanford, CA 94305; ¶Department of Biology, University of Kentucky, Lexington, KY 40506; and †Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne-Dorigny, Switzerland Contributed by Steven L. McKnight, March 13, 2006 Because the transcription factor neuronal Per-Arnt-Sim-type sig- delta frequency range is a sensitive marker of time spent awake (4, nal-sensor protein-domain protein 2 (NPAS2) acts both as a sensor 7) and local cortical activation (8) and is therefore widely used as and an effector of intracellular energy balance, and because sleep an index of NREMS need and intensity. is thought to correct an energy imbalance incurred during waking, The PAS-domain proteins, CLOCK, BMAL1, PERIOD-1 we examined NPAS2’s role in sleep homeostasis using npas2 (PER1), and PER2, play crucial roles in circadian rhythm gener- knockout (npas2؊/؊) mice. We found that, under conditions of ation (9). The NPAS2 paralog CLOCK, like NPAS2, can induce the increased sleep need, i.e., at the end of the active period or after transcription of per1, per2, cryptochrome-1 (cry1), and cry2. PER and sleep deprivation (SD), NPAS2 allows for sleep to occur at times CRY proteins, in turn, inhibit CLOCK- and NPAS2-induced when mice are normally awake. Lack of npas2 affected electroen- transcription, thereby closing a negative-feedback loop that is cephalogram activity of thalamocortical origin; during non-rapid thought to underlie circadian rhythm generation. -
TWIST1 and TWIST2 Regulate Glycogen Storage and Inflammatory
J M MUDRY and others TWIST regulation of metabolism 224:3 303–313 Research in muscle TWIST1 and TWIST2 regulate glycogen storage and inflammatory genes in skeletal muscle Correspondence 1 1 2 1,2 Jonathan M Mudry , Julie Massart , Ferenc L M Szekeres and Anna Krook should be addressed to A Krook 1Section for Integrative Physiology, Department of Molecular Medicine and Surgery, and 2Section for Integrative Email Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden [email protected] Abstract TWIST proteins are important for development of embryonic skeletal muscle and play a role Key Words in the metabolism of tumor and white adipose tissue. The impact of TWIST on metabolism " TWIST in skeletal muscle is incompletely studied. Our aim was to assess the impact of TWIST1 " metabolism and TWIST2 overexpression on glucose and lipid metabolism. In intact mouse muscle, " glycogen overexpression of Twist reduced total glycogen content without altering glucose uptake. " skeletal muscle Expression of TWIST1 or TWIST2 reduced Pdk4 mRNA, while increasing mRNA levels of Il6, Tnfa, and Il1b. Phosphorylation of AKT was increased and protein abundance of acetyl CoA carboxylase (ACC) was decreased in skeletal muscle overexpressing TWIST1 or TWIST2. Glycogen synthesis and fatty acid oxidation remained stable in C2C12 cells overexpressing TWIST1 or TWIST2. Finally, skeletal muscle mRNA levels remain unaltered in ob/ob mice, type 2 diabetic patients, or in healthy subjects before and after 3 months of exercise training. Journal of Endocrinology Collectively, our results indicate that TWIST1 and TWIST2 are expressed in skeletal muscle. Overexpression of these proteins impacts proteins in metabolic pathways and mRNA level of cytokines. -
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.