Regulation of Translation and the Unfolded Protein Response in Pituitary Gonadotropes
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Molecular Genetic Analysis of Two Loci (Ity2 and Ity3) Involved in The
Copyright Ó 2007 by the Genetics Society of America DOI: 10.1534/genetics.107.075523 Molecular Genetic Analysis of Two Loci (Ity2 and Ity3) Involved in the Host Response to Infection With Salmonella Typhimurium Using Congenic Mice and Expression Profiling Vanessa Sancho-Shimizu,*,† Rabia Khan,*,† Serge Mostowy,† Line Larivie`re,† Rosalie Wilkinson,† Noe´mie Riendeau,† Marcel Behr† and Danielle Malo*,†,‡,1 *Department of Human Genetics, McGill University, Montreal, Quebec H3G 1A4, Canada and †Center for the Study of Host Resistance, McGill University Health Center, Montreal, Quebec H3G 1A4, Canada and ‡Department of Medicine, McGill University, Montreal, Quebec H3G 1A4, Canada Manuscript received May 4, 2007 Accepted for publication July 27, 2007 ABSTRACT Numerous genes have been identified to date that contribute to the host response to systemic Sal- monella Typhimurium infection in mice. We have previously identified two loci, Ity2 and Ity3, that control survival to Salmonella infection in the wild-derived inbred MOLF/Ei mouse using a (C57BL/6J 3 MOLF/ Ei)F2cross. We validated the existence of these two loci by creating congenic mice carrying each quan- titative trait locus (QTL) in isolation. Subcongenic mice generated for each locus allowed us to define the critical intervals underlying Ity2 and Ity3. Furthermore, expression profiling was carried out with the aim of identifying differentially expressed genes within the critical intervals as potential candidate genes. Genomewide expression arrays were used to interrogate expression differences in the Ity2 congenics, leading to the identification of a new candidate gene (Havcr2, hepatitis A virus cellular receptor 2). Interval-specific oligonucleotide arrays were created for Ity3, identifying one potential candidate gene (Chi3l1, chitinase 3-like 1) to be pursued further. -
Genetic Screens in Isogenic Mammalian Cell Lines Without Single Cell Cloning
ARTICLE https://doi.org/10.1038/s41467-020-14620-6 OPEN Genetic screens in isogenic mammalian cell lines without single cell cloning Peter C. DeWeirdt1,2, Annabel K. Sangree1,2, Ruth E. Hanna1,2, Kendall R. Sanson1,2, Mudra Hegde 1, Christine Strand 1, Nicole S. Persky1 & John G. Doench 1* Isogenic pairs of cell lines, which differ by a single genetic modification, are powerful tools for understanding gene function. Generating such pairs of mammalian cells, however, is labor- 1234567890():,; intensive, time-consuming, and, in some cell types, essentially impossible. Here, we present an approach to create isogenic pairs of cells that avoids single cell cloning, and screen these pairs with genome-wide CRISPR-Cas9 libraries to generate genetic interaction maps. We query the anti-apoptotic genes BCL2L1 and MCL1, and the DNA damage repair gene PARP1, identifying both expected and uncharacterized buffering and synthetic lethal interactions. Additionally, we compare acute CRISPR-based knockout, single cell clones, and small- molecule inhibition. We observe that, while the approaches provide largely overlapping information, differences emerge, highlighting an important consideration when employing genetic screens to identify and characterize potential drug targets. We anticipate that this methodology will be broadly useful to comprehensively study gene function across many contexts. 1 Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA. 2These authors contributed equally: Peter C. DeWeirdt, -
Recent Advances of M6a Methylation Modification in Esophageal Squamous Cell Carcinoma
Zhang et al. Cancer Cell Int (2021) 21:421 https://doi.org/10.1186/s12935-021-02132-2 Cancer Cell International REVIEW Open Access Recent advances of m6A methylation modifcation in esophageal squamous cell carcinoma Xiaoqing Zhang1†, Ning Lu1†, Li Wang2†, Yixuan Wang1, Minna Li1, Ying Zhou3, Manli Cui1*, Mingxin Zhang1,3* and Lingmin Zhang4* Abstract In recent years, with the development of RNA sequencing technology and bioinformatics methods, the epigenetic modifcation of RNA based on N6-methyladenosine (m6A) has gradually become a research hotspot in the feld of bioscience. m6A is the most abundant internal modifcation in eukaryotic messenger RNAs (mRNAs). m6A methylation modifcation can dynamically and reversibly regulate RNA transport, localization, translation and degradation through the interaction of methyltransferase, demethylase and reading protein. m6A methylation can regulate the expression of proto-oncogenes and tumor suppressor genes at the epigenetic modifcation level to afect tumor occurrence and metastasis. The morbidity and mortality of esophageal cancer (EC) are still high worldwide. Esophageal squamous cell carcinoma (ESCC) is the most common tissue subtype of EC. This article reviews the related concepts, biological functions and recent advances of m6A methylation in ESCC, and looks forward to the prospect of m6A methylation as a new diagnostic biomarker and potential therapeutic target for ESCC. Keywords: N6-methyladenosine, Methylation, Esophageal squamous cell carcinoma Introduction surgical resection, combined radiotherapy and chemo- Esophageal cancer (EC) is one of the most invasive malig- therapy have improved the prognosis of patients with nant tumors of digestive tract in the world, and its mor- ESCC, the 5-year overall survival rate is still very low [5], bidity and mortality are still high in China [1]. -
Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
FLRT Proteins Are Endogenous Latrophilin Ligands and Regulate Excitatory Synapse Development
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Neuron Report FLRT Proteins Are Endogenous Latrophilin Ligands and Regulate Excitatory Synapse Development Matthew L. O’Sullivan,1,5 Joris de Wit,1,5 Jeffrey N. Savas,2 Davide Comoletti,3 Stefanie Otto-Hitt,1,6 John R. Yates III,2 and Anirvan Ghosh1,4,* 1Neurobiology Section, Division of Biology, University of California San Diego, La Jolla, CA 92093, USA 2Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA 3Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, UMDNJ/Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA 4CNS Discovery, F. Hoffmann-La Roche, 4070 Basel, Switzerland 5These authors contributed equally to this work 6Present address: Department of Natural Sciences, Carroll College, Helena, MT 59625, USA *Correspondence: [email protected] DOI 10.1016/j.neuron.2012.01.018 SUMMARY much effort has been expended investigating the mechanisms of a-latrotoxin action (Su¨ dhof, 2001), nothing is known about Latrophilins (LPHNs) are a small family of G protein- the endogenous function of latrophilins in vertebrates. Further coupled receptors known to mediate the massive evidence for the importance of latrophilins in the proper synaptic exocytosis caused by the black widow functioning of neural circuits comes from recent human spider venom a-latrotoxin, but their endogenous genetics studies that have linked LPHN3 mutations to attention ligands and function remain unclear. Mutations in deficit hyperactivity disorder (ADHD), a common and highly LPHN3 are strongly associated with attention deficit heritable developmental psychiatric disorder (Arcos-Burgos et al., 2010; Domene´ et al., 2011; Jain et al., 2011; Ribase´ s hyperactivity disorder, suggesting a role for latrophi- et al., 2011). -
Edinburgh Research Explorer
Edinburgh Research Explorer International Union of Basic and Clinical Pharmacology. LXXXVIII. G protein-coupled receptor list Citation for published version: Davenport, AP, Alexander, SPH, Sharman, JL, Pawson, AJ, Benson, HE, Monaghan, AE, Liew, WC, Mpamhanga, CP, Bonner, TI, Neubig, RR, Pin, JP, Spedding, M & Harmar, AJ 2013, 'International Union of Basic and Clinical Pharmacology. LXXXVIII. G protein-coupled receptor list: recommendations for new pairings with cognate ligands', Pharmacological reviews, vol. 65, no. 3, pp. 967-86. https://doi.org/10.1124/pr.112.007179 Digital Object Identifier (DOI): 10.1124/pr.112.007179 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Pharmacological reviews Publisher Rights Statement: U.S. Government work not protected by U.S. copyright General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 02. Oct. 2021 1521-0081/65/3/967–986$25.00 http://dx.doi.org/10.1124/pr.112.007179 PHARMACOLOGICAL REVIEWS Pharmacol Rev 65:967–986, July 2013 U.S. -
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. -
A Helicase-Independent Activity of Eif4a in Promoting Mrna Recruitment to the Human Ribosome
A helicase-independent activity of eIF4A in promoting mRNA recruitment to the human ribosome Masaaki Sokabea and Christopher S. Frasera,1 aDepartment of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616 Edited by Alan G. Hinnebusch, National Institutes of Health, Bethesda, MD, and approved May 5, 2017 (received for review December 12, 2016) In the scanning model of translation initiation, the decoding site and at the solvent side of the mRNA entry channel (14). Importantly, latch of the 40S subunit must open to allow the recruitment and that study showed that a short mRNA that does not extend into the migration of messenger RNA (mRNA); however, the precise molec- entry channel fails to displace eIF3j. A similar observation was also ular details for how initiation factors regulate mRNA accommodation found for initiation mediated by the hepatitis C virus internal ribo- into the decoding site have not yet been elucidated. Eukaryotic some entry site, where an mRNA truncated after the initiation co- initiation factor (eIF) 3j is a subunit of eIF3 that binds to the mRNA don failed to displace eIF3j (11). Taken together, these studies entry channel and A-site of the 40S subunit. Previous studies have suggest a model in which a full accommodation of mRNA in the shown that a reduced affinity of eIF3j for the 43S preinitiation mRNA entry channel of the 40S subunit corresponds to a reduced complex (PIC) occurs on eIF4F-dependent mRNA recruitment. Because affinity of eIF3j for the 40S subunit. This model has allowed us to eIF3j and mRNA bind anticooperatively to the 43S PIC, reduced eIF3j exploit the change in eIF3j affinity for the 43S PIC to quantitatively affinity likely reflects a state of full accommodation of mRNA into the monitor the process of mRNA recruitment. -
Ten Commandments for a Good Scientist
Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds Ana María Sotoca Covaleda Wageningen 2010 Thesis committee Thesis supervisors Prof. dr. ir. Ivonne M.C.M. Rietjens Professor of Toxicology Wageningen University Prof. dr. Albertinka J. Murk Personal chair at the sub-department of Toxicology Wageningen University Thesis co-supervisor Dr. ir. Jacques J.M. Vervoort Associate professor at the Laboratory of Biochemistry Wageningen University Other members Prof. dr. Michael R. Muller, Wageningen University Prof. dr. ir. Huub F.J. Savelkoul, Wageningen University Prof. dr. Everardus J. van Zoelen, Radboud University Nijmegen Dr. ir. Toine F.H. Bovee, RIKILT, Wageningen This research was conducted under the auspices of the Graduate School VLAG Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds Ana María Sotoca Covaleda Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Tuesday 14 September 2010 at 4 p.m. in the Aula Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds. Ana María Sotoca Covaleda Thesis Wageningen University, Wageningen, The Netherlands, 2010, With references, and with summary in Dutch. ISBN: 978-90-8585-707-5 “Caminante no hay camino, se hace camino al andar. Al andar se hace camino, y al volver la vista atrás se ve la senda que nunca se ha de volver a pisar” - Antonio Machado – A mi madre. -
Initiation Factor Eif5b Catalyzes Second GTP-Dependent Step in Eukaryotic Translation Initiation
Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation Joon H. Lee*†, Tatyana V. Pestova†‡§, Byung-Sik Shin*, Chune Cao*, Sang K. Choi*, and Thomas E. Dever*¶ *Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2716; ‡Department of Microbiology and Immunology, State University of New York Health Science Center, Brooklyn, NY 11203; and §A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia Edited by Harry F. Noller, University of California, Santa Cruz, CA, and approved October 31, 2002 (received for review September 19, 2002) Initiation factors IF2 in bacteria and eIF2 in eukaryotes are GTPases In addition, when nonhydrolyzable GDPNP was substituted Met that bind Met-tRNAi to the small ribosomal subunit. eIF5B, the for GTP, eIF5B catalyzed subunit joining; however, the factor eukaryotic ortholog of IF2, is a GTPase that promotes ribosomal was unable to dissociate from the 80S ribosome after subunit subunit joining. Here we show that eIF5B GTPase activity is re- joining (7). quired for protein synthesis. Mutation of the conserved Asp-759 in To dissect the function of the eIF5B G domain and test the human eIF5B GTP-binding domain to Asn converts eIF5B to an model that two GTP molecules are required in translation XTPase and introduces an XTP requirement for subunit joining and initiation, we mutated conserved residues in the eIF5B G translation initiation. Thus, in contrast to bacteria where the single domain and tested the function of the mutant proteins in GTPase IF2 is sufficient to catalyze translation initiation, eukaryotic translation initiation. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Ss-TEA: Entropy Based Identification of Receptor Specific Ligand Binding
Sanders et al. BMC Bioinformatics 2011, 12:332 http://www.biomedcentral.com/1471-2105/12/332 RESEARCHARTICLE Open Access ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs Marijn PA Sanders1, Wilco WM Fleuren1, Stefan Verhoeven2, Sven van den Beld1, Wynand Alkema2, Jacob de Vlieg1,2 and Jan PG Klomp2* Abstract Background: G-protein coupled receptors (GPCRs) are involved in many different physiological processes and their function can be modulated by small molecules which bind in the transmembrane (TM) domain. Because of their structural and sequence conservation, the TM domains are often used in bioinformatics approaches to first create a multiple sequence alignment (MSA) and subsequently identify ligand binding positions. So far methods have been developed to predict the common ligand binding residue positions for class A GPCRs. Results: Here we present 1) ss-TEA, a method to identify specific ligand binding residue positions for any receptor, predicated on high quality sequence information. 2) The largest MSA of class A non olfactory GPCRs in the public domain consisting of 13324 sequences covering most of the species homologues of the human set of GPCRs. A set of ligand binding residue positions extracted from literature of 10 different receptors shows that our method has the best ligand binding residue prediction for 9 of these 10 receptors compared to another state-of-the-art method. Conclusions: The combination of the large multi species alignment and the newly introduced residue selection method ss-TEA can be used to rapidly identify subfamily specific ligand binding residues.