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List of 1124 Genes Whose Binding to Eif4e Was Induced by Radiation

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Supplemental Table S1: List of 1124 genes whose binding to eIF4E was induced by radiation Fold Increase Gene Symbol Gene Description 1.5 AP4M1 adaptor-related protein 2.2 ABCA11 ATP-binding cassette, complex 4, mu 1 subunit sub-family A (ABC1), 1.7 APBB1 amyloid beta (A4) member 11 precursor protein- (pseudogene) binding, family B, 3.1 ABHD4 abhydrolase domain member 1 (Fe65) containing 4 2 APLP2 amyloid beta (A4) 1.9 ABHD6 abhydrolase domain precursor-like protein 2 containing 6 1.5 APOL3 apolipoprotein L, 3 1.5 ABT1 activator of basal 1.5 APTX aprataxin transcription 1 2.9 ARF3 ADP-ribosylation factor 1.8 ACAD8 acyl-Coenzyme A 3 dehydrogenase family, 1.5 ARL6IP5 ADP-ribosylation-like member 8 factor 6 interacting 1.8 ACAT1 acetyl-Coenzyme A protein 5 acetyltransferase 1 10.8 ARPC2 actin related protein 2/3 (acetoacetyl Coenzyme complex, subunit 2, A thiolase) 34kDa 1.7 ACOT7 acyl-CoA thioesterase 7 1.5 ARRB2 arrestin, beta 2 1.5 ACOT9 acyl-CoA thioesterase 9 1.8 ASB13 ankyrin repeat and 1.6 ACTR5 ARP5 actin-related SOCS box-containing 13 protein 5 homolog 11.2 ASCIZ ATM/ATR-Substrate (yeast) Chk2-Interacting Zn2+- 3 ADCK2 aarF domain containing finger protein kinase 2 2.3 ATP1B3 ATPase, Na+/K+ 1.8 ADPGK ADP-dependent transporting, beta 3 glucokinase polypeptide 2.4 ADSL adenylosuccinate lyase 1.7 ATP5B ATP synthase, H+ 2.2 AGPAT2 1-acylglycerol-3- transporting, phosphate O- mitochondrial F1 acyltransferase 2 complex, beta (lysophosphatidic acid polypeptide acyltransferase, beta) 1.6 ATP5C1 ATP synthase, H+ 1.5 AIM1L absent in melanoma 1- transporting, like mitochondrial F1 1.5 AKR1C2 aldo-keto reductase complex, gamma family 1, member C2 polypeptide 1 (dihydrodiol 1.5 ATP5L ATP synthase, H+ dehydrogenase 2; bile transporting, acid binding protein; 3- mitochondrial F0 alpha hydroxysteroid complex, subunit g dehydrogenase, type III) 2 ATP6V0E ATPase, H+ 1.8 AKR7A2 aldo-keto reductase transporting, lysosomal family 7, member A2 9kDa, V0 subunit e (aflatoxin aldehyde 1.6 ATP6V1D ATPase, H+ reductase) transporting, lysosomal 4.1 ALKBH alkB, alkylation repair 34kDa, V1 subunit D homolog (E. coli) 1.8 ATP8A2 ATPase, 1.9 AMFR autocrine motility factor aminophospholipid receptor transporter-like, Class I, 1.7 ANAPC5 anaphase promoting type 8A, member 2 complex subunit 5 1.8 ATPAF2 ATP synthase 1.8 ANKRD40 ankyrin repeat domain mitochondrial F1 40 complex assembly factor 4.5 ANXA11 annexin A11 2 1 2.2 B4GALT4 UDP-Gal:betaGlcNAc 7.4 C1orf163 chromosome 1 open beta 1,4- reading frame 163 galactosyltransferase, 1.7 C1orf174 chromosome 1 open polypeptide 4 reading frame 174 8.6 BBP Beta-amyloid binding 1.8 C1orf33 chromosome 1 open protein precursor reading frame 33 2.1 BBS4 Bardet-Biedl syndrome 4 4.8 C20orf111 chromosome 20 open 1.7 BCAT1 branched chain reading frame 111 aminotransferase 1, 1.7 C20orf24 chromosome 20 open cytosolic reading frame 24 2.6 BCL10 B-cell CLL/lymphoma 3 C20orf29 chromosome 20 open 10 reading frame 29 4.7 BCL2L11 BCL2-like 11 (apoptosis 5.3 C20orf44 chromosome 20 open facilitator) reading frame 44 3.5 BIRC5 baculoviral IAP repeat- 3.8 C20orf45 chromosome 20 open containing 5 (survivin) reading frame 45 2.1 BMPR1A bone morphogenetic 3 C21orf91 chromosome 21 open protein receptor, type IA reading frame 91 1.7 BNIP2 BCL2/adenovirus E1B 4.8 C2orf43 chromosome 2 open 19kDa interacting reading frame 43 protein 2 1.5 C3orf18 chromosome 3 open 1.9 BNIP3 BCL2/adenovirus E1B reading frame 18 19kDa interacting 1.7 C3orf37 chromosome 3 open protein 3 reading frame 37 1.7 BRE brain and reproductive 1.8 C5orf30 chromosome 5 open organ-expressed reading frame 30 (TNFRSF1A modulator) 3.7 C6orf106 chromosome 6 open 2.3 BTG1 B-cell translocation gene reading frame 106 1, anti-proliferative 4 C6orf49 chromosome 6 open 1.6 C10orf57 chromosome 10 open reading frame 49 reading frame 57 1.8 C6orf82 chromosome 6 open 2.7 C10orf61 chromosome 10 open reading frame 82 reading frame 61 1.6 C7orf26 chromosome 7 open 2 C10orf97 chromosome 10 open reading frame 26 reading frame 97 10 C8orf30A chromosome 8 open 1.7 C11orf24 chromosome 11 open reading frame 30A reading frame 24 3 C9orf78 chromosome 9 open 4.8 C12orf41 chromosome 12 open reading frame 78 reading frame 41 5.4 C9orf82 chromosome 9 open 1.6 C12orf49 chromosome 12 open reading frame 82 reading frame 49 4.1 CABIN1 calcineurin binding 1.6 C12orf52 chromosome 12 open protein 1 reading frame 52 6.1 CALM1 calmodulin 1 1.7 C14orf138 chromosome 14 open (phosphorylase kinase, reading frame 138 delta) 1.5 C14orf172 chromosome 14 open 4.3 CAMLG calcium modulating reading frame 172 ligand 1.5 C16orf45 chromosome 16 open 2.3 CAMTA2 calmodulin binding reading frame 45 transcription activator 2 1.7 C16orf58 chromosome 16 open 4.7 CASP3 caspase 3, apoptosis- reading frame 58 related cysteine 1.6 C17orf39 chromosome 17 open peptidase reading frame 39 1.8 CASP9 caspase 9, apoptosis- 1.8 C19orf2 chromosome 19 open related cysteine reading frame 2 peptidase 1.5 C19orf50 chromosome 19 open 1.5 CAV2 caveolin 2 reading frame 50 2.2 CCDC132 coiled-coil domain 8.2 C1orf144 chromosome 1 open containing 132 reading frame 144 3.9 CCNA1 cyclin A1 2 1.7 CCNA2 cyclin A2 channel 4 1.6 CCNB1IP1 cyclin B1 interacting 2 CLINT1 clathrin interactor 1 protein 1 1.5 CLN5 ceroid-lipofuscinosis, 2.5 CCNE2 cyclin E2 neuronal 5 1.9 CCS copper chaperone for 1.7 CLTA clathrin, light superoxide dismutase polypeptide (Lca) 3 CD164 CD164 antigen, 7.5 CNGA1 cyclic nucleotide gated sialomucin channel alpha 1 1.7 CD59 CD59 antigen p18-20 2.3 CNIH3 cornichon homolog 3 (antigen identified by (Drosophila) monoclonal antibodies 1.9 CNKSR1 connector enhancer of 16.3A5, EJ16, EJ30, kinase suppressor of Ras EL32 and G344) 1 4.3 CD63 CD63 antigen 5.5 CNP 2',3'-cyclic nucleotide 3' (melanoma 1 antigen) phosphodiesterase 1.6 CDC2 cell division cycle 2, G1 9.9 COG2 component of oligomeric to S and G2 to M golgi complex 2 4.9 CDC25C cell division cycle 25C 1.7 COPS2 COP9 constitutive 2.2 CDC42EP2 CDC42 effector protein photomorphogenic (Rho GTPase binding) 2 homolog subunit 2 1.6 CDCA4 cell division cycle (Arabidopsis) associated 4 6.1 COPS7B COP9 constitutive 1.7 CDKL3 cyclin-dependent kinase- photomorphogenic like 3 homolog subunit 7B 1.9 CDKN1A cyclin-dependent kinase (Arabidopsis) inhibitor 1A (p21, Cip1) 1.5 COPS8 COP9 constitutive photomorphogenic 1.7 CDKN2C cyclin-dependent kinase homolog subunit 8 inhibitor 2C (p18, (Arabidopsis) inhibits CDK4) 1.9 COQ2 coenzyme Q2 homolog, 1.5 CDKN3 cyclin-dependent kinase prenyltransferase (yeast) inhibitor 3 (CDK2- associated dual 1.8 COTL1 coactosin-like 1 specificity phosphatase) (Dictyostelium) 2.3 CDYL chromodomain protein, 3.5 COX11 COX11 homolog, Y-like cytochrome c oxidase 2 CENPB centromere protein B, assembly protein (yeast) 80kDa 1.5 COX7A2 cytochrome c oxidase 3.2 CENPO centromere protein O subunit VIIa polypeptide 2 (liver) 6.1 CEP57 centrosomal protein 1.8 COX7B cytochrome c oxidase 57kDa subunit VIIb 1.5 CEPT1 choline/ethanolamine 1.5 CREB1 cAMP responsive phosphotransferase 1 element binding protein 2.3 CHCHD7 coiled-coil-helix-coiled- 1 coil-helix domain 2.3 CREG1 cellular repressor of containing 7 E1A-stimulated genes 1 7.6 CHEK1 CHK1 checkpoint 2.1 CRELD1 cysteine-rich with EGF- homolog (S. pombe) like domains 1 3.1 CHST10 carbohydrate 15.7 CRI1 CREBBP/EP300 sulfotransferase 10 inhibitor 1 1.8 CIDEC cell death-inducing 1.5 CSNK1A1 casein kinase 1, alpha 1 DFFA-like effector c 1.6 CINP cyclin-dependent kinase 6.2 CTBP2 C-terminal binding 2-interacting protein protein 2 2.2 CIR CBF1 interacting 4.4 CTDSP1 CTD (carboxy-terminal corepressor domain, RNA 3.1 CLIC1 chloride intracellular polymerase II, channel 1 polypeptide A) small 5.5 CLIC4 chloride intracellular phosphatase 1 3 2.5 CTDSP2 CTD (carboxy-terminal 2.1 DNAJB12 DnaJ (Hsp40) homolog, domain, RNA subfamily B, member 12 polymerase II, 1.7 DNAJB9 DnaJ (Hsp40) homolog, polypeptide A) small subfamily B, member 9 phosphatase 2 2.1 DNAJC17 DnaJ (Hsp40) homolog, 1.7 CTDSPL CTD (carboxy-terminal subfamily C, member 17 domain, RNA 2 DNAJC8 DnaJ (Hsp40) homolog, polymerase II, subfamily C, member 8 polypeptide A) small 1.9 DNAJC9 DnaJ (Hsp40) homolog, phosphatase-like subfamily C, member 9 2.4 CTGLF1 centaurin, gamma-like 4.7 DR1 down-regulator of family, member 1 transcription 1, TBP- 6.5 CTH cystathionase binding (negative (cystathionine gamma- cofactor 2) lyase) 2.5 DSTN destrin (actin 1.7 CTSB cathepsin B depolymerizing factor) 1.8 CTSS cathepsin S 4.4 DTX2 deltex homolog 2 (Drosophila) 1.9 CXorf12 chromosome X open 1.8 DUSP1 dual specificity reading frame 12 phosphatase 1 3.9 CXorf15 chromosome X open 1.5 DYNLL1 dynein, light chain, LC8- reading frame 15 type 1 5.5 CYB5B cytochrome b5 type B 1.8 DYNLT1 dynein, light chain, (outer mitochondrial Tctex-type 1 membrane) 1.7 DYNLT3 dynein, light chain, 2.5 CYB5R3 cytochrome b5 reductase Tctex-type 3 3 7.1 E2F6 E2F transcription factor 4.3 DBT dihydrolipoamide 6 branched chain 1.6 EBAG9 estrogen receptor transacylase E2 binding site associated, 24.9 DCLRE1B DNA cross-link repair antigen, 9 1B (PSO2 homolog, S. 3.9 EEF1B2 eukaryotic translation cerevisiae) elongation factor 1 beta 1.6 DCTD dCMP deaminase 2 2.2 DCTN4 dynactin 4 (p62) 1.5 EFCAB2 EF-hand calcium 2.9 DCTN5 dynactin 5 (p25) binding domain 2 165.8 EFEMP2 EGF-containing fibulin- 1.6 DDX19A DEAD (Asp-Glu-Ala- like extracellular matrix As) box polypeptide 19A protein 2 1.6 DDX28 DEAD (Asp-Glu-Ala- 3.2 EFNA4 ephrin-A4 Asp) box polypeptide 28 3.1 DDX50 DEAD (Asp-Glu-Ala- 1.8 EGFL9 EGF-like-domain, Asp) box polypeptide
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    AP-4 mediates export of ATG9A from the trans-Golgi PNAS PLUS network to promote autophagosome formation Rafael Matteraa,1, Sang Yoon Parka,1, Raffaella De Pacea, Carlos M. Guardiaa, and Juan S. Bonifacinoa,2 aCell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892 Edited by Pietro De Camilli, Howard Hughes Medical Institute and Yale University, New Haven, CT, and approved November 6, 2017 (received for review October 2, 2017) AP-4 is a member of the heterotetrameric adaptor protein (AP) mediated by a noncanonical YRYRF sequence in the receptor- complex family involved in protein sorting in the endomembrane associated, transmembrane AMPA receptor regulatory proteins system of eukaryotic cells. Interest in AP-4 has recently risen with (TARPs) (17). Finally, in the δ2 glutamate receptor protein, the discovery that mutations in any of its four subunits cause a binding to μ4 depends on several phenylalanine residues in a form of hereditary spastic paraplegia (HSP) with intellectual noncanonical context (18). disability. The critical sorting events mediated by AP-4 and the Interest in AP-4 has recently risen because of the discovery of pathogenesis of AP-4 deficiency, however, remain poorly under- mutations in genes encoding each of the subunits of AP-4 in stood. Here we report the identification of ATG9A, the only a subset of autosomal recessive hereditary spastic paraplegias multispanning membrane component of the core autophagy ma- (HSPs), namely, SPG47 (AP4B1/β4), SPG50 (AP4M1/μ4), SPG51 chinery, as a specific AP-4 cargo. AP-4 promotes signal-mediated (AP4E1/e), and SPG52 (AP4S1/σ4) (19–21).
  • Spatial Protein Interaction Networks of the Intrinsically Disordered Transcription Factor C(%3$

    Spatial Protein Interaction Networks of the Intrinsically Disordered Transcription Factor C(%3$

    Spatial protein interaction networks of the intrinsically disordered transcription factor C(%3$ Dissertation zur Erlangung des akademischen Grades Doctor rerum naturalium (Dr. rer. nat.) im Fach Biologie/Molekularbiologie eingereicht an der Lebenswissenschaftlichen Fakultät der Humboldt-Universität zu Berlin Von Evelyn Ramberger, M.Sc. Präsidentin der Humboldt-Universität zu Berlin Prof. Dr.-Ing.Dr. Sabine Kunst Dekan der Lebenswissenschaftlichen Fakultät der Humboldt-Universität zu Berlin Prof. Dr. Bernhard Grimm Gutachter: 1. Prof. Dr. Achim Leutz 2. Prof. Dr. Matthias Selbach 3. Prof. Dr. Gunnar Dittmar Tag der mündlichen Prüfung: 12.8.2020 For T. Table of Contents Selbstständigkeitserklärung ....................................................................................1 List of Figures ............................................................................................................2 List of Tables ..............................................................................................................3 Abbreviations .............................................................................................................4 Zusammenfassung ....................................................................................................6 Summary ....................................................................................................................7 1. Introduction ............................................................................................................8 1.1. Disordered proteins
  • The Mammalian Adult Neurogenesis Gene Ontology (MANGO) Provides a Structural Framework for Published Information on Genes Regulating Adult Hippocampal Neurogenesis

    The Mammalian Adult Neurogenesis Gene Ontology (MANGO) Provides a Structural Framework for Published Information on Genes Regulating Adult Hippocampal Neurogenesis

    The Mammalian Adult Neurogenesis Gene Ontology (MANGO) Provides a Structural Framework for Published Information on Genes Regulating Adult Hippocampal Neurogenesis Rupert W. Overall1, Maciej Paszkowski-Rogacz2, Gerd Kempermann1,3* 1 CRTD – Center for Regenerative Therapies Dresden, Technische Universita¨t Dresden, Dresden, Germany, 2 UCC – University Cancer Center, Medical Faculty, Technische Universita¨t Dresden, Dresden, Germany, 3 DZNE, German Center for Neurodegenerative Diseases, Dresden, Germany Abstract Background: Adult hippocampal neurogenesis is not a single phenotype, but consists of a number of sub-processes, each of which is under complex genetic control. Interpretation of gene expression studies using existing resources often does not lead to results that address the interrelatedness of these processes. Formal structure, such as provided by ontologies, is essential in any field for comprehensive interpretation of existing knowledge but, until now, such a structure has been lacking for adult neurogenesis. Methodology/Principal Findings: We have created a resource with three components 1. A structured ontology describing the key stages in the development of adult hippocampal neural stem cells into functional granule cell neurons. 2. A comprehensive survey of the literature to annotate the results of all published reports on gene function in adult hippocampal neurogenesis (257 manuscripts covering 228 genes) to the appropriate terms in our ontology. 3. An easy-to- use searchable interface to the resulting database made freely available online. The manuscript presents an overview of the database highlighting global trends such as the current bias towards research on early proliferative stages, and an example gene set enrichment analysis. A limitation of the resource is the current scope of the literature which, however, is growing by around 100 publications per year.