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YBX1 and Its Interactors Derived from Unihi, Metamatched and TRRUST Databases

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Supplementary 1: YBX1 and its Interactors derived from UniHi, Metamatched and TRRUST databases. Gene_Id Description ABCB1|5243 ATP binding cassette subfamily B member 1 ACTB|60 actin beta AFF4|27125 AF4/FMR2 family member 4 AGT|183 angiotensinogen AKT1|207 AKT serine/threonine kinase 1 AMOTL1|154810 angiomotin like 1 ANAPC4|29945 anaphase promoting complex subunit 4 ANKRD2|26287 ankyrin repeat domain 2 APBB1|322 amyloid beta precursor protein binding family B member 1 APEX1|328 apurinic/apyrimidinic endodeoxyribonuclease 1 AR|367 androgen receptor ARID1A|8289 AT-rich interaction domain 1A ARRB1|408 arrestin beta 1 ARRB2|409 arrestin beta 2 ATF1|466 activating transcription factor 1 ATF2|1386 activating transcription factor 2 ATP6V1E1|529 ATPase H+ transporting V1 subunit E1 BARD1|580 BRCA1 associated RING domain 1 BCL6|604 B-cell CLL/lymphoma 6 BRCA1|672 BRCA1, DNA repair associated C19orf2|8725 URI1, prefoldin like chaperone C1QBP|708 complement C1q binding protein carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and CAD|790 dihydroorotase CALM1|801 calmodulin 1 CAND1|55832 cullin associated and neddylation dissociated 1 CBX8|57332 chromobox 8 CCAR1|55749 cell division cycle and apoptosis regulator 1 CCDC40|55036 coiled-coil domain containing 40 CCNB1|891 cyclin B1 CCNC|892 cyclin C CD2BP2|10421 CD2 cytoplasmic tail binding protein 2 CDC20|991 cell division cycle 20 CDH1|999 cadherin 1 CDK9|1025 cyclin dependent kinase 9 CDKN3|1033 cyclin dependent kinase inhibitor 3 CHD1|1105 chromodomain helicase DNA binding protein 1 CHTF18|63922 chromosome transmission fidelity factor 18 CKS2|1164 CDC28 protein kinase regulatory subunit 2 CLP1|10978 cleavage and polyadenylation factor I subunit 1 CMYA5|202333 cardiomyopathy associated 5 COBRA1|25920 negative elongation factor complex member B COPS5|10987 COP9 signalosome subunit 5 CPSF1|29894 cleavage and polyadenylation specific factor 1 CPSF2|53981 cleavage and polyadenylation specific factor 2 CPSF3|51692 cleavage and polyadenylation specific factor 3 CPSF6|11052 cleavage and polyadenylation specific factor 6 CPSF7|79869 cleavage and polyadenylation specific factor 7 CREB1|1385 cAMP responsive element binding protein 1 CSAD|51380 cysteine sulfinic acid decarboxylase CSDA|8531 Y-box binding protein 3 CSNK2A1|1457 casein kinase 2 alpha 1 CSTF1|1477 cleavage stimulation factor subunit 1 CSTF2|1478 cleavage stimulation factor subunit 2 CSTF3|1479 cleavage stimulation factor subunit 3 CTCF|10664 CCCTC-binding factor CUL1|8454 cullin 1 CUL2|8453 cullin 2 CUL3|8452 cullin 3 CUL4B|8450 cullin 4B CXCR4|7852 C-X-C motif chemokine receptor 4 DDX1|1653 DEAD-box helicase 1 DDX23|9416 DEAD-box helicase 23 DDX3X|1654 DEAD-box helicase 3, X-linked DHX30|22907 DExH-box helicase 30 DHX38|9785 DEAH-box helicase 38 DHX9|1660 DExH-box helicase 9 DIAPH1|1729 diaphanous related formin 1 DIMT1L|27292 DIM1 dimethyladenosine transferase 1 homolog DMXL1|1657 Dmx like 1 DNAJC8|22826 DnaJ heat shock protein family (Hsp40) member C8 DNMT1|1786 DNA methyltransferase 1 DYNC1H1|1778 dynein cytoplasmic 1 heavy chain 1 DYNC1I2|1781 dynein cytoplasmic 1 intermediate chain 2 DYNC1LI2|1783 dynein cytoplasmic 1 light intermediate chain 2 E2F1|1869 E2F transcription factor 1 EEF1A1|1915 eukaryotic translation elongation factor 1 alpha 1 EFTUD2|9343 elongation factor Tu GTP binding domain containing 2 EGFR|1956 epidermal growth factor receptor EGR1|1958 early growth response 1 EIF2B2|8892 eukaryotic translation initiation factor 2B subunit beta EIF2C1|26523 argonaute 1, RISC catalytic component EIF2C4|192670 argonaute 4, RISC catalytic component EIF2S1|1965 eukaryotic translation initiation factor 2 subunit alpha EIF3K|27335 eukaryotic translation initiation factor 3 subunit K EIF4A3|9775 eukaryotic translation initiation factor 4A3 ELK1|2002 ELK1, ETS transcription factor EP300|2033 E1A binding protein p300 EPRS|2058 glutamyl-prolyl-tRNA synthetase ERBB2|2064 erb-b2 receptor tyrosine kinase 2 ERBB3|2065 erb-b2 receptor tyrosine kinase 3 ESR1|2099 estrogen receptor 1 ETS1|2113 ETS proto-oncogene 1, transcription factor ETV4|2118 ETS variant 4 EWSR1|2130 EWS RNA binding protein 1 EZH2|2146 enhancer of zeste 2 polycomb repressive complex 2 subunit FAS|355 Fas cell surface death receptor FBXO33|254170 F-box protein 33 FKBP3|2287 FK506 binding protein 3 FLOT1|10211 flotillin 1 FMR1|2332 fragile X mental retardation 1 FN1|2335 fibronectin 1 FOXM1|2305 forkhead box M1 FUS|2521 FUS RNA binding protein G3BP1|10146 G3BP stress granule assembly factor 1 GATA3|2625 GATA binding protein 3 GATA4|2626 GATA binding protein 4 GIGYF2|26058 GRB10 interacting GYF protein 2 GIPC1|10755 GIPC PDZ domain containing family member 1 GRINL1A|81488 RNA polymerase II subunit M GSK3B|2932 glycogen synthase kinase 3 beta GTF2F1|2962 general transcription factor IIF subunit 1 GTF2F2|2963 general transcription factor IIF subunit 2 GZF1|64412 GDNF inducible zinc finger protein 1 HABP4|22927 hyaluronan binding protein 4 HDAC1|3065 histone deacetylase 1 HDAC2|3066 histone deacetylase 2 HDAC3|8841 histone deacetylase 3 HDGF|3068 heparin binding growth factor HIF1A|3091 hypoxia inducible factor 1 alpha subunit HIST1H1C|3006 histone cluster 1 H1 family member c HLA-C|3107 major histocompatibility complex, class I, C HNF4A|3172 hepatocyte nuclear factor 4 alpha HNRNPA0|10949 heterogeneous nuclear ribonucleoprotein A0 HNRNPA1|3178 heterogeneous nuclear ribonucleoprotein A1 HNRNPA2B1|318 1 heterogeneous nuclear ribonucleoprotein A2/B1 HNRNPA3|220988 heterogeneous nuclear ribonucleoprotein A3 HNRNPAB|3182 heterogeneous nuclear ribonucleoprotein A/B HNRNPC|3183 heterogeneous nuclear ribonucleoprotein C (C1/C2) HNRNPD|3184 heterogeneous nuclear ribonucleoprotein D HNRNPF|3185 heterogeneous nuclear ribonucleoprotein F HNRNPH1|3187 heterogeneous nuclear ribonucleoprotein H1 HNRNPH2|3188 heterogeneous nuclear ribonucleoprotein H2 HNRNPK|3190 heterogeneous nuclear ribonucleoprotein K HNRNPL|3191 heterogeneous nuclear ribonucleoprotein L HNRNPM|4670 heterogeneous nuclear ribonucleoprotein M HNRNPR|10236 heterogeneous nuclear ribonucleoprotein R HNRNPU|3192 heterogeneous nuclear ribonucleoprotein U HNRNPUL1|1110 0 heterogeneous nuclear ribonucleoprotein U like 1 HOXB7|3217 homeobox B7 HSPA1A|3303 heat shock protein family A (Hsp70) member 1A HSPA2|3306 heat shock protein family A (Hsp70) member 2 HSPA5|3309 heat shock protein family A (Hsp70) member 5 IFIT1|3434 interferon induced protein with tetratricopeptide repeats 1 IFIT2|3433 interferon induced protein with tetratricopeptide repeats 2 IFIT3|3437 interferon induced protein with tetratricopeptide repeats 3 IL7R|3575 interleukin 7 receptor ILF2|3608 interleukin enhancer binding factor 2 IQCB1|9657 IQ motif containing B1 IREB2|3658 iron responsive element binding protein 2 IRF1|3659 interferon regulatory factor 1 IRS1|3667 insulin receptor substrate 1 ITGA4|3676 integrin subunit alpha 4 JAM2|58494 junctional adhesion molecule 2 JUN|3725 Jun proto-oncogene, AP-1 transcription factor subunit KHDRBS2|202559 KH RNA binding domain containing, signal transduction associated 2 KIAA0101|9768 PCNA clamp associated factor KLF4|9314 Kruppel like factor 4 KLF5|688 Kruppel like factor 5 KPNA2|3838 karyopherin subunit alpha 2 LARP1|23367 La ribonucleoprotein domain family member 1 LCP2|3937 lymphocyte cytosolic protein 2 LMAN1|3998 lectin, mannose binding 1 LSM2 homolog, U6 small nuclear RNA and mRNA degradation LSM2|57819 associated LSM3 homolog, U6 small nuclear RNA and mRNA degradation LSM3|27258 associated MAGOH|4116 mago homolog, exon junction complex core component MAP2|4133 microtubule associated protein 2 MAP3K14|9020 mitogen-activated protein kinase kinase kinase 14 MAPK1|5594 mitogen-activated protein kinase 1 MAPK13|5603 mitogen-activated protein kinase 13 MCCC2|64087 methylcrotonoyl-CoA carboxylase 2 MECP2|4204 methyl-CpG binding protein 2 MED6|10001 mediator complex subunit 6 MEPCE|56257 methylphosphate capping enzyme MET|4233 MET proto-oncogene, receptor tyrosine kinase METAP2|10988 methionyl aminopeptidase 2 MMP13|4322 matrix metallopeptidase 13 MMP2|4313 matrix metallopeptidase 2 MNAT1|4331 MNAT1, CDK activating kinase assembly factor MTA1|9112 metastasis associated 1 MVP|9961 major vault protein MYC|4609 MYC proto-oncogene, bHLH transcription factor MYCN|4613 MYCN proto-oncogene, bHLH transcription factor NAP1L1|4673 nucleosome assembly protein 1 like 1 NAT10|55226 N-acetyltransferase 10 NCBP1|4686 nuclear cap binding protein subunit 1 NCBP2|22916 nuclear cap binding protein subunit 2 NCOR2|9612 nuclear receptor corepressor 2 neural precursor cell expressed, developmentally down-regulated 4, E3 NEDD4|4734 ubiquitin protein ligase NEDD8|4738 neural precursor cell expressed, developmentally down-regulated 8 NFKB1|4790 nuclear factor kappa B subunit 1 NFX1|4799 nuclear transcription factor, X-box binding 1 NFYA|4800 nuclear transcription factor Y subunit alpha NFYB|4801 nuclear transcription factor Y subunit beta NFYC|4802 nuclear transcription factor Y subunit gamma NHP2L1|4809 SNU13 homolog, small nuclear ribonucleoprotein (U4/U6.U5) NMT1|4836 N-myristoyltransferase 1 NOP56|10528 NOP56 ribonucleoprotein NOS2|4843 nitric oxide synthase 2 NPM1|4869 nucleophosmin NR4A1|3164 nuclear receptor subfamily 4 group A member 1 NUDT21|11051 nudix hydrolase 21 PA2G4|5036 proliferation-associated 2G4 PABPN1|8106 poly(A) binding protein nuclear 1 PAN2|9924 PAN2 poly(A) specific ribonuclease subunit PAPOLA|10914 poly(A) polymerase alpha PARP1|142 poly(ADP-ribose) polymerase 1 PAX3|5077 paired box 3 PAX5|5079 paired
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    ab207227 Sp1/Sp3 Transcription Factor Assay Kit (Colorimetric) Instructions for use: For quantitative measurement of Sp1/Sp3 Activation in human, mouse and rat nuclear extracts. This product is for research use only and is not intended for diagnostic use. Version 2 Last Updated 24 August 2017 Table of Contents INTRODUCTION 1 1. BACKGROUND 1 2. ASSAY SUMMARY 3 GENERAL INFORMATION 4 3. PRECAUTIONS 4 4. STORAGE AND STABILITY 4 5. LIMITATIONS 5 6. MATERIALS SUPPLIED 5 7. MATERIALS REQUIRED, NOT SUPPLIED 6 8. TECHNICAL HINTS 7 ASSAY PREPARATION 8 9. REAGENT PREPARATION 8 10. SAMPLE PREPARATION 14 ASSAY PROCEDURE 16 11. ASSAY PROCEDURE 16 DATA ANALYSIS 18 12. TYPICAL DATA 18 RESOURCES 19 13. QUICK ASSAY PROCEDURE 19 14. TROUBLESHOOTING 20 15. INTERFERENCES 21 16. NOTES 22 INTRODUCTION INTRODUCTION 1. BACKGROUND Sp1/Sp3 Transcription Factor Assay Kit (Colorimetric) (ab207227) is a high throughput assay to quantify Sp1/Sp3 activation. This assay combines a quick ELISA format with a sensitive and specific non- radioactive assay for transcription factor activation. A specific double stranded DNA sequence containing the Sp1/Sp3 consensus binding site (5’ – GGGGCGGGG – 3’) has been immobilized onto a 96-well plate. Active Sp1/Sp3 present in the nuclear extract specifically binds to the oligonucleotide. Sp1/Sp3 is detected by a primary antibody that recognizes an epitope of Sp1/Sp3 accessible only when the protein is activated and bound to its target DNA. An HRP- conjugated secondary antibody provides sensitive colorimetric readout at OD 450 nm. This product detects human, mouse and rat Sp1/Sp3. Key performance and benefits: Assay time: 3.5 hours (cell extracts preparation not included).
  • Mrna Editing, Processing and Quality Control in Caenorhabditis Elegans

    Mrna Editing, Processing and Quality Control in Caenorhabditis Elegans

    | WORMBOOK mRNA Editing, Processing and Quality Control in Caenorhabditis elegans Joshua A. Arribere,*,1 Hidehito Kuroyanagi,†,1 and Heather A. Hundley‡,1 *Department of MCD Biology, UC Santa Cruz, California 95064, †Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, and ‡Medical Sciences Program, Indiana University School of Medicine-Bloomington, Indiana 47405 ABSTRACT While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in Caenorhabditis elegans, with a focus on those that occur on protein-coding genes after transcription initiation. In addition, we will describe the genetic and technical approaches that have allowed studies in C. elegans to reveal important mechanistic insight into these processes. KEYWORDS Caenorhabditis elegans; splicing; RNA editing; RNA modification; polyadenylation; quality control; WormBook TABLE OF CONTENTS Abstract 531 RNA Editing and Modification 533 Adenosine-to-inosine RNA editing 533 The C. elegans A-to-I editing machinery 534 RNA editing in space and time 535 ADARs regulate the levels and fates of endogenous dsRNA 537 Are other modifications present in C.