Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S12-A-36-AU-L_36-non-M_Contrl-H_WellB2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S12-A-27nonAu-L_Contr-M_27Au-H_WellB2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S05-A-27-AU-L_27-non-M_Contrl-H_WellA4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S05-A-Contr-L_27Au-M_27nonAu-H_WellA4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S34-A-36nonAu-L_Contr-M_36Au-H_WellD6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S29-A-36nonAu-L_Contr-M_36Au-H_WellD1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S22-A-Contr-L_36Au-M_36nonAu-H_WellC3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S13-A-36-AU-L_36-non-M_Contrl-H_WellB3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S15-A-27nonAu-L_Contr-M_27Au-H_WellB5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S31-A-36nonAu-L_Contr-M_36Au-H_WellD3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S04-A-27-AU-L_27-non-M_Contrl-H_WellA3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S20-A-Contr-L_36Au-M_36nonAu-H_WellC1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S13-A-27nonAu-L_Contr-M_27Au-H_WellB3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S25-A-Contr-L_36Au-M_36nonAu-H_WellC6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S04-A-Contr-L_27Au-M_27nonAu-H_WellA3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S14-A-36-AU-L_36-non-M_Contrl-H_WellB4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S32-A-36nonAu-L_Contr-M_36Au-H_WellD4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S03-A-27-AU-L_27-non-M_Contrl-H_WellA2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S14-A-27nonAu-L_Contr-M_27Au-H_WellB4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S21-A-Contr-L_36Au-M_36nonAu-H_WellC2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S15-A-36-AU-L_36-non-M_Contrl-H_WellB5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S33-A-36nonAu-L_Contr-M_36Au-H_WellD5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S02-A-27-AU-L_27-non-M_Contrl-H_WellA1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S03-A-Contr-L_27Au-M_27nonAu-H_WellA2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S24-A-Contr-L_36Au-M_36nonAu-H_WellC5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S07-A-27-AU-L_27-non-M_Contrl-H_WellA6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S16-A-36-AU-L_36-non-M_Contrl-H_WellB6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S11-A-27nonAu-L_Contr-M_27Au-H_WellB1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S11-A-36-AU-L_36-non-M_Contrl-H_WellB1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S06-A-Contr-L_27Au-M_27nonAu-H_WellA5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1001-S06-A-27-AU-L_27-non-M_Contrl-H_WellA5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S07-A-Contr-L_27Au-M_27nonAu-H_WellA6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S30-A-36nonAu-L_Contr-M_36Au-H_WellD2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S23-A-Contr-L_36Au-M_36nonAu-H_WellC4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S16-A-27nonAu-L_Contr-M_27Au-H_WellB6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/HOR1026-S02-A-Contr-L_27Au-M_27nonAu-H_WellA1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD001463/Agcaetal2014_MaxQuantresults.zipprimaryOK200004320Karsten BoldtNot availableRmc-1 CellCell CulturerMC-1 cells were cells were grown in SILAC DMEM (PAA) supplemented with 3 mM L-Glutamine (PAA), 10% dialyzed fetal bovine serum (PAA) and 0.55 mM lysine, 0.4 mM arginine. Light SILAC medium was supplemented with 12C6, 14N2 lysine and 12C6, 14N4 arginine. Heavy SILAC medium was supplemented with either 13C6 lysine and 13C6, 15N4 arginine or 13C6, 15N2 lysine and 13C6, 15N4 arginine. 0.5 mM proline was added to all SILAC media to prevent arginine to proline conversion2. All amino acids were purchased from Silantes. 25 µg of biotin-labelled RNA was bound to Strep-tactin beads (IBA) in RNA binding buffer (150 mM NaCl, 50 mM Hepes-HCl pH 7.5, 0.5% NP40 (v/v), 10 mM MgCl2) and incubated on a rotation wheel at 4°C. Beads were washed three times with RNA wash buffer containing 250 mM NaCl, 50 mM Hepes-HCl pH 7.5, 0.5% NP40 and 10 mM MgCl2 before incubation at 4°C for 30 min with 400 µg of cytoplasmic extract; 40 units RNase inhibitor (Fermentas) and 20 µg salomon sperm RNA. After incubation beads were washed another three times with RNA wash buffer and RNA was eluted from the beads with Strep elution buffer (IBA). The methanol-chloroform precipitated proteins were then subjected to in-gel tryptic cleavage as described elsewhere (Texier et al: PMID: 24563533.PrideDr. Karsten BoldtLTQ Orbitrap VelosPARTIALMedical Proteome Center Eberhard-Karls University of Tuebingen25907681 Agca C, Boldt K, Gubler A, Meneau I, Corpet A, Samardzija M, Stucki M, Ueffing M, Grimm C. Expression of leukemia inhibitory factor in Müller glia cells is regulated by a redox-dependent mRNA stability mechanism. BMC Biol. 2015 Apr 25;13:30 10.1186/s12915-015-0137-1Medical Bioanalyticskarsten.boldt@uni-tuebingen.deAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryShotgun proteomicsBlindnessLtq orbitrap velosMaxquantSilacRna-pulldownhttp://www.ebi.ac.uk/pride/archive/projects/PXD001463SILACiodoacetamide derivatized residuedeamidated residueacetylated residueLC-MS/MS analysis was performed on an Ultimate3000 nano RSLC system (Thermo Fisher Scientific) coupled to a LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific) by a nano spray ion source. Tryptic peptide mixtures were automatically injected and separated by a linear gradient from 5% to 40% of buffer B in buffer A (2% acetonitrile, 0.1% formic acid in HPLC grade water) in buffer A (0.1% formic acid in HPLC grade water) at a flow rate of 300 nl/min over 90 minutes. Remaining peptides were eluted by a short gradient from 40% to 100% buffer B in 5 minutes. The eluted peptides were analyzed by the LTQ Orbitrap Velos mass spectrometer. From the high resolution MS pre-scan with a mass range of 300 to 1500, the ten most intense peptide ions were selected for fragment analysis in the linear ion trap if they exceeded an intensity of at least 500 counts and if they were at least doubly charged. The normalized collision energy for CID was set to a value of 35 and the resulting fragments were detected with normal resolution in the linear ion trap. The lock mass option was activated, the background signal with a mass of 445.12002 was used as lock mass 5. Every ion selected for fragmentation, was excluded for 20 seconds by dynamic exclusion. All acquired spectra were processed and analyzed using the MaxQuant software 6 (version 1.3.0.5) and the human specific IPI database version 3.52 (http://www.maxquant.org/) in combination with Mascot ((Matrix Science, version 2.2). Cysteine carbamidomethylation was selected as fixed modification, methionine oxidation and protein acetylation were allowed as variable modifications. The peptide and protein false discovery rates were set to 1%. Contaminants like keratins were removed. Proteins, identified and quantified by at least two unique peptides were considered for further analysis. The significance values were determined by Perseus tool (part of MaxQuant) using significance A.ProteomicsRattus Norvegicus (rat)karsten.boldt@uni-tuebingen.deBiomedicalGermany<h4>Background</h4>Photoreceptor degeneration is a main hallmark of many blinding diseases making protection of photoreceptors crucial to prevent vision loss. Thus, regulation of endogenous neuroprotective factors may be key for cell survival and attenuation of disease progression. Important neuroprotective factors in the retina include H2O2 generated by injured photoreceptors, and leukemia inhibitory factor (LIF) expressed in Müller glia cells in response to photoreceptor damage.<h4>Results</h4>We present evidence that H2O2 connects to the LIF response by inducing stabilization of Lif transcripts in Müller cells. This process was independent of active gene transcription and p38 MAPK, but relied on AU-rich elements (AREs), which we identified within the highly conserved Lif 3'UTR. Affinity purification combined with quantitative mass spectrometry identified several proteins that bound to these AREs. Among those, interleukin enhancer binding factor 3 (ILF3) was confirmed to participate in the redox-dependent Lif mRNA stabilization. Additionally we show that KH-type splicing regulatory protein (KHSRP) was crucial for maintaining basal Lif expression levels in non-stressed Müller cells.<h4>Conclusions</h4>Our results suggest that H2O2-induced redox signaling increases Lif transcript levels through ILF3 mediated mRNA stabilization. Generation of H2O2 by injured photoreceptors may thus enhance stability of Lif mRNA and therefore augment neuroprotective LIF signaling during degenerative conditions in vivo.Expression of leukemia inhibitory factor in Müller glia cells is regulated by a redox-dependent mRNA stability mechanism.Agca Cavit C, Boldt Karsten K, Gubler Andrea A, Meneau Isabelle I, Corpet Armelle A, Samardzija Marijana M, Stucki Manuel M, Ueffing Marius M, Grimm Christian C432D factor, Emfilermin, Leukemia, Differentiation-Stimulating Factor, Differentiation Factor, D Factor (Leukemia Inhibitory Factor), Myeloid, Cholinergic, neuroglia, emfilermin, Cell, Myeloid Differentiation-Stimulating Factor, Cholinergic Differentiation Factor, LIF, Myeloid Differentiation Stimulating Factor, Differentiation Stimulating Factor, MLPLI, melanoma-derived LPL inhibitor, HILDA, leukemia inhibitory factor receptor ligand, differentiation-stimulating factor, leukemia inhibitory factor, macromolecular stability of mRNA., AM424, Inhibitory FactorMethane, Ribonucleic, vitamin B7, Lysine Hydrochloride, L-arginine, DL-Arginine Acetate, Aminosaeure, classic hairy cell leukaemia, Amino acid, Monohydrate, HEPES Monosodium Salt, Visible Light, Hydrogenchlorid, extracted material, L-(+)-glutamine, trichloro-, aortic arch artery, L-glutamine, Lysine Acetate, halite, L-Glutaminsaeure-5-amid, hydrogen chloride, 5-[(3aS, Magnesium chloride, Biotin, hnu, L-Proline, HCL-C, L-2-aminoglutaramic acid, 2, branchial aortic arches, 6aR)-Hexahydro-2-oxo-1H-thieno[3, Arg, foton, Non Polyadenylated, RNA Gene Products, L Lysine, wood alcohol, X-Chromosome-Bearing Sperm, HEPES Monosodium, sperm cell, (S)-2-amino-5-guanidinopentanoic acid, X-Bearing, amino acids, K, DmelCG13176, (3aS, (S)-2-Amino-5-guanidinovaleric acid, Q, cis-Hexahydro-2-oxo-1H-thieno(3, Salt, R, biotina, epsilon-diaminocaproic acid, Arginine, ORF19, Monohydrate DL-Arginine Acetate, biotine, proteins, BIOTIN, cloruro sodico, salt, Y Chromosome Bearing Sperm, Wasserstoffchlorid, LYS, Hermes, 1-Piperazineethanesulfonic acid, Y-Bearing Sperm, X Chromosome Bearing Sperm, Lysin, Y-Chromosome-Bearing Sperms, Rotations, PAA, biotinum, Sodium Methoxide, gamma, L-Arginin, ejaculate, embryonic aortic arch artery, Medobiotin, Y-Chromosome-Bearing, pharyngeal arch arteries, rock salt, Radiation, Alcohol, Rombellin, ribose nucleic acid, Aminokarbonsaeure, [MgCl2], Sxv, Arginine Hydrochloride, ribonucleic acids, arginine, Light, Streptococcal Infections, classic hairy cell leukemia, alpha-amino carboxylic acids, cleavage., 4S, 4-d)imidazole-4-pentanoic acid, (3aS-(3aalpha, MgCl2, common salt, LIGHT, poly-A RNA binding, Ribonukleinsaeure, lysine, HCL, Chlorwasserstoff, Biotin Ratiopharm, pentosenucleic acids, Ribonucleic acids, 1110049F14Rik, WASH, 4-d)imidazoline-4-valeric acid, leukemic reticuloendotheliosis, Carbinol, D-Biotin, pharyngeal arch artery, carbinol, L-Arginine, Visible Radiations, Clinorotations, Amino Acid, Acid, 1H-Thieno(3, X-Chromosome-Bearing, Visible Radiation, Biotine Roche, HVEML, Amino acids, HCl, DMEM, alpha, (S)-2, natrii chloridum, spermatozoid, RCB2299, X Bearing Sperm, magnesium dichloride, Trichloromethane, L-glutamic acid gamma-amide, Clinorotation, seminal fluid, METHANOL, Wood, light quantum, rotation, spirit of wood, Sperms, branchial arch artery, cis-(+)-Tetrahydro-2-oxothieno[3, Acids, HEPES, chlorane, XR, D-(+)-biotin, Biokur, aortic arch, Methyl Alcohol, a. arcuum pharyngeorum, GLUTAMINE, 4-d]imidazol-4-yl)pentanoic acid, Sperm, Deacura, 5-diamino-5-oxopentanoic acid, chlorure d'hydrogene, Biotine, Aminocarbonsaeure, L Isomer, Medebiotin, Levoglutamide, Gene, high weight, Methyl, CH3OH, alpha-amino acid, Vitamin H, (2S)-2-amino-4-carbamoylbutanoic acid, Y-Chromosome-Bearing Sperm, Methylalkohol, L-(+)-arginine, Ly113, Buffer, (2S)-2-amino-5-(carbamimidamido)pentanoic acid, p63, 4beta, p65, heavy, Gene Products, Spermatozoon, Wood Alcohol, Lysine, light, 6aalpha))-, Gelfert, Y Bearing Sperm, cloruro de hidrogeno, Biotin Hermes, FAM39E, Coenzyme R, poly(A) RNA binding, Hydrogen chloride, (2S)-2, Lichtquant, Monosodium Salt, chlorure de sodium, inhibiteur, X-Bearing Sperms, Visible, methanol, X-Chromosome-Bearing Sperms, Non-Polyadenylated RNA, 4-d]imidazole-4-valeric acid, hairy cell leukemia, inhibidor, sperm, wood naphtha, (+)-cis-Hexahydro-2-oxo-1H-thieno[3, poly(A)-RNA binding, L Proline, Kochsalz, photon, L-Arg, L-Glutamine, N-2-Hydroxyethylpiperazine-N'-2'-ethanesulfonic Acid, SPERM, TR2, base pairing with RNA, 4-(2-hydroxyethyl)-, D-MEM, inhibitors, RNA, X-Bearing Sperm, Magnesiumchlorid, post-anaphase array, Proteins, Roche, inhibitor, Biotin Gelfert, Methyl alcohol, RNS, Syg1, L-2-Aminoglutaramic acid, alpha-amino acids, chloridohydrogen, L-Isomer, DL Arginine Acetate, CD258, 5-(2-oxohexahydro-1H-thieno[3, buffer, Cell, 4]imidazole-4-valeric acid, spermatozoon, Methanol, 6aR)-2-oxohexahydro-1H-thieno[3, [HCl], Wash2, Wash1, cis-Tetrahydro-2-oxothieno(3, 4]imidazoline-4-valeric acid, biotin, Natriumchlorid, L-Isomer Arginine, RMC-1, Acetate, yeast nucleic acid, 4-d]imidazol-4-yl]pentanoic acid, Protein, Hydrochloride, Glutamic acid 5-amide, table salt, Sodium, L Arginine, MeOH, L-Glutamin, NaCl, Rmc-1, L-Lysine, Y-Bearing, Magnesium chloride anhydrous, Biodermatin, CG13176, Radiations, Biotin-Ratiopharm, ribonucleic acid, Gabunat, Glutamic acid amide, HVEM-L, Non Polyadenylated RNA, (2S)-2-amino-5-guanidinopentanoic acid, Photoradiation, hexahydro-2-oxo-, Non-Polyadenylated, N 2 Hydroxyethylpiperazine N' 2' ethanesulfonic Acid, Ribonucleic Acid, Amino, 4)imidazole-4-valeric acid, LTg, arteriae arcuum pharyngeorum, Protein Gene Products, Gene Proteins, Y-Bearing Sperms, Photoradiations, aortic arches, wood spirit, Rmc1, 6-diaminohexanoic acid, Enisyl, hydrochloric acid, Methoxide, sodium chlorideds RNA-Binding, CDF, Ribonucleic, Hunter Carpenter Macdonald syndrome, Differentiation-Stimulating Factor, neurodegeneration, vitamin B7, D Factor (Leukemia Inhibitory Factor), Myeloid, Wound, phospholipase A2-associated neurodegeneration, Physical, inborn disorder, genetic disorder, protein, injury, element, Protoplasm, trauma, mRNA degradation, protein polypeptide chains, genetic condition, Double Stranded RNA Binding Proteins, neurodegeneration with brain iron accumulation caused by mutation in PLA2G6, 5-[(3aS, Biotin, responsivity, 6aR)-Hexahydro-2-oxo-1H-thieno[3, Analysis, protein aggregate, Non Polyadenylated, Research-Related, RNA Gene Products, Inhibitory Factor, RNA Binding Proteins, Mass Spectrum Analysis, Analyses, (3aS, cis-Hexahydro-2-oxo-1H-thieno(3, biotina, mRNA breakdown, proteins, biotine, procedures, BIOTIN, INSDC_feature:ncRNA, DIA, INSDC_qualifier:siRNA, Double-Stranded RNA-Binding Protein, Hermes, LIF, ds RNA-Binding Proteins, biotinum, RNA Binding Protein, AM424, D factor, molecular disease, Medobiotin, hereditary diseases, early onset of peripheral gangrene, Rombellin, small interfering RNA, ribose nucleic acid, neuroaxonal dystrophy, Injury and Wounds, Cytoplasms, ds, ribonucleic acids, Physical Traumas, emfilermin, Double-Stranded, Spectrum Analysis, genetic disease, results, familial disorder, 4S, 4-d)imidazole-4-pentanoic acid, (3aS-(3aalpha, Cholinergic Differentiation Factor, Spectroscopy, infantile neuroaxonal dystrophy/atypical neuroaxonal dystrophy, poly-A RNA binding, Double-Stranded RNA-Binding Proteins, Ribonukleinsaeure, Biotin Ratiopharm, pentosenucleic acids, atomo, Ribonucleic acids, Hunter-Carpenter-McDonald syndrome, Physical Trauma, 4-d)imidazoline-4-valeric acid, atome, Double-Stranded RNA-Binding, region, RNA-Binding Protein, D-Biotin, 1H-Thieno(3, Acid, Element, Biotine Roche, positional polypeptide feature, protein_coding_transcript, Seitelberger disease, RNA-Binding Proteins, Cholinergic, atoms, Spectrometry, hereditary disease, Research-Related Injuries, cis-(+)-Tetrahydro-2-oxothieno[3, Research-Related Injury, D-(+)-biotin, Biokur, INAD1, Research Related Injuries, 4-d]imidazol-4-yl)pentanoic acid, photoreceptor, Deacura, PLA2G6-associated, region or site annotation, inherited genetic disease, PLAN, hereditary disease or disorder, Biotine, Double Stranded RNA Binding Protein, Medebiotin, Gene, PLA2G6 neurodegeneration with brain iron accumulation, Vitamin H, Spectrum Analyses, protein-containing complex, Injuries and Wounds, Differentiation-stimulating factor, Pla2g6-associated, mRNA decay, infantile, Wounds, polypeptide chain, Differentiation Stimulating Factor, A230075M04Rik, 4beta, HILDA, Gene Products, Mass, Cholinergic neuronal differentiation factor, leukemia inhibitory factor receptor ligand, differentiation-stimulating factor, 6aalpha))-, Gelfert, Mass Spectroscopy, reactivity, positional, ds RNA-Binding Protein, Biotin Hermes, Leukemia, Injury, Differentiation Factor, Coenzyme R, poly(A) RNA binding, neurodegeneration with brain iron accumulation 2A, messenger RNA, ds RNA Binding Protein, Pla2G6-associated, Non-Polyadenylated RNA, 4-d]imidazole-4-valeric acid, template RNA, Myeloid Differentiation Stimulating Factor, (+)-cis-Hexahydro-2-oxo-1H-thieno[3, poly(A)-RNA binding, Traumas, melanoma-derived LPL inhibitor, site, elements, inherited disease, base pairing with RNA, atom, RNA, KARAK syndrome, infantile neuroaxonal dystrophy 1, protein complex, degeneration, Proteins, Roche, Biotin Gelfert, RNS, 5-(2-oxohexahydro-1H-thieno[3, AW061234, Cell, 4]imidazole-4-valeric acid, Myeloid Differentiation-Stimulating Factor, mRNA catabolism, 6aR)-2-oxohexahydro-1H-thieno[3, cis-Tetrahydro-2-oxothieno(3, 4]imidazoline-4-valeric acid, biotin, native protein, natural protein, traumatic injury, Wounds and Injury, yeast nucleic acid, Trauma, MLPLI, Protein, 4-d]imidazol-4-yl]pentanoic acid, sequence, INSDC_feature:mRNA, atomus, techniques, Mass Spectrum Analyses, Biodermatin, neurodegeneration with brain iron accumulation type 2a, Emfilermin, Biotin-Ratiopharm, ribonucleic acid, Mass Spectrum, NBIA2A, Gabunat, neuroaxonal dystrophy presenting with neonatal dysmorphic features, mRNA, Protein., Non Polyadenylated RNA, wound, hexahydro-2-oxo-, Non-Polyadenylated, Ribonucleic Acid, 4)imidazole-4-valeric acid, inaD, primary structure of sequence macromolecule, included, Injuries, Protein Gene Products, neurodegeneration with brain iron accumulation type 2A, infantile neuroaxonal dystrophy, Gene Proteins, Protoplasms, Melanoma-derived LPL inhibitor, regulation, response, leukemia inhibitory factor, Mendelian disease, methodologyprojections, CDF, Differentiation-Stimulating Factor, D Factor (Leukemia Inhibitory Factor), Myeloid, H2O2, Oxydol, A4, via spliceosome, HYDROGEN PEROXIDE, D-p38, Viabilities, dihydrogen dioxide, MAGE-E1 antigen, element, blindness, diseases, responsivity, CG9063, bacterial-type proximal promoter sequence-specific DNA binding, Dp38, diseases and disorders, Analysis, Mpk34C, IKKg, Viability, bacterial-type cis-regulatory region sequence-specific DNA binding, KEY, Key, Inhibitory Factor, p38B, Progression, Mass Spectrum Analysis, perhydrol, Fubp2, human disease, Analyses, tunica interna of eyeball, present in organism, proteins, Dm p38b, BcDNA:GH03694, DIA, NFAR-1, LIF, HCA1, Dmp38b, papilla, signaling process, Exacerbation, core promoter proximal region DNA binding, Homo sapiens disease, FUBP2, bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding, DmelCG9063, AM424, ESTS:186F5S, single organism signaling, D factor, anatomical protrusion, NF-AT-90, Disease Exacerbation, lamina, flanges, emfilermin, vision impairment, inner layer of eyeball, Spectrum Analysis, INSDC_feature:misc_RNA, results, Cholinergic Differentiation Factor, D-p38b, Spectroscopy, DmIKKgamma, dIKK, DAMAGE, Hepatocellular carcinoma-associated protein 1, Diseases, Kenny, shelf, atomo, atome, ilf3, Hydrogen peroxide, Interleukin, TCP80, Element, protein_coding_transcript, dioxidane, Cholinergic, shelves, BcDNAGH03694, atoms, IKK-gamma, Spectrometry, promoter proximal region sequence-specific DNA binding, neuroglia, p38, projection, ridge, 3L6, disease, MPP4, bacterial-type RNA polymerase enhancer sequence-specific DNA binding, DMDA, DmelCG16910, rich, spine, NF90, enhancer sequence-specific DNA binding, 186F5S, MPHOSPH4, mMage-e1, bis(hydridooxygen)(O--O), HOOH, NF110b, D-p38 MAPK, NFAR2, other disease, biological signaling, photoreceptor, nuclear mRNA cis splicing, lamellae, CG7393, CBTF, number, Gene, Spectrum Analyses, NF90b, NF90a, splicing, process of organ, presence, dIKK-gamma, TYPE, Differentiation-stimulating factor, protrusion, DAGA4, lamella, dp38b, ubp3, ubp4, Differentiation Stimulating Factor, DmIKK-gamma, Survival, p38 MAPK, A230075M04Rik, Clinical Progression, HILDA, Mass, Gene Products, disease or disorder, Cholinergic neuronal differentiation factor, NF110, dmIKKgamma, leukemia inhibitory factor receptor ligand, bacterial-type RNA polymerase upstream activating sequence (UAS) sequence-specific DNA binding, differentiation-stimulating factor, IKK[[gamma]], MAM, SCG3, Mass Spectroscopy, Netzhaut, p38beta, reactivity, Leukemia, Clinical, Differentiation Factor, retinas, retina of camera-type eye, p38Kb, messenger RNA, eubacterial-type RNA polymerase regulatory transcription factor sequence-specific DNA binding, cbtf122, ridges, dihydrogen peroxide, AI847422, non-neoplastic, via U2-type spliceosome, template RNA, IKK, Clinical Course, Myeloid Differentiation Stimulating Factor, [OH(OH)], Ora Serrata, melanoma-derived LPL inhibitor, disorder, DRBF, core promoter proximal region sequence-specific DNA binding, proximal promoter sequence-specific DNA binding, elements, laminae, vision loss, atom, Dp38b, signalling., TCP110, Disease, KSRP, degeneration, anatomical process, dihydrogen(peroxide), Alpha-dystrobrevin-associated MAGE Protein, Proteins, disorders, anon-sts23, cis-regulatory region binding, enhancer binding, medical condition, DRBP76, Marta1, MBII-26, Cell, AW061234, DmelCG7393, Myeloid Differentiation-Stimulating Factor, LGMD2C, MMP4, Cell Viabilities, IKKgamma, count in organism, xilf3, hydrogen peroxide, MLPLI, Protein, INSDC_feature:mRNA, condition, atomus, background, p38 beta, 6330409F21Rik, flange, Mass Spectrum Analyses, organ process, FBP2, Fbp2, Emfilermin, Mass Spectrum, DMDA1, mRNA, RGD1560259, Dmikkgamma, NFAR, 4F.1, visual impairment, CG16910, introduction, signalling, Protein Gene Products, processes, process, Gene Proteins, Ksrp, signalling process, ilf3-A, SCARMD2, Melanoma-derived LPL inhibitor, processus, regulation, BG:DS00797.3, response, quantitative, Cell Viability, leukemia inhibitory factor, presence or absence in organismliquid chromatography tandem mass spectroscopy, sodium salt, l(4)17, CPD photolyase activity, l(4)13, IPP2A2, ammonium formate, Gli, 13C-labeled, MeCN, cadmium salt, NCMe, PhrB photolyase activity, ion, determination, Cid[Mel], Ci[D], zinc formate, Keratin-Associated Proteins, lead salt, magnesium formate, protein, combined T cell and B cell immunodeficiency, pigmented epithelium, zinc salt, CENP-A, CENP-C, 5730420M11Rik, peptide, Polypeptides, L-Isomer Methionine, protein polypeptide chains, ammonium tetraformate, Methionine, ClvPrd, peptido, cobalt(II) formate dihydrate, CH3-C#N, Keratin Associated, Min, 3, NUP96, Software Engineering, outer pigmented layer of retina, Gpi-1, protein aggregate, epithelium, WMS, Computer Program, DmelCG42273, C79691, CG13329, average, SET, Divorced, BcDNA:RE21270, F, LCMSMS, peptides, TAF-I, Nlk, M, phosphatase 2A inhibitor I2PP2A, Open, pigmented retina, min, Computer Programs and Programming, chemical analysis., mAPC, Divorces, proteins, copper, SCAN, Keratin Associated Proteins, DNA cyclobutane dipyrimidine photolyase activity, HPLC, alpha-Keratin, SUPPRESSOR OF AUXIN RESISTANCE 3, AI047805, DmelCG4299, Lccp, set, IGAAD, pigment epithelium of retina, lithium salt, CI, DmelCG10574, n, Cenp-A, pigmented retina epithelium, Half Cystine, GPHYSD2, Racemethionine, ammonium (2:1) salt, nickel salt, SGS, CiD, NK/GPI, LC-MS2, phapii, Gpi, PRE, Ce, Ci, cobalt (+2) salt, Zinc Cysteinate, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, LC-MS/MS, 2-Amino-4-(methylthio)butyric acid, Keratin, Dmel_CG7826, StF-IT-1, Normalcy, pigmented retinal epithelium, not genetically inherited, collisionally activated dissociation, Source Softwares, CID, ciD, Cid, Software Tools, ACMICD, Programs, shortened, Program, Computer Applications, sodium (4:1:1) salt, mOC-X, magnesium salt, Dm1, retinal pigment, Ionen, Computer Applications Software, Computer Applications Softwares, dipyrimidine photolyase (photosensitive), ci-D, Methionin, NK|GPI, methionine, Softwares, Hmet, nickel (+2) salt, retinal pigment layer, Dmel_CG7835, Hydrogen Oxide, cenpA, Mnb, MNB, ammonium salt, ORG, Org, Software Applications, HLA-DR-associated protein II, Ci/Gli, Ci/GLI, CenH3/CID, CENP-A/Cid, CENP-A/CID, DI-2, retinal pigmented epithelium, CENPA, Source Software, I-2Dm, formate, cobaltous formate, Gpi1-r, cromium (+3), Gpi1-s, MASCOT, L-Cysteine, MASS, CG4299, inhibitor of granzyme A-activated DNase, AW124434, Gpi1-t, human, alpha Keratin, organ system, congenital combined immunodeficiency, I-2PP1, phr A photolyase activity, Applications, Health, DNA-photoreactivating enzyme, TAF-IBETA, liquid chromatography-tandem mass spectroscopy, copper salt, ammonium (4:1) salt, TAF-Ibeta, Polypeptide, methyl cyanide, lead (+2) salt, short, i2pp2a, Liquimeth, Ci-155, Bglap-rs1, Gpi1s, Computer Software Applications, Cytokeratin, human being, Cysteine Hydrochloride, 2-amino-4-(methylsulfanyl)butanoic acid, nickel formate dihydrate, lead formate, AI461847, AW549739, False, aluminum salt, cesium salt, L Isomer, FBN, Gene, Computer, photoreactivating enzyme activity, protein-containing complex, body system, combined T and B cell immunodeficiency, CG7826, deoxyribodipyrimidine photolyase activity, PHAPII, LC-MS-MS, stratum pigmentosum retinae, Buffer, formic acid, CenpA, l(4)102ABc, potassium salt, template-activating factor I, polypeptide chain, ECTOL1, 14C-labeled, LC-MSMS, CG7835, Gene Products, CG42273, L-Methionine, system, Pgi, stratum pigmentosa retinae, Half-Cystine, Keratin Associated Protein, Separated, Siah, Pedameth, Application, CenH3[Cid], CenH3[CID], Normalities, Open Source Softwares, anatomical systems, MOS3, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, PRECOCIOUS, thallium (+1) salt, Gpi-1r, iones, Software Application, Gpi-1s, L Cysteine, protein amino acid acetylation, ipp2a2, Phi, rubidium salt, Gpi-1t, stubby, F23A5.3, DmelCG13329, Open Source Software, 2pp2a, Sciences, calcium formate, methanoic acid, ions, man, CG10574, Computer Software Application, OCTD, X-linked combined immunodeficiency, mKIAA0989, 2PP2A, 2-amino-4-(methylthio)butanoic acid, Tools, taf-ibeta, dSET, dSet, CG2125, peptidos, cromium (+3) salt, Associated Protein, metionina, sodium formate, F23A5_3, combined immunodeficiency, Applications Software, Open Source, DYRK1, Computer Software, 1-(14)C-labeled, nickel formate, 3H-labeled, DL-Methionine, protein complex, Proteins, igaad, strontium formate, cenH3, potassium formate, copper (+2) salt, MF, acetonitrile, strontium salt, L-Isomer, buffer, Amf, Peptide, Tool, polypeptide, stratum pigmentosum (retina), LC/MS/MS, MODIFIER OF SNC1, Software Tool, CAD, native protein, natural protein, ci[D], I-2PP2A, Ci155, cupric formate, chemical analysis, Dm I-2, Protein, deoxyribonucleic photolyase activity, I2PP2A, MFS1, Dyrk1, background, connected anatomical system, aluminum formate, Software, ACETONITRILE, cyanomethane, WMS2, NK, Met, AU020952, Separation, 10^[-9], lithium formate, RPE, DmelCG2125, ci155, CenH3, photolyase activity, Normality, Separations, CC1, Engineering, ethanenitrile, retinal pigment epithelium, chromic formate, introduction, ME-IV, p. pigmentosa retinae, Protein Gene Products, Computer Programs, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, Applications Softwares, Ion, SSKS, calcium salt, alpha-amino-gamma-methylmercaptobutyric acid, liquid chromatography tandem mass spectrometry, Peptid, deoxyribonucleate pyrimidine dimer lyase (photosensitive), assay, variable, AA407739, CenpA/CID, CID/CENP-AD factor, Emfilermin, ds RNA-Binding, ds RNA-Binding Protein, CDF, Element, RNA-Binding Proteins, ds, Double Stranded RNA Binding Protein, atoms, Differentiation-stimulating factor., emfilermin, Double-Stranded, AW061234, DIA, ds RNA Binding Protein, element, Double-Stranded RNA-Binding Protein, Double Stranded RNA Binding Proteins, LIF, ds RNA-Binding Proteins, Double-Stranded RNA-Binding Proteins, Protein, A230075M04Rik, MLPLI, melanoma-derived LPL inhibitor, HILDA, Melanoma-derived LPL inhibitor, atomo, atomus, Cholinergic neuronal differentiation factor, elements, differentiation-stimulating factor, RNA Binding Protein, atome, Double-Stranded RNA-Binding, atom, RNA-Binding Protein, RNA Binding ProteinstrueIdentification of RNA binding proteins that interact with AU-rich elements of Lif 3`UTRLeukemia inhibitory factor (LIF) is an important endogenous factor for photoreceptor protection. Lif is known to be upregulated both in induced and inherited disease models of photoreceptor degeneration only in a subset of Muller cells. Since Lif is induced in Muller cells in response to photoreceptor injury, we studied its regulation in Muller cells. We have recently identified several AU-rich elements (AREs) within the 3′ untranslated region (UTR) of Lif . We also showed that as a result of these elements Lif encodes a highly unstable mRNA. mRNAs containing AREs in the 3`UTR undergo rapid ARE-mediated mRNA decay in the cytoplasm which is mediated by the RNA–binding proteins. In order to identify the RNA-binding proteins that are involved in the regulation of Lif transcripts, we will use the biotin-labelled RNA. By using this methodology, we will isolate the related RNA binding proteins. We plan to analyze the isolated proteins by mass spectrometry, and compare the mass spectrometry results of different regions with or without AREs . Once we identify the specific proteins that bind only to AREs, we will do the functional characterization of these proteins by cotransfecting the constructs with AREs and the siRNA that inhibits the expression of related RNA binding protein.2016-07-202016-07-20PXD00146328065516460991804982953585111454224942024527872842188090368093270429330845811363336351524260119834300662758385NCBITaxon:128068888561896111430118726355557114526236493461364031952065126957366649274670738538836411354615821582310665688954762721123294422291180992323122586365458333460792519365914320597129386558195851149315242592637371250232NCBITaxon:127211195774818661488584310430024513586722175543740816918045426683429531945305861266835149822505814963674452158554528113208147956410039237514636942049433208964208963445974137979138712728384400667453293529367156759388036478434716052165994048321659721659545501315282693042165915627161696833218321729204277944762376454317203094980197525556978159509439843948840479NCBITaxon:21575253381053551531051067439899037122857759515205968762262311210884555588845587077918178081736309431794571698936160488409859NCBITaxon:3716210478267940150590714836432042106132049138169363035554320466326333119945651110245351102541110321745921612926420128867641002642036945694101676341021076127735152486713165823925472793342814613584301417298760917463345774449167547604893212873567568403013506219172651813019411192943936711041131023932025559863258278839659104759347495109716049016529983552566317585439801102432608663102459808757417555183201964471452680457966313670190832331156114155355104219325552113834397634981812359871069955529NCBITaxon:4751850298335476113615741465477180066556484337677144137929976798251021699823897641400820840741400821137351155711089725482444474153NCBITaxon:5055789969844100036465349334147147493548019467512991143597412764731370863265478765658936398353221595893669838192011106775772710348198523487802655544794640986099586157187176685991915729513722117110129292107687834974198602028091488406334249234235152335985988655913249746499870392021110727113994331136352721598741908503711708271170828418235024145113969293190219782247463604614712374940237593972328758172253256648905079452659600131972211915853101774208588596NCBITaxon:615750521028307989515586411051989972375059576131720002634196102641088878176179212190659407121906772275885815689964975151950582873757244NCBITaxon:22023717NCBITaxon:17036122019998570506050617476792745062724915961533355418400524643213686150596487844612286662941786661347515363291018194301086731018510184NCBITaxon:176357303963558633149286287670580132165085271848461051865368595105135553482260710185687294296110091416333NCBITaxon:619184023210007348824123363630710470058127187878645159812894555663577553470951451225786425011449447260704NCBITaxon:133562626070526070765845740541636774831672331502951803561007133705654195NCBITaxon:305550445791399878168119011928752829126806315327341478281055524NCBITaxon:9606135858469008111167815022830519302836728593008529005NCBITaxon:5693826883064017946991510118499435258759131515901448242838111394422584416041937047592721204414370860423281677285035158199011951953267386370137024924053608838581622488186156227748817562615835583715333760572671193501998086119350216787910857913711371272407190650371475917262981288057125627457572709030903113335503728142433747924910078711082NCBITaxon:96157243359463318586260799141262200298492670NCBITaxon:12637192812492125283038568385695911692661006581373523756127504542666255151978813566383750644223360094129349790546322453524721401257515115199764990851515143899237453747445446415243235937605920222887051580595536555088157932716029385157811497863389229382894535936479437509173NCBITaxon:685441275422511775299159010901341673871589552101296610306129671585158451584937659393432715910022637673388990461423451287689591198332966467041464792936576164280341160221641331599280382803536909108917688149894621812141080348179392287889295027113133295282829445686174934681911265269972273218903821076012471904007273915215973699782811431140206411981087135547743658142450722953379698204232124223129163218033470871453720916457332153581575469928777020206032811431933829355083329129221148643745725264999728303573908718308726727103790855071762997076789268370415573729214053651388294128160783956392431426265489822737756115596207322086595882735551693605330797255181135491432137159749535026115955614321384060725878141447335215094933491949634016143347280059360463164610466038151845474485001561972356709747777195124017484185560133575554792042741580536076994688103762014887100594120037582890931643542826885007123038399001389464940838283538283494144242322197857742171598921409212205853939621157781154756929793244704749906604162103591905158114452749907312987779913112273170187546991103589915NCBITaxon:3729610360983341871049113079813367953164072994671034015786582645303337330638301130641399253064236365059116965478854698112116203431765261610337286129940445862073401153571119529652611745531114716133865413131663430552132312017983602532373127612552329935129938505731631764261979401151345844577267872862321933415134618620862116079139222798351681196125522814953932232311676175731225024091080772134879999488618569628140843410335177879963218496209948873213924882097115338209611533920953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