{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/v01/MSV000080920/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"submitter":["Laurence Florens"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=062e30bb29d8471c9a398ff5a4f42294"],"submitter_email":["laf@stowers.org"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["142"],"ptm_modification":["MOD:01060 - \"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\""],"data_protocol":[""],"omics_type":["Proteomics"],"instrument_platform":["LTQ"],"species":["Mus Musculus (ncbitaxon:10090)"],"submitter_affiliation":["The Stowers Institute for Medical Research"],"pubmed_abstract":["Bilateral symmetry is a striking feature of the vertebrate body plan organization. Vertebral precursors, called somites, provide one of the best illustrations of embryonic symmetry. Maintenance of somitogenesis symmetry requires retinoic acid (RA) and its coactivator Rere/Atrophin2. Here, using a proteomic approach we identify a protein complex, containing Wdr5, Hdac1, Hdac2 and Rere (named WHHERE), which regulates RA signaling and controls embryonic symmetry. We demonstrate that Wdr5, Hdac1, and Hdac2 are required for RA signaling in vitro and in vivo. Mouse mutants for Wdr5 and Hdac1 exhibit asymmetrical somite formation characteristic of RA-deficiency. We also identify the Rere-binding histone methyltransferase Ehmt2/G9a, as a RA coactivator controlling somite symmetry. Upon RA treatment, WHHERE and Ehmt2 become enriched at RA target genes to promote RNA polymerase II recruitment. Our work identifies a protein complex linking key epigenetic regulators acting in the molecular control of embryonic bilateral symmetry.Retinoic acid (RA) regulates the maintenance of somitogenesis symmetry. Here, the authors use a proteomic approach to identify a protein complex of Wdr5, Hdac1, Hdac2 that act together with RA and coactivator Rere/Atrophin2 and a histone methyltransferase Ehmt2 to regulate embryonic symmetry."],"pubmed_title":["The WHHERE coactivator complex is required for retinoic acid-dependent regulation of embryonic symmetry."],"pubmed_authors":["Vilhais-Neto Gonçalo C GC, Fournier Marjorie M, Plassat Jean-Luc JL, Sardiu Mihaela E ME, Saraf Anita A, Garnier Jean-Marie JM, Maruhashi Mitsuji M, Florens Laurence L, Washburn Michael P MP, Pourquié Olivier O"],"pubmed_abstract_synonyms":["Hunter Carpenter Macdonald syndrome, dmBest1, epimere, Materials, 2410041A17Rik, Laboratory, Refissa, Hdac1-ps, Non-Governmental Organizations, fs(1)M34, House Mouse, DmelCG6264, CFAP89, prevention, DmelCG7471, DmelCG12051, Embryonic., neurodegeneration with brain iron accumulation caused by mutation in PLA2G6, INAD, DHDAC1, D17Ertd710e, HEL-176, CG4601, 3, 4, 6, dRPD3, epimere mesoderm, dRpd3, hdac1, treatment, A, C, cyt5C, DHO, anabolism, Salt, CG18572, Epigenomic, DNA Dependent RNA Polymerase II, Histone H5, Histone H4, Histone H7, ACT, Act, Organizations, Vitamin A Acid, (2E, Histone H1, single organism signaling, Histone H3, eye-lt-m03Jus-gt-, preventive therapy, DmelCG17437, early onset of peripheral gangrene, Actin/BAP47, CTE-II, AACT, CTE-IIa, act, Ach1, hBACH, ACH1, zw8, rpd[3], GAT8, act42A, KMT1C, GIG25, DmIKKgamma, Biacna, Su(b), Retin A, dIKK, AFFX-Dros-ACTIN_M_r_at, GIG24, actin, all-trans-Retinoic, LACH, TU15B, Acid, AA408785, tretinoina, drpd3, DmelCG4027, whole organism, Seitelberger disease, Nongovernmental, administrative structure, dbest1, Swiss Mouse, IKK-gamma, beta-all-trans-Retinoic Acid, tretinoinum, xwdr5, Big, Zinc Salt, Sodium Salt, 7-dimethyl-9-(2, actin5C, all-(E)-retinoic acid, Material, Koerper, Mouse, Phospholipase A2-associated neurodegeneration, Epigenetics, tretinoine, BACH, INAD1, l(1)Ab, Act5c, dHDAC-1, somitus, ACT5C, organization and administration, PLA2G6 neurodegeneration with brain iron accumulation, biosynthesis, 8E-tetraenoic acid, protein-containing complex, Bach, dIKK-gamma, infantile, RPD3L1, DmIKK-gamma, Mus musculus domesticus, Cell growth-inhibiting gene 24|25 protein, Retin-A, Stieva-A, Histone H3.3, BIG-3, Organization, GON-10, Methyltransferase, VMD2, ligand, BRWS2, Renova, dHDAC1, Big-3, BMD, l(3)04556, synthesis, fs(1)829, anon-EST:fe2D2, Altreno, Non-Governmental Organization, DmelCG18572, T11, Act-5C, trans-Retinoic, RP50, 42A, swd3, CPS, organizational structure, body, Atr2, zw-8, dJ393D12.2, whole body, Hdac1, Tretinoin Potassium, WDR5, YAF1, Histone, Tri-luma, Tretinoin, IKKgamma, Tretinoin Sodium, wdr5, MommeD5, beta-actin, G9A, M32055, Act42, Nongovernmental Organizations, Acide retinoique (French), Embryonic, beta-Retinoic acid, macromolecular complex, HDAC1, best, Dmikkgamma, prophylaxis, PYR1, G9a, protein containing complex, Tretinoin Zinc, House Mice, eyes3, Ng36, CG16910, Histone H1(s), included, Yy1bp, signalling process, control, vitamin A acid, RNA Polymerase B, DRORUD, rpd3l1, SWD3, DmHDAC1, BAP47, DNA-Dependent RNA Polymerase II, ACTSG, NG36, Nongovernmental Organization, BEST, Bap47, protein-protein complex, 1110033A15Rik, Tretin M, ACTG, ACTE, Mus domesticus, protein, DNB1, mesodermal cluster, csp2, Act5, l(1)G0420, Retinoic Acid, Histone H2b, Histone H2a, Cordes vas, epithelial somite, ARB, ARG, protein aggregate, animal, 2410008O07Rik, prevention and control, IKKg, Retinoic acid, Arp, multicellular organismal biosynthetic process, KEY, Key, ARP, HDAC, Retinoic, single-organism biosynthetic process, mKIAA0458, all-trans-beta-Retinoic acid, reference sample, ATN1L, AA960360, Swiss Mice, Tretinoin Potassium Salt, Betarretin, 8E)-3, trans Retinoic Acid, 6-trimethyl-1-cyclohexenyl)nona-2, preventive measures, act 42A, disease management, Ac5C, Therapies, CG4027, house mouse, Somite, D10Wsu179e, Therapy, l(1)G0330, CG6264, organisation, neuroaxonal dystrophy, CG7471, 4E, mouse, macromolecule complex, DRpd3, LACH1, Ro 1-5488, trans-retinoic acid, all-trans retinoic acid, 8-nonatetraenoic acid, infantile neuroaxonal dystrophy/atypical neuroaxonal dystrophy, all-trans-vitamin A acid, 6-trimethylcyclohex-1-enyl)nona-2, Alpha-1-antichymotrypsin His-Pro-less, dmHDA401, Kenny, DFNA26, retinoic acid, Genetic Materials, all-trans-tretinoin, Hunter-Carpenter-McDonald syndrome, HD1, C6orf30, Su(var)3-26, HD2, GAT, DFNA20, Genetic Material, dBest1, Mus musculus, l(1)3Ad, RNA Pol II, Epigenetic, mice, l(1)G0117, 6E, gon-10, Actin, 6-trimethylcyclohexen-1-yl)nona-2E, E(var)3-64BC, Treatments, beta-actin/Bap47, domesticus, l(1)G0486, l(1)G0245, DmelCG16910, l(1)G0009, ACTL3, Lach1, Cistron, (all-E)-3, 8-tetraenoic acid, HDAC-1, Bat8, BAT8, l(1)G0251, l(1)G0010, tretinoin, l(3)64Cc, RPD3, PLAN, trans-Retinoic Acid, l(1)16-94, Vitamin A, Gene, CG12051, Serpin A3, anon-WO0118547.380, beta all trans Retinoic Acid, 6-trimethyl-1-cyclohexen-1-yl)-2, AGN 100335, Potassium Salt, somites, l(1)G0025, WDS, Wds, House, big-3, Non-Governmental, dmIKKgamma, rpd3, IKK[[gamma]], Mice, Vesanoid, 6-trimethylcyclohex-1-en-1-yl)nona-2, mRPD3, act5C, Genetic, formation, Swiss, all trans Retinoic Acid, Atralin, AW742570, Maintenances, Tretinoin Sodium Salt, Act42a, beta-all-trans-Retinoic, 1700027G07Rik, IKK, organization, EG:BACR25B3.7, Cte-II, Veltin, Controlled, all-trans-vitamin A1 acid, l(1)G0177, Controlling, KARAK syndrome, Tretinoin Zinc Salt, protein complex, 8-all-trans-tetraenoic acid, Dermairol, Cistrons, all-trans-Retinoic Acid, CAD, formation of mesodermal clusters, Mus, Su(var)326, Su(var)328, Vertebrate, ACTA3, 6-trimethyl-1-cyclohexene-1-yl)-2, AI414665, administrative management, l(1)G0079, Dbest, Exhibit, neuroaxonal dystrophy presenting with neonatal dysmorphic features, hdac1b, VSCM, act 5C, Rpd3/HDAC, Laboratory Mice, Non Governmental Organizations, Therapeutic, Avita, l(1)zw8, somitic mesoderm, organizational management, Treatment, Retisol-A, CG17437, Laboratory Mouse, Actin5C"],"description_synonyms":["MGC130048, 1110033A15Rik, Laboratory, Mus domesticus, leg, A4, CASP-14, SDH, protein, Basodexan, DNB1, House Mouse, prevention, l(1)AA33, peptide, Polypeptides, SDS, protein polypeptide chains, %, halite, peptido, diseases, congenital, ionic compounds, Extracts, 1, Msal-1, 2, diseases and disorders, ARG, protein aggregate, prevention and control, Arp, ARP, gamma sarcoglycan, mKIAA0458, me75, human disease, peptides, reference sample, ATN1L, E927b, Tissue, Salt, hypoplasia, Swiss Mice, Msal, purification, proteins, sel, Salz, D17Mit170, free, T1, lipomatosis of pancreas, salts, cloruro sodico, isolation and purification, preventive measures, salt, SOLO DANCERS, l(1)B2/13.1, RUN, Run, gamma-sarcoglycan, Homo sapiens disease, Shwachman-Bodian syndrome, house mouse, eye-lt-m03Jus-gt-, rock salt, l(1)LB9, preventive therapy, Arts, mouse, SG-gamma, AI836084, Tl3, antibodies, Tl2, ur, AA33, carbamide, common salt, Mini-ICE, sarcoglycan, Mus musculus, Industrial, Industrial Arts, Caspase-14 subunit p10, Spalt, ionic compound, mice, Swiss Mouse, Shwachman-Diamond type metaphyseal dysplasia, Caspase-14 subunit p19, Shwachman syndrome, MICE, natrii chloridum, study protocol, gamma (35kDa dystrophin-associated glycoprotein), beta Trypsin, domesticus, disease, H2NC(O)NH2, DMDA, Cell Extract, 35kD dystrophin-associated glycoprotein, label, Mouse, Polypeptide, 1728, 3.4.22.-, F10B6_15, other disease, CG1849, SGCG_HUMAN, Extract, Peptidomics, number, Gene, mini-ICE, Carbamide, protein-containing complex, presence, TYPE, F10B6.15, Buffer, DAGA4, Karbamid, method, polypeptide chain, reduced, House, isolation, method used in an experiment, Harnstoff, 35DAG, Gene Products, Mus musculus domesticus, disease or disorder, Low, tiny, Carmol, MAM, gamma-SG, Mice, SCG3, Swiss, ligand, Runt, beta-Trypsin, chlorure de sodium, 4733401P19Rik, AW742570, non-neoplastic, sels, congenital lipomatosis of pancreas, Kochsalz, disorder, peptidos, LB5, Controlled, small, Controlling, cou, 35 kDa dystrophin-associated glycoprotein, Atr2, protein complex, sales, Proteins, disorders, DmelCG1849, medical condition, Rnt, buffer, Cell, Peptide, SGCG, LGMD2C, lLB5, polypeptide, count in organism, Lr, native protein, Natriumchlorid, natural protein, Mus, carbonyldiamide, Protein, condition, table salt, NaCl, AI414665, Sal, PRSS, DMDA1, underdeveloped, uree, Protein., prophylaxis, Tripcellim, SWDS, House Mice, B130022O04Rik, Shwachman-Bodian-Diamond syndrome, eyes3, Salze, l(1)19Ea, CGI-97, Laboratory Mice, sal, Protein Gene Products, plan specification, P235, Gene Proteins, Trypure, control, Dietary Sodium, Pancreatic insufficiency and bone marrow dysfunction, SCARMD2, Bra, Peptid, Laboratory Mouse, Females"],"pubmed_title_synonyms":["all-trans-vitamin A1 acid, Regulations, Tretin M, tretinoin, Formal Social Control, Tretinoin Zinc Salt, Refissa, trans-Retinoic Acid, 8-all-trans-tetraenoic acid, 4E, Vitamin A, 8E-tetraenoic acid, Dermairol, Tretinoin Potassium, beta all trans Retinoic Acid, Ro 1-5488, Tri-luma, Social Controls, Tretinoin, trans-retinoic acid, 6-trimethyl-1-cyclohexen-1-yl)-2, AGN 100335, all-trans retinoic acid, Potassium Salt, all-trans-Retinoic Acid, Retinoic Acid, 8-nonatetraenoic acid, Tretinoin Sodium, Embryonic., all-trans-vitamin A acid, Biacna, 6-trimethylcyclohex-1-enyl)nona-2, Social Control, Retin A, Cordes vas, retinoic acid, 3, all-trans-tretinoin, all-trans-Retinoic, 4, 6, Retin-A, 6-trimethyl-1-cyclohexene-1-yl)-2, Vesanoid, Acide retinoique (French), Stieva-A, Formal Social Controls, 6-trimethylcyclohex-1-en-1-yl)nona-2, Retinoic acid, Retinoic, beta-Retinoic acid, Acid, tretinoina, all-trans-beta-Retinoic acid, 6E, Renova, Salt, Tretinoin Zinc, Control, all trans Retinoic Acid, beta-all-trans-Retinoic Acid, tretinoinum, Atralin, Tretinoin Potassium Salt, Betarretin, 8E)-3, 6-trimethylcyclohexen-1-yl)nona-2E, Controls, trans Retinoic Acid, Tretinoin Sodium Salt, 6-trimethyl-1-cyclohexenyl)nona-2, Social, Zinc Salt, Sodium Salt, 7-dimethyl-9-(2, beta-all-trans-Retinoic, Altreno, all-(E)-retinoic acid, Avita, vitamin A acid, regulation, Retisol-A, (all-E)-3, 8-tetraenoic acid, Vitamin A Acid, tretinoine, Regulation, (2E, trans-Retinoic, Veltin"],"name_synonyms":["1110033A15Rik, Tretin M, tretinoin, determination, Laboratory, Refissa, trans-Retinoic Acid, Mus domesticus, Vitamin A, Gene, 8E-tetraenoic acid, DNB1, beta all trans Retinoic Acid, House Mouse, 6-trimethyl-1-cyclohexen-1-yl)-2, AGN 100335, Potassium Salt, Retinoic Acid, House, Cordes vas, Gene Products, Mus musculus domesticus, 3, 4, 6, Retin-A, ARG, Mice, Vesanoid, Stieva-A, 6-trimethylcyclohex-1-en-1-yl)nona-2, Retinoic acid, Arp, ARP, Retinoic, Laboratory Mice., mKIAA0458, all-trans-beta-Retinoic acid, Swiss, ATN1L, Renova, Salt, all trans Retinoic Acid, Atralin, Swiss Mice, Tretinoin Potassium Salt, Betarretin, AW742570, 8E)-3, trans Retinoic Acid, Tretinoin Sodium Salt, 6-trimethyl-1-cyclohexenyl)nona-2, beta-all-trans-Retinoic, Altreno, house mouse, Vitamin A Acid, (2E, trans-Retinoic, Veltin, all-trans-vitamin A1 acid, eye-lt-m03Jus-gt-, Tretinoin Zinc Salt, Atr2, 8-all-trans-tetraenoic acid, Proteins, 4E, mouse, Dermairol, Tretinoin Potassium, Ro 1-5488, Tri-luma, Tretinoin, trans-retinoic acid, all-trans retinoic acid, all-trans-Retinoic Acid, 8-nonatetraenoic acid, Tretinoin Sodium, all-trans-vitamin A acid, Biacna, 6-trimethylcyclohex-1-enyl)nona-2, Mus, Retin A, chemical analysis, Protein, retinoic acid, all-trans-tretinoin, all-trans-Retinoic, 6-trimethyl-1-cyclohexene-1-yl)-2, Acide retinoique (French), AI414665, beta-Retinoic acid, Acid, Mus musculus, tretinoina, mice, 6E, Swiss Mouse, Tretinoin Zinc, beta-all-trans-Retinoic Acid, tretinoinum, House Mice, eyes3, 6-trimethylcyclohexen-1-yl)nona-2E, domesticus, Protein Gene Products, Gene Proteins, Zinc Salt, Sodium Salt, 7-dimethyl-9-(2, all-(E)-retinoic acid, Avita, vitamin A acid, Mouse, assay, Retisol-A, (all-E)-3, 8-tetraenoic acid, tretinoine, Laboratory Mouse"],"citation_count":["0"],"additional_accession":["PXD006303"]},"is_claimable":true,"name":"MudPIT analysis of proteins interacting with the retinoic acid coactivator Rere/Atrophin2 in mouse embryos","description":"To identify proteins binding to Rere, we first generated a mouse colony homozygous for both the T-Cre transgene and the RS-Rere-HA allele. Thus, all the embryos generated by crossing these mice expressed Rere-HA only in mesodermal tissues. We collected around 600 E10.5 embryos and prepared whole-cell extracts using either a low salt (350 mM NaCl) or a high salt (420 mM NaCl) extraction buffer. For the low salt condition, affinity purification was done at 150 mM NaCl; whereas for the high salt protocol, it was performed at 300 mM NaCl. Each affinity purification was performed on biological replicates of protein extracts from about 50-70 embryos prepared on different days. Two different anti-HA antibodies from Sigma and Roche were used for the affinity purification. For each of the conditions, six elutions were performed with HA peptide, and the last elution with 2 percent SDS to completely remove all the proteins attached to the beads. Samples were analyzed by MudPIT as follows: elution 1 run alone; elution 2 and 3 combined; and elutions 4 to 7 combined. A total of 11 and 12 MudPIT analyses were performed for the low and high salt conditions, respectively. The same purification strategy was applied to embryos from wild-type females to use as a negative control. Proteins were extracted in either low or high salt conditions from 108 x 2 and 100 x 2 embryos prepared on different days, then split in half and affinity purified using either the Sigma or Roche anti-HA antibodies; elutions were combined into 3 digested samples as described above and analyzed independently for a total of 12 MudPIT analyses. After TCA-precipitation, proteins were urea-denatured, reduced, alkylated, then digested with endoproteinase LysC followed by trypsin. The resulting peptide mixtures were analyzed by Multidimensional Protein Identification Technology (MudPIT). Label-free quantitative proteomics was used to identify and quantify the relative abundance of affinity-enriched proteins.","dates":{"publication":"Thu Apr 13 11:25:00 BST 2017"},"accession":"MSV000080920","cross_references":{"pubmed":["28959017"]}}