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Probe Set Gene Title Gene Symbol Fold Change Down/Up P

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Supplementary Table 1. Regulated genes in mice skeletal muscle after DHT and E2 Probe Set Gene Title Gene Symbol Fold Change Down/Up P Genes regulated after DHT 1419487_at myosin binding protein H Mybph 11.9 down 0.000 1415927_at Actin. alpha. cardiac Actc1 3.8 down 0.000 1419606_a_at troponin T1. skeletal. slow Tnnt1 2.8 down 0.004 1448553_at myosin. heavy polypeptide 7. cardiac muscle. beta Myh7 2.6 down 0.001 1417765_a_at amylase 1. salivary Amy1 2.5 down 0.000 1416411_at glutathione S-transferase. mu 2 Gstm2 2.5 down 0.000 1418492_at gremlin 2 homolog. cysteine knot superfamily (Xenopus laevis) Grem2 2.4 down 0.000 1424392_at alcohol dehydrogenase. iron containing. 1 Adhfe1 2.2 down 0.000 1418370_at troponin C. cardiac/slow skeletal Tnnc1 2.2 down 0.002 1448394_at myosin. light polypeptide 2. regulatory. cardiac. slow Myl2 2.2 down 0.004 1450813_a_at troponin I. skeletal. slow 1 Tnni1 2.1 down 0.001 1449996_a_at tropomyosin 3. gamma Tpm3 2.1 down 0.017 1449118_at dihydrolipoamide branched chain transacylase E2 Dbt 1.8 down 0.002 1418507_s_at suppressor of cytokine signaling 2 Socs2 1.8 down 0.038 1449059_a_at 3-oxoacid CoA transferase 1 Oxct1 1.8 down 0.000 1453552_at RIKEN cDNA 2310014F07 gene 2310014F07Rik 1.8 down 0.012 1436913_at CDC14 cell division cycle 14 homolog A (S. cerevisiae) Cdc14a 1.8 down 0.014 1448554_s_at myosin. heavy polypeptide 6. cardiac muscle. alpha Myh6 1.7 down 0.008 1427168_a_at procollagen. type XIV. alpha 1 Col14a1 1.7 down 0.005 1423607_at lumican Lum 1.7 down 0.005 1451310_a_at cathepsin L Ctsl 1.7 down 0.001 1452363_a_at ATPase. Ca++ transporting. cardiac muscle. slow twitch 2 Atp2a2 1.7 down 0.002 1452203_at oligonucleotide/oligosaccharide-binding fold containing 2A Obfc2a 1.7 down 0.007 1420523_at coiled-coil domain containing 50 Ccdc50 1.6 down 0.008 1417719_at sin3 associated polypeptide Sap30 1.6 down 0.007 1418152_at nucleosome binding protein 1 Nsbp1 1.6 down 0.012 1424649_a_at tetraspanin 8 Tspan8 1.6 down 0.003 1425090_s_at potassium voltage gated channel. Shaw-related subfamily. member 4 Kcnc4 1.6 down 0.001 1421891_at ST3 beta-galactoside alpha-2.3-sialyltransferase 2 St3gal2 1.6 down 0.014 1455007_s_at glutamic pyruvate transaminase (alanine aminotransferase) 2 Gpt2 1.6 down 0.004 1427343_at RASD family. member 2 Rasd2 1.6 down 0.014 1460451_at transmembrane protein 52 Tmem52 1.6 down 0.003 1427769_x_at myosin. light polypeptide 3 Myl3 1.6 down 0.002 1423606_at periostin. osteoblast specific factor Postn 1.6 down 0.025 1443299_at PDZ and LIM domain 3 (Pdlim3). mRNA Pdlim3 1.5 down 0.011 1426236_a_at glutamate-ammonia ligase (glutamine synthetase) Glul 1.5 down 0.014 1438855_x_at tumor necrosis factor. alpha-induced protein 2 Tnfaip2 1.5 down 0.028 1448181_at Kruppel-like factor 15 Klf15 1.5 down 0.002 1451047_at integral membrane protein 2A Itm2a 1.5 down 0.000 1425458_a_at growth factor receptor bound protein 10 Grb10 1.5 down 0.001 1424151_at JTV1 gene Jtv1 1.5 down 0.000 1450637_a_at AE binding protein 1 Aebp1 1.5 down 0.000 1451031_at secreted frizzled-related sequence protein 4 Sfrp4 1.5 down 0.001 1427153_at branched chain ketoacid dehydrogenase E1. beta polypeptide Bckdhb 1.5 down 0.003 1437273_at HtrA serine peptidase 4 Htra4 1.5 down 0.004 1422982_at androgen receptor Ar 1.5 down 0.001 1435148_at ATPase. Na+/K+ transporting. beta 2 polypeptide Atp1b2 1.5 down 0.000 1433711_s_at sestrin 1 Sesn1 1.5 down 0.000 1438641_x_at RIKEN cDNA 1500016O10 gene 1500016O10Rik 1.5 down 0.041 1433924_at --- --- 1.6 down 0.002 1436092_at --- --- 1.7 down 0.000 AFFX-18SRNAMur/X00686_M_at 1.5 down 0.029 AFFX-18SRNAMur/X00686_3_at 1.6 down 0.007 AFFX-18SRNAMur/X00686_5_at 3.4 down 0.003 1451601_a_at spinster homolog 2 (Drosophila) Spns2 3.4 up 0.000 1455031_at cell division cycle 2-like 6 (CDK8-like) Cdc2l6 3.0 up 0.000 1427339_at solute carrier family 30 (zinc transporter). member 2 Slc30a2 3.0 up 0.000 1427364_a_at ornithine decarboxylase. structural 1 Odc1 2.8 up 0.000 1424268_at spermine oxidase Smox 2.6 up 0.000 1427722_at RIKEN cDNA 9830102E05 gene 9830102E05Rik 2.6 up 0.001 1419423_at stabilin 2 Stab2 2.5 up 0.000 1455898_x_at solute carrier family 2 (facilitated glucose transporter). member 3 Slc2a3 2.5 up 0.000 1455377_at tubulin tyrosine ligase-like family. member 7 Ttll7 2.5 up 0.000 1448881_at haptoglobin Hp 2.4 up 0.020 1457587_at Voltage-gated potassium channel KCNQ5 (Kcnq5) Kcnq5 2.3 up 0.001 1451465_at ubiquitin-like 7 (bone marrow stromal cell-derived) Ubl7 2.3 up 0.000 1416835_s_at S-adenosylmethionine decarboxylase 1 /// S-adenosylmethionine decarboxylase 2 Amd1 /// Amd2 2.3 up 0.000 1460241_a_at ST3 beta-galactoside alpha-2.3-sialyltransferase 5 St3gal5 2.3 up 0.000 1428111_at solute carrier family 38. member 4 Slc38a4 2.3 up 0.010 1418509_at carbonyl reductase 2 Cbr2 2.2 up 0.000 1452035_at procollagen. type IV. alpha 1 Col4a1 2.2 up 0.000 1416138_at annexin A7 Anxa7 2.2 up 0.000 1438676_at macrophage activation 2 like Mpa2l 2.2 up 0.002 1448747_at F-box only protein 32 Fbxo32 2.1 up 0.004 1455794_at smoothelin-like 2 Smtnl2 2.1 up 0.000 1417611_at transmembrane protein 37 Tmem37 2.1 up 0.013 1435605_at ARP3 actin-related protein 3 homolog B (yeast) Actr3b 2.1 up 0.001 1424514_at ring finger protein 126 Rnf126 2.0 up 0.000 1450138_a_at serine (or cysteine) peptidase inhibitor. clade B. member 6a Serpinb6a 2.0 up 0.000 1418003_at RIKEN cDNA 1190002H23 gene 1190002H23Rik 2.0 up 0.004 1434548_at serine incorporator 3 Serinc3 2.0 up 0.002 1418091_at transcription factor CP2-like 1 Tcfcp2l1 1.9 up 0.002 1455399_at connector enhancer of kinase suppressor of Ras 1 Cnksr1 1.9 up 0.001 1433702_at endoplasmic reticulum metallopeptidase 1 Ermp1 1.9 up 0.016 1418697_at indolethylamine N-methyltransferase Inmt 1.9 up 0.002 1415897_a_at microsomal glutathione S-transferase 1 Mgst1 1.9 up 0.004 1424854_at histone 1. H4i Hist1h4i 1.9 up 0.008 1436309_at neuropilin (NRP) and tolloid (TLL)-like 2 Neto2 1.9 up 0.002 1424051_at procollagen. type IV. alpha 2 Col4a2 1.9 up 0.001 1432001_at zinc finger. MYND domain containing 17 Zmynd17 1.9 up 0.024 1415698_at golgi phosphoprotein 2 Golph2 1.9 up 0.002 1453851_a_at growth arrest and DNA-damage-inducible 45 gamma Gadd45g 1.9 up 0.002 1435902_at nudix (nucleoside diphosphate linked moiety X)-type motif 18 Nudt18 1.9 up 0.005 1426464_at nuclear receptor subfamily 1. group D. member 1 Nr1d1 1.9 up 0.015 1448300_at microsomal glutathione S-transferase 3 Mgst3 1.8 up 0.000 1449005_at solute carrier family 16 (monocarboxylic acid transporters). member 3 Slc16a3 1.8 up 0.000 1427883_a_at procollagen. type III. alpha 1 Col3a1 1.8 up 0.013 1423086_at Niemann Pick type C1 Npc1 1.8 up 0.012 1451342_at spondin 1. (f-spondin) extracellular matrix protein Spon1 1.8 up 0.000 1423296_at proteasome (prosome. macropain) 26S subunit. non-ATPase. 8 Psmd8 1.8 up 0.000 1452661_at transferrin receptor Tfrc 1.8 up 0.002 1416125_at FK506 binding protein 5 Fkbp5 1.8 up 0.002 1424126_at aminolevulinic acid synthase 1 Alas1 1.8 up 0.001 1427992_a_at RAB12. member RAS oncogene family Rab12 1.7 up 0.000 1436715_s_at CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase) Cdipt 1.7 up 0.003 1434947_at kinesin family member 3C Kif3c 1.7 up 0.001 1423110_at collagen. type I. alpha 2 Col1a2 1.7 up 0.049 1431213_a_at hypothetical gene LOC433762 LOC433762 1.7 up 0.003 1424795_a_at RIKEN cDNA 1700001O22 gene 1700001O22Rik 1.7 up 0.003 1416514_a_at fascin homolog 1. actin bundling protein (Strongylocentrotus) purpuratus) Fscn1 1.7 up 0.011 1455628_at erythrocyte protein band 4.1-like 4b Epb4.1l4b 1.7 up 0.013 1417562_at eukaryotic translation initiation factor 4E binding protein 1 Eif4ebp1 1.7 up 0.000 1417279_at inositol 1.4.5-triphosphate receptor 1 Itpr1 1.7 up 0.004 1428357_at RIKEN cDNA 2610019F03 gene 2610019F03Rik 1.7 up 0.000 1422437_at procollagen. type V. alpha 2 Col5a2 1.7 up 0.015 1448566_at solute carrier family 40 (iron-regulated transporter). member 1 Slc40a1 1.7 up 0.000 1450914_at protein phosphatase 1. regulatory (inhibitor) subunit 14B Ppp1r14b 1.7 up 0.000 1453898_at integrin beta 1 binding protein 3 Itgb1bp3 1.7 up 0.043 1428536_at potassium voltage-gated channel. subfamily G. member 4 Kcng4 1.7 up 0.003 1421413_a_at PDZ and LIM domain 5 Pdlim5 1.7 up 0.000 1423596_at NIMA (never in mitosis gene a)-related expressed kinase 6 Nek6 1.7 up 0.002 1455493_at synaptic nuclear envelope 1 Syne1 1.7 up 0.001 1440085_at ectodysplasin A2 isoform receptor Eda2r 1.6 up 0.037 1416589_at secreted acidic cysteine rich glycoprotein Sparc 1.6 up 0.003 1426951_at cysteine rich transmembrane BMP regulator 1 (chordin like) Crim1 1.6 up 0.022 1435950_at hairless Hr 1.6 up 0.001 1449533_at transmembrane protein 100 Tmem100 1.6 up 0.033 1422324_a_at parathyroid hormone-like peptide Pthlh 1.6 up 0.001 1417409_at Jun oncogene Jun 1.6 up 0.011 1455494_at procollagen. type I. alpha 1 Col1a1 1.6 up 0.044 1429273_at BMP-binding endothelial regulator Bmper 1.6 up 0.001 1424842_a_at Rho GTPase activating protein 24 Arhgap24 1.6 up 0.004 1438426_at shisa homolog 4 (Xenopus laevis) Shisa4 1.6 up 0.005 1455548_at discs.
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    RyR1 Deficiency in Congenital Myopathies Disrupts Excitation-Contraction Coupling Haiyan Zhou1, Ori Rokach2, Lucy Feng1, Iulia Munteanu1, Kamel Mamchaoui3, Jo M. Wilmshurst4, Caroline Sewry1, Adnan Y. Manzur1, Komala Pillay5, Vincent Mouly2, Michael Duchen6, Heinz Jungbluth7,8,9, Susan Treves2,10* and Francesco Muntoni1* 1 Dubowitz Neuromuscular Centre, Institute of Child Health, University College London WC1N 1EH, UK. 2 Department of Anaesthesia and Biomedicine, Basel University and University Hospital Basel, 4031 Basel, Switzerland 3 UM76 Université Pierre et Marie Curie, UMRS974 INSERM, UMR 7215 CNRS, Institut de Myologie AIM, Groupe hospitalier Pitié-Salpétrière, 47 bd de I’Hôpital, 75013 Paris, France 4 Department of Paediatric Neurology, School of Child and Adolescent Health, University of Cape Town, Red Cross Children’s Hospital, Cape Town, South Africa 5 Department of Paediatric Pathology, School of Child and Adolescent Health, University of Cape Town, Red Cross Children’s Hospital, Cape Town, South Africa 6 Cell and Developmental Biology, University College London, London WC1E 6BT, UK 7 Department of Paediatric Neurology, Evelina Children’s Hospital, London SE1 7EH, UK 8 Clinical Neuroscience Division, IoP, King’s College, London, UK 9 Randall Division of Cell and Molecular Biophysics, Muscle Signalling Group, King's College London, UK 10 Department of Life Sciences, University of Ferrara, Ferrara, Italy 1 *To whom correspondence should be addressed. Emails: [email protected] (Tel: 0044- 2079052136; Fax: 0044-2079052832) and
  • S1 Table Protein

    S1 Table Protein

    S1 Table dFSHD12_TE dFSHD12_NE aFSHD51_TE aFSHD51_NE Accession Gene Protein H/L SD # bold H/L SD # bold H/L SD # bold H/L SD # bold Intermediate filament (or associated proteins) P17661 DES Desmin 0.91 N.D. 37 1.06 1.35 19 0.89 1,13 33 * 1.20 1.21 17 * P02545 LMNA Prelamin-A/C 0.90 1.25 30 * 1.07 1.26 20 0.96 1.23 34 1.21 1.24 19 * P48681 NES Nestin 0.91 N.D. 60 0.94 1.25 27 0.72 1.20 50 * 0.89 1.27 31 * P08670 VIM Vimentin 1.04 N.D. 35 1.24 1.24 14 * 1.21 1.18 36 * 1.39 1.17 16 * Q15149 PLEC Plectin-1 1.10 1.28 19 1.05 1.10 3 1.07 1.23 26 1.25 1.27 7 * P02511 CRYAB Alpha-crystallin B chain (HspB5) 1.47 1.17 2 1.17 2 1.14 1.12 2 Tubulin (or associated proteins) P62158 CALM1 Calmodulin (CaM) 0.83 0.00 1 0.93 0.00 1 Programmed cell death 6- Q8WUM4 PDCD6IP 1.34 0.00 1 interacting protein Q71U36 TUBA1A Tubulin α-1A chain (α-tubulin 3) 1.44 1.12 3 * Tubulin β chain (Tubulin β-5 P07437 TUBB 1.52 0.00 1 chain) Nuclear mitotic apparatus Q14980 NUMA1 0.68 0.00 1 0.75 0.00 1 protein 1 Microtubule-associated protein P27816 MAP4 1.10 1 4 Microtubule-associated protein P78559 MAP1A 0.76 0.00 1 1A Q6PEY2 TUBA3E Tubulin α-3E chain (α-tubulin 3E) 0.91 0.00 1 1.12 0.00 1 0.98 1.12 3 Tubulin β-2C chain (Tubulin β-2 P68371 TUBB2C 0.93 1.13 7 chain) Q3ZCM7 TUBB8 Tubulin β-8 chain 0.97 1.09 4 Serine P34897 SHMT2 hydroxymethyltransferase 0.93 0.00 1 (serine methylase) Cytoskeleton-associated protein Q07065 CKAP4 0.98 1.24 5 0.96 0.00 1 1.08 1.28 6 0.75 0.00 1 4 (p63) Centrosomal protein of 135 kDa Q66GS9 CEP135 0.84 0.00 1 (Centrosomal protein 4) Pre-B cell leukemia transcription Q96AQ6 PBXIP1 0.74 0.00 1 0.80 1 factor-interacting protein 1 T-complex protein 1 subunit P17897 TCP1 0.84 0.00 1 alpha (CCT-alpha) Cytoplasmic dynein Q13409 DYNC1I2 1.01 0.00 1 intermediate chain 2 (DH IC-2) Dynein heavy chain 3 (Dnahc3- Q8TD57 DNAH3 b) Microtubule-actin cross- linking Q9UPN3 MACF1 factor 1 (Trabeculin-alpha) Actin (or associated including myofibril-associated porteins) P60709 ACTB Actin, cytoplasmic 1 (β-actin) 1.11 N.D.
  • Analysis of the Dystrophin Interactome

    Analysis of the Dystrophin Interactome

    Analysis of the dystrophin interactome Dissertation In fulfillment of the requirements for the degree “Doctor rerum naturalium (Dr. rer. nat.)” integrated in the International Graduate School for Myology MyoGrad in the Department for Biology, Chemistry and Pharmacy at the Freie Universität Berlin in Cotutelle Agreement with the Ecole Doctorale 515 “Complexité du Vivant” at the Université Pierre et Marie Curie Paris Submitted by Matthew Thorley born in Scunthorpe, United Kingdom Berlin, 2016 Supervisor: Simone Spuler Second examiner: Sigmar Stricker Date of defense: 7th December 2016 Dedicated to My mother, Joy Thorley My father, David Thorley My sister, Alexandra Thorley My fiancée, Vera Sakhno-Cortesi Acknowledgements First and foremost, I would like to thank my supervisors William Duddy and Stephanie Duguez who gave me this research opportunity. Through their combined knowledge of computational and practical expertise within the field and constant availability for any and all assistance I required, have made the research possible. Their overarching support, approachability and upbeat nature throughout, while granting me freedom have made this year project very enjoyable. The additional guidance and supported offered by Matthias Selbach and his team whenever required along with a constant welcoming invitation within their lab has been greatly appreciated. I thank MyoGrad for the collaboration established between UPMC and Freie University, creating the collaboration within this research project possible, and offering research experience in both the Institute of Myology in Paris and the Max Delbruck Centre in Berlin. Vital to this process have been Gisele Bonne, Heike Pascal, Lidia Dolle and Susanne Wissler who have aided in the often complex processes that I am still not sure I fully understand.