Supplementary Materials for

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1 Supplementary Materials for MuSK is a BMP co-receptor that shapes BMP responses and calcium signaling in muscle cells Atilgan Yilmaz, Chandramohan Kattamuri, Rana N. Ozdeslik, Carolyn Schmiedel, Sarah Mentzer, Christoph Schorl, Elena Oancea, Thomas B. Thompson, Justin R. Fallon* This PDF file includes: *Corresponding author. justin_fallon@brown.edu Published 6 September 2016, Sci. Signal. 9, ra87 (2016) DOI: /scisignal.aaf0890 Fig. S1. SPR binding analysis of MuSK with BMP2 and BMP7. Fig. S2. Soluble MuSK ectodomain inhibits BMP4 activity. Fig. S3. Equivalent binding of biglycan to MuSK ectodomain either containing (FL) or lacking ( Ig3) the third Ig domain. Fig. S4. BMP4 treatment stimulates Rgs4 expression in wild-type but not MuSK / myoblasts. Fig. S5. MuSK favors the transcription of signaling- and transcription-related genes. Fig. S6. Abundant phosphorylated SMAD1/5/8 in cytosolic granules in wild-type but not MuSK / myoblasts. Table S1. Association and dissociation rate constants and overall Kd values for the interaction of MuSK with BMP2, BMP4, and BMP7, as determined by SPR. Table S2. Transcripts induced by BMP4 only in wild-type myoblasts. Table S3. Transcripts induced by BMP4 in both wild-type and MuSK / myoblasts. Table S4. Transcripts induced by BMP4 only in MuSK / myoblasts. Table S5. Transcripts induced by BMP4 only in wild-type myotubes. Table S6. Transcripts induced by BMP4 in both wild-type and MuSK / myotubes. Table S7. Transcripts induced by BMP4 only in MuSK / myotubes. Table S8. Transcripts induced by BMP4 in a MuSK-dependent manner in both myoblasts and myotubes. Table S9. Transcripts induced by BMP4 in a MuSK-dependent manner only in myoblasts. Table S10. Transcripts induced by BMP4 in a MuSK-dependent manner only in myotubes.

2 A MuSK over BMP2 B MuSK over BMP7 Response (RU) Response (RU) Time (s) Time (s) Fig. S1. SPR binding analysis of MuSK with BMP2 and BMP7. (A and B) MuSK binding to BMP2 and BMP7 immobilized on a biosensor chip. Representative SPR profiles are shown for various concentrations of MuSK binding to BMP2 (A); and BMP7 (B). Sensograms were normalized for MuSK binding to a mock-coupled flow cell. The black lines show the experimental measurements of a two-fold serial dilution over the concentration range [2 mm nm] of each sensorgram and the red lines correspond to global fits of the data to a 1:1 model using a heterogeneous surface model with the program EVILFIT.

3 Fig. S2. Soluble MuSK ectodomain inhibits BMP4 activity. BMP4 (45pM) was preincubated with the indicated concentrations of MuSK ectodomain or a control His-tagged protein (Histagged TEV-protease) and the mixture was then added to C2C12BRA cells for 8 hours. Data are representative of three independent experiments. Values indicate the average from eight replicates and are means ± SEM. (**p < 0.01; *p, 0.05; ns, not significant versus BMP4-only treatment, one-way ANOVA with Bonferroni correction).

4 Normalized horseradish peroxidase activity Immobilized protein: Soluble protein: ns ns ** ** BSA BSA BSA biglycan biglycan FLectoMuSK ectomusk ectomusk ΔIg3- FL- ΔIg3- - ectomusk Fig. S3. Equivalent binding of biglycan to MuSK ectodomain either containing (FL) or lacking ( Ig3) the third Ig domain. 6 µg biglycan was immobilized on 96-well plates and incubated with µg/ml soluble MuSK ectodomain fusions. Bound MuSK was detected by ELISA. Data are means ± SEM. (n=4, **p < 0.01; ns, not significant versus BSA-only condition, one way ANOVA with Bonferroni correction).

5 Relative RGS4 transcript level * Relative RGS4 transcript level BMP4: wild type MuSK -/- Fig. S4. BMP4 treatment stimulates Rgs4 expression in wild-type but not MuSK -/- myoblasts. Wild-type H-2Kb-tsA58 or MuSK -/- myoblasts were serum-deprived for 5 6 hours and then treated with 3.25ng/ml BMP4 for 2 hours. Rgs4 transcript abundance was measured by qrt- PCR. Data are means ± SEM from three biological replicate experiments (*p < 0.05, unpaired, two-sided Student s t-test).

6 1.00E E E E E E+00 A B Growth factors Transcription factors Cell surface receptors Extracellular matrix proteins Intracellular signaling proteins Other Myoblasts Myotubes C Inverse FDR value D Inverse FDR value MuSK-dependent gene ontology terms Limb morphogenesis Appendage morphogenesis Embryonic appendage morphogenesis Embroyonic limb morphogenesis Appendage development Limb development Mesenchymal cell differentiation Mesenchyme development Bone development Cartilage development Tube morphogenesis Mesenchymal cell development Wnt receptor signaling pathway Negative regulation of nucleic acid metabolic process Negative regulation of N 2 compound metabolic process Regulation of transcription, DNA-dependent Regulation of RNA metabolic proceess Negative regulation of cellular biosynthetic process Negative regulation of biosynthetic process Regionalization Negative regulation of transcription Neural crest cell development Neural crest cell differentiation Heart development Morphogenesis of an epithelium Myoblasts MuSK-dependent gene ontology terms Skeletal system development Angiogenesis Regulation of RNA metabolic process Regulation of transcription, DNA-dependent Tube morphogenesis Regulation of transcription from RNA pol. II promoter Response to protein stimulus Embryonic morphogenesis Pattern specification process Regulation of transcription Skeletal system morphogenesis Chordate embryonic development Embryonic development ending in birth or egg hatching Gland development Embryonic skeletal system development Gland morphogenesis Embryonic cranial skeleton morphogenesis Embryonic organ development Morphogenesis of an epithelium Mammary gland development Mammary gland duct morphogenesis Positive regulation of developmental process Regionalization Negative regulation of transcription Artery morphogenesis Myotubes Fig. S5. MuSK favors the transcription of signaling- and transcription-related genes. (A) Approximately half of MuSK-dependent BMP4 transcriptional responses in myoblasts comprise secreted and intracellular signaling molecules or transcription factors. Transcripts that are upregulated by BMP4 only in wild-type myoblasts were manually assigned to functional categories related to signaling. (B) More than half of MuSK-dependent BMP4 responses in myotubes comprise secreted and intracellular signaling molecules and transcription factors. Transcripts that are upregulated by BMP4 only in wild-type myotubes were manually assigned to functional categories related to signaling. Note that MuSK favors the transcription of signalingand transcription-related genes that are distinct in myoblasts and myotubes. (C, D) Gene Ontology (GO) analysis of MuSK-dependent transcripts in myoblasts and myotubes, respectively. MuSK-regulated GO terms were determined by subtracting GO terms enriched

7 among BMP4 responses in MuSK -/- cells from those of wild-type cells. A false discovery rate (FDR) cut-off of 0.05 was applied to the selection criteria of the terms (C) Transcripts encoding limb morphogenesis factors and transcriptional regulators are enriched among the MuSKdependent BMP4 transcriptional responses in myoblasts. (D) Transcripts encoding transcriptional regulators are among the most enriched MuSK-dependent BMP4 transcriptional responses in myotubes. Note that only 4/25 GO terms are shared between MuSK-dependent transcripts in myoblasts and myotubes.

8 A wild type MuSK -/- psmad1/5/8 psmad1/5/8 B % cells expressing cyctosolic psmad5 granules * wild type MuSK -/- Fig. S6. Abundant phosphorylated SMAD1/5/8 in cytosolic granules in wild-type but not MuSK -/- myoblasts. (A) Resting wild-type H-2Kb-tsA58 or MuSK -/- myoblasts were fixed and immunostained for phosphorylated SMAD1/5/8 (psmad1/5/8). Note the abundant cytosolic psmad1/5/8 puncta in wild-type cells. Such puncta were sparse in MuSK -/- cells. (B) Quantification of the percentage of wildtype H-2Kb-tsA58 and MuSK -/- myoblasts with detectable psmad1/5/8 granules. Data are means ± SEM from three independent experiments with sixty cells analyzed in each (n=3, *p < 0.05, unpaired, two-sided Student s t-test).

9 Table S1. Association and dissociation rate constants and overall Kd values for the interaction of MuSK with BMP2, BMP4, and BMP7, as determined by SPR. Immobilized ligand Analyte MuSK k on (M -1 s -1 ) k off (s -1 ) K D (M) BMP2 1.7x x x10-9 BMP4 2.6x x x10-9 BMP7 1.1x x x10-9

10 Table S2. Transcripts induced by BMP4 only in wild-type myoblasts. Fold-changes indicate the upregulation of the listed transcript by BMP4..Gene Symbol gene_assignment fold change p-value Rgs4 NM_ // Rgs4 // regulator of G-protein signaling 4 // 1 H cm // E-05 Msx2 NM_ // Msx2 // homeobox, msh-like 2 // 13 B cm // /// BC E-05 Avpr1a NM_ // Avpr1a // arginine vasopressin receptor 1A // 10 D3 // /// EN E L13Rik ENSMUST // L13Rik // RIKEN cdna L13 gene // 18 E E-04 Kazald1 NM_ // Kazald1 // Kazal-type serine peptidase inhibitor domain 1 // 19 C E-05 Foxc2 NM_ // Foxc2 // forkhead box C2 // 8 E cm // /// ENSMUST E-05 Sema6d NM_ // Sema6d // sema domain, transmembrane domain (TM), and cytoplasmic d E-05 Lgr4 NM_ // Lgr4 // leucine-rich repeat-containing G proteincoupled receptor E-05 Ptx3 NM_ // Ptx3 // pentraxin related gene // 3 E cm // /// ENSMU E-05 Serpinb2 NM_ // Serpinb2 // serine (or cysteine) peptidase inhibitor, clade B, memb E-04 Ptger4 NM_ // Ptger4 // prostaglandin E receptor 4 (subtype EP4) // 15 A E-05 Timp3 NM_ // Timp3 // tissue inhibitor of metalloproteinase 3 // 10 C1 10 C1-D E-04 Nog NM_ // Nog // noggin // 11 C cm // /// ENSMUST // E-05 Pcp4l1 NM_ // Pcp4l1 // Purkinje cell protein 4-like 1 // 1 H3 // /// ENSMU E-04 Orai2 NM_ // Orai2 // ORAI calcium release-activated calcium modulator 2 // 5 G E-04 Slc5a7 NM_ // Slc5a7 // solute carrier family 5 (choline transporter), member 7 / E-04 Gprin3 NM_ // Gprin3 // GPRIN family member 3 // 6 B3 // /// ENSMUST E-04 Plcb1 NM_ // Plcb1 // phospholipase C, beta 1 // 2 F cm // /// NM_ E-05 Slc25a13 NM_ // Slc25a13 // solute carrier family 25 (mitochondrial carrier, adenin E-04 Snai2 NM_ // Snai2 // snail homolog 2 (Drosophila) // 16 A cm // / E-05 Inhba NM_ // Inhba // inhibin beta-a // 13 A cm // /// ENSMUST E-05 Prr9 NM_ // Prr9 // proline rich 9 // 3 F1 // /// ENSMUST // E-04 Lef1 NM_ // Lef1 // lymphoid enhancer binding factor 1 // 3 G cm // E-04 Insc NM_ // Insc // inscuteable homolog (Drosophila) // 7 F1 // /// ENSM E-05 Hoxc13 NM_ // Hoxc13 // homeo box C13 // 15 F cm // /// ENSMUST E-04 Asphd2 NM_ // Asphd2 // aspartate beta-hydroxylase domain containing 2 // 5 F // E-04 Tiam2 NM_ // Tiam2 // T-cell lymphoma invasion and metastasis 2 // cm E-04

11 Rasl11a Ptch1 Itgb1bp3 Dio2 Tmem56 Erc1 Dlx3 Trps1 Hoxc11 Prr5l Kcnf1 Myf5 Pappa Skil Cpne4 A630033H20Rik Thsd7a Pdk4 Vasn Lpl Rarres1 Ttc39b Ier3 Tm4sf1 Hoxa11 Fzd1 Has2 Car8 Htr1b Erc1 NM_ // Rasl11a // RAS-like, family 11, member A // 5 G3 // /// ENSMU E-04 NM_ // Ptch1 // patched homolog 1 // 13 B cm // /// ENSMUST E-04 NM_ // Itgb1bp3 // integrin beta 1 binding protein 3 // 10 C1 // /// E-04 NM_ // Dio2 // deiodinase, iodothyronine, type II // 12 D3 // /// EN E-04 NM_ // Tmem56 // transmembrane protein 56 // 3 G3 // /// ENSMUST E-06 NM_ // Erc1 // ELKS/RAB6-interacting/CAST family member 1 // 6 F1 // E-05 NM_ // Dlx3 // distal-less homeobox 3 // 11 D cm // /// ENSM E-05 NM_ // Trps1 // trichorhinophalangeal syndrome I (human) // 15 C c E-04 NM_ // Hoxc11 // homeo box C11 // 15 F cm // /// ENSMUS E-06 NM_ // Prr5l // proline rich 5 like // 2 E2 // /// NM_ // P E-04 NM_ // Kcnf1 // potassium voltage-gated channel, subfamily F, member 1 // E-04 NM_ // Myf5 // myogenic factor 5 // 10 D cm // /// ENSMUST E-04 NM_ // Pappa // pregnancy-associated plasma protein A // 4 C cm // E-03 NM_ // Skil // SKI-like // 3 A cm // /// NM_ // Ski E-05 NM_ // Cpne4 // copine IV // 9 F1 // /// ENSMUST // Cpne E-05 NM_ // A630033H20Rik // RIKEN cdna A630033H20 gene // X D // /// NM E-04 ENSMUST // Thsd7a // thrombospondin, type I, domain containing 7A // E-05 NM_ // Pdk4 // pyruvate dehydrogenase kinase, isoenzyme 4 // 6 A c E-04 NM_ // Vasn // vasorin // 16 A1 // /// ENSMUST // Vasn / E-04 NM_ // Lpl // lipoprotein lipase // 8 B cm // /// ENSMUST E-04 ENSMUST // Rarres1 // retinoic acid receptor responder (tazarotene in E-04 NM_ // Ttc39b // tetratricopeptide repeat domain 39B // 4 C3 // /// E-05 NM_ // Ier3 // immediate early response 3 // 17 B1 // /// ENSMUST E-04 NM_ // Tm4sf1 // transmembrane 4 superfamily member 1 // 3 D // /// E-06 NM_ // Hoxa11 // homeo box A11 // 6 B cm // /// ENSMUST E-04 NM_ // Fzd1 // frizzled homolog 1 (Drosophila) // 5 A cm // / E-04 NM_ // Has2 // hyaluronan synthase 2 // 15 D cm // /// ENSM E-05 NM_ // Car8 // carbonic anhydrase 8 // 4 A cm // /// BC E-03 NM_ // Htr1b // 5-hydroxytryptamine (serotonin) receptor 1B // 9 E E-04 NM_ // Erc1 // ELKS/RAB6-interacting/CAST family member 1 // 6 F1 // E-04

12 Pcdh7 Pcolce2 Ptpru Mab21l1 Smoc1 Fzd7 Papss2 Col10a1 Tmeff1 Ssfa2 Junb Gcnt4 Prss35 Itgb L11Rik Klf10 Rpgrip1l F19Rik Ccdc34 Smpdl3a Flrt2 Jak2 Pi15 Cpm Il17ra Cldn1 Mpp2 Ppap2b Alpk1 Grb14 NM_ // Pcdh7 // protocadherin 7 // 5 C3-D // /// NM_ // Pcd E-05 NM_ // Pcolce2 // procollagen C-endopeptidase enhancer 2 // 9 E3.3 // E-04 NM_ // Ptpru // protein tyrosine phosphatase, receptor type, U // 4 D E-04 NM_ // Mab21l1 // mab-21-like 1 (C. elegans) // 3 E3-F1 // /// ENSMU E-04 NM_ // Smoc1 // SPARC related modular calcium binding 1 // 12 D1 // E-05 NM_ // Fzd7 // frizzled homolog 7 (Drosophila) // 1 C cm // E-04 NM_ // Papss2 // 3'-phosphoadenosine 5'-phosphosulfate synthase 2 // 19 C E-04 NM_ // Col10a1 // collagen, type X, alpha 1 // cm // /// ENS E-04 NM_ // Tmeff1 // transmembrane protein with EGF-like and two follistatin-l E-05 NM_ // Ssfa2 // sperm specific antigen 2 // 2 D // /// ENSMUST E-04 NM_ // Junb // Jun-B oncogene // 8 C2-D cm // /// ENSMUST E-05 AK // Gcnt4 // glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-n-a E-05 NM_ // Prss35 // protease, serine, 35 // 9 E3.1 // /// ENSMUST E-06 NM_ // Itgb8 // integrin beta 8 // 12 F2 // /// ENSMUST E-05 NR_ // L11Rik // signal peptidase complex subunit 3 homolog pseudog E-03 NM_ // Klf10 // Kruppel-like factor 10 // 15 B3.1 // /// ENSMUST E-04 NM_ // Rpgrip1l // Rpgrip1-like // 8 C cm // /// ENSMUST E-04 NM_ // F19Rik // RIKEN cdna F19 gene // 10 A4 // / E-03 NM_ // Ccdc34 // coiled-coil domain containing 34 // 2 E3 // /// ENS E-04 NM_ // Smpdl3a // sphingomyelin phosphodiesterase, acid-like 3A // 10 B4 / E-05 NM_ // Flrt2 // fibronectin leucine rich transmembrane protein 2 // 12 E / E-05 NM_ // Jak2 // Janus kinase 2 // 19 C cm // /// NM_ E-05 NM_ // Pi15 // peptidase inhibitor 15 // 1 A4 // /// ENSMUST E-03 NM_ // Cpm // carboxypeptidase M // 10 D2 // /// ENSMUST E-03 NM_ // Il17ra // interleukin 17 receptor A // 6 F cm // /// E-05 NM_ // Cldn1 // claudin 1 // 16 B2 // /// ENSMUST // Cldn E-04 NM_ // Mpp2 // membrane protein, palmitoylated 2 (MAGUK p55 subfamily memb E-04 NM_ // Ppap2b // phosphatidic acid phosphatase type 2B // 4 C cm / E-04 ENSMUST // Alpk1 // alpha-kinase 1 // 3 H1 // /// AK // A E-04 NM_ // Grb14 // growth factor receptor bound protein 14 // 2 C1.3 // E-04

13 Tmeff2 Clcf1 Epha7 Lrrc8c Podnl1 Rusc2 Rhou Jhdm1d Cxcr4 Irx5 Mtmr11 Ephb2 Fmn2 Sh3bp4 Egr2 Asap1 Kremen1 Fam135a Twist2 Syn1 Dok4 Mapkapk3 Zfp462 Angptl2 Tsc22d1 Cenpp Sstr2 Col12a1 Rai14 Stmn2 NM_ // Tmeff2 // transmembrane protein with EGF-like and two follistatin-l E-06 NM_ // Clcf1 // cardiotrophin-like cytokine factor 1 // 19 A // /// E-05 NM_ // Epha7 // Eph receptor A7 // 4 A cm // /// NM_ E-04 NM_ // Lrrc8c // leucine rich repeat containing 8 family, member C // 5 E E-05 NM_ // Podnl1 // podocan-like 1 // 8 C3 // /// ENSMUST E-04 NM_ // Rusc2 // RUN and SH3 domain containing 2 // 4 A5 // /// N E-03 NM_ // Rhou // ras homolog gene family, member U // 8 E2 // /// ENSM E-04 NM_ // Jhdm1d // jumonji C domain-containing histone demethylase 1 homo E-04 NM_ // Cxcr4 // chemokine (C-X-C motif) receptor 4 // 1 E cm // E-04 NM_ // Irx5 // Iroquois related homeobox 5 (Drosophila) // 8 C cm E-04 NM_ // Mtmr11 // myotubularin related protein 11 // 3 F2.1 // /// E E-04 NM_ // Ephb2 // Eph receptor B2 // 4 D-E cm // /// ENSMUST E-04 NM_ // Fmn2 // formin 2 // 1 H cm // /// ENSMUST E-04 NM_ // Sh3bp4 // SH3-domain binding protein 4 // 1 D // /// ENSMUST E-04 NM_ // Egr2 // early growth response 2 // 10 B cm // /// EN E-04 NM_ // Asap1 // ArfGAP with SH# domain, ankyrin repeat and PH domain1 // E-05 NM_ // Kremen1 // kringle containing transmembrane protein 1 // 11 A1 // E-06 NM_ // Fam135a // family with sequence similarity 135, member A // 1 A5 // E-05 NM_ // Twist2 // twist homolog 2 (Drosophila) // 1 D // /// ENSMUST E-04 NM_ // Syn1 // synapsin I // X A1-A4 X 6.2 cm // /// NM_ // E-04 NM_ // Dok4 // docking protein 4 // 8 D1 // /// NM_ // Polr2c E-04 NM_ // Mapkapk3 // mitogen-activated protein kinaseactivated protein kina E-04 NM_ // Zfp462 // zinc finger protein 462 // 4 B3 // /// ENSMUST E-04 NM_ // Angptl2 // angiopoietin-like 2 // 2 B // /// ENSMUST E-04 NM_ // Tsc22d1 // TSC22 domain family, member 1 // 14 D cm // E-05 NM_ // Cenpp // centromere protein P // 13 B1 // /// ENSMUST E-03 NM_ // Sstr2 // somatostatin receptor 2 // 11 E cm // /// N E-04 NM_ // Col12a1 // collagen, type XII, alpha 1 // 9 E cm // / E-04 NM_ // Rai14 // retinoic acid induced 14 // 15 A2 // /// ENSMUST E-04 NM_ // Stmn2 // stathmin-like 2 // 3 A cm // /// ENSMUST E-04

14 Stra6 Pdgfra Zbtb2 Tmem45a Tnfrsf12a Timp1 Musk Retsat Prickle1 Pgm2l1 Isl1 Itpripl2 Stbd1 Glis1 Wnt5a Mmp28 Pax3 Rgnef Msx1 Abcc4 Ephb6 Phldb2 Rnf125 Rab3a Btg3 Aaas Ikzf E14Rik E01Rik Kalrn NM_ // Stra6 // stimulated by retinoic acid gene 6 // 9 C // /// NM_ E-04 NM_ // Pdgfra // platelet derived growth factor receptor, alpha polypeptid E-04 NM_ // Zbtb2 // zinc finger and BTB domain containing 2 // 10 A1 // E-04 NM_ // Tmem45a // transmembrane protein 45a // 16 C1.1 // /// ENSMUS E-04 NM_ // Tnfrsf12a // tumor necrosis factor receptor superfamily, member 12a E-03 NM_ // Timp1 // tissue inhibitor of metalloproteinase 1 // X A1.3 X E-04 NM_ // Musk // muscle, skeletal, receptor tyrosine kinase // 4 B E-04 NM_ // Retsat // retinol saturase (all trans retinol 13,14 reductase) // E-04 NM_ // Prickle1 // prickle like 1 (Drosophila) // 15 E3 // /// E E-04 NM_ // Pgm2l1 // phosphoglucomutase 2-like 1 // 7 F1 // /// ENSMUST E-04 NM_ // Isl1 // ISL1 transcription factor, LIM/homeodomain // 13 D2.3 // E-04 NM_ // Itpripl2 // inositol 1,4,5-triphosphate receptor interacting pro E-04 NM_ // Stbd1 // starch binding domain 1 // 5 E cm // /// ENS E-04 NM_ // Glis1 // GLIS family zinc finger 1 // 4 C6 // /// ENSMUST E-04 NM_ // Wnt5a // wingless-related MMTV integration site 5A // 14 A E-05 NM_ // Mmp28 // matrix metallopeptidase 28 (epilysin) // 11 C // // E-04 NM_ // Pax3 // paired box gene 3 // 1 C cm // /// NM_ E-05 NM_ // Rgnef // Rho-guanine nucleotide exchange factor // 13 D cm E-04 NM_ // Msx1 // homeobox, msh-like 1 // 5 B cm // /// ENSMUST E-04 NM_ // Abcc4 // ATP-binding cassette, sub-family C (CFTR/MRP), member E-04 NM_ // Ephb6 // Eph receptor B6 // 6 B2.1 // /// NM_ // Eph E-04 NM_ // Phldb2 // pleckstrin homology-like domain, family B, member 2 // E-05 NM_ // Rnf125 // ring finger protein 125 // 18 A2 // /// ENSMUST E-04 NM_ // Rab3a // RAB3A, member RAS oncogene family // 8 B cm // E-04 NM_ // Btg3 // B-cell translocation gene 3 // 16 C3.1 // /// NR_ E-04 NM_ // Aaas // achalasia, adrenocortical insufficiency, alacrimia // 15 F E-04 NM_ // Ikzf2 // IKAROS family zinc finger 2 // 1 C3 // /// ENSMUST E-04 NM_ // E14Rik // RIKEN cdna E14 gene // 13 C1 // // E-04 NM_ // E01Rik // RIKEN cdna E01 gene // 2 A2 // /// EN E-03 BC // Kalrn // kalirin, RhoGEF kinase // 16 B3 // /// BC // K E-04

15 Tmem119 Rgl1 Rufy3 B3gnt2 Btg3 Fam161a Srxn1 Rab39b Zfp365 Prrx1 Rab27b Cc2d2a Slc39a14 Phtf2 Ell2 Arl10 Dnajb14 Golim4 Manea Lrrk2 Kif21b Rnf41 Slc44a2 Dusp8 Sertad1 Mupcdh E2f5 Prkaa1 Nr1d1 Pqlc3 NM_ // Tmem119 // transmembrane protein 119 // 5 F // /// ENSMUST E-06 NM_ // Rgl1 // ral guanine nucleotide dissociation stimulator,-like 1 // E-04 NM_ // Rufy3 // RUN and FYVE domain containing 3 // 5 E cm // E-04 NM_ // B3gnt2 // UDP-GlcNAc:betaGal beta-1,3-nacetylglucosaminyltransfera E-04 NM_ // Btg3 // B-cell translocation gene 3 // 16 C3.1 // /// NR_ E-04 BC // Fam161a // family with sequence similarity 161, member A // 11 A E-04 NM_ // Srxn1 // sulfiredoxin 1 homolog (S. cerevisiae) // 2 H1 // // E-04 NM_ // Rab39b // RAB39B, member RAS oncogene family // X A7.3 // /// E-04 NM_ // Zfp365 // zinc finger protein 365 // 10 B5.1 // /// ENSMUST E-04 NM_ // Prrx1 // paired related homeobox 1 // 1 H cm // /// E-04 NM_ // Rab27b // RAB27b, member RAS oncogene family // 18 E cm E-04 NM_ // Cc2d2a // coiled-coil and C2 domain containing 2A // 5 B3 // E-04 NM_ // Slc39a14 // solute carrier family 39 (zinc transporter), member E-05 NM_ // Phtf2 // putative homeodomain transcription factor 2 // 5 A3 // E-04 NM_ // Ell2 // elongation factor RNA polymerase II 2 // 13 C1 // // E-04 NM_ // Arl10 // ADP-ribosylation factor-like 10 // 13 B1 // /// ENSM E-04 NM_ // Dnajb14 // DnaJ (Hsp40) homolog, subfamily B, member 14 // 3 G E-04 NM_ // Golim4 // golgi integral membrane protein 4 // 3 E3 // /// EN E-04 NM_ // Manea // mannosidase, endo-alpha // 4 A3 // /// ENSMUST E-04 NM_ // Lrrk2 // leucine-rich repeat kinase 2 // 15 F1 // /// ENSMUST E-05 NM_ // Kif21b // kinesin family member 21B // 1 E cm // / E-04 NM_ // Rnf41 // ring finger protein 41 // 10 D cm // /// EN E-04 NM_ // Slc44a2 // solute carrier family 44, member 2 // 9 A3 // /// E-04 NM_ // Dusp8 // dual specificity phosphatase 8 // 7 F cm // E-04 NM_ // Sertad1 // SERTA domain containing 1 // 7 A3 // /// ENSMUST E-04 NM_ // Mupcdh // mucin-like protocadherin // 7 F5 // /// NM_ E-04 NM_ // E2f5 // E2F transcription factor 5 // 3 A1 // /// ENSMUST E-04 NM_ // Prkaa1 // protein kinase, AMP-activated, alpha 1 catalytic subun E-04 NM_ // Nr1d1 // nuclear receptor subfamily 1, group D, member 1 // 11 D // E-05 NM_ // Pqlc3 // PQ loop repeat containing // 12 A1.1 // /// NM_ E-04

16 Epb4.1l3 Slc1a4 Slc9a2 Wwc2 Zeb2 Elk3 Slc7a1 Tmem104 Derl3 Akap2 Carf Rnf138 Adamts12 Eml3 Sash1 Cdc2l6 Ddr1 Bag3 Bcor Ppt2 Tmem54 Fdxr E11Rik Slc10a7 Dbc1 Rnf149 Chpf2 Purg Svep P08Rik NM_ // Epb4.1l3 // erythrocyte protein band 4.1-like 3 // 17 E E-04 NM_ // Slc1a4 // solute carrier family 1 (glutamate/neutral amino acid tra E-04 NM_ // Slc9a2 // solute carrier family 9 (sodium/hydrogen exchanger), m E-04 NM_ // Wwc2 // WW, C2 and coiled-coil domain containing 2 // 8 B E-04 NM_ // Zeb2 // zinc finger E-box binding homeobox 2 // 2 C1 // /// E E-04 NM_ // Elk3 // ELK3, member of ETS oncogene family // 10 C-D cm / E-05 NM_ // Slc7a1 // solute carrier family 7 (cationic amino acid transporter, E-04 NM_ // Tmem104 // transmembrane protein 104 // 11 E2 // /// ENSM E-04 NM_ // Derl3 // Der1-like domain family, member 3 // 10 C1 // /// EN E-03 NM_ // Akap2 // A kinase (PRKA) anchor protein 2 // 4 B3 // /// N E-04 NM_ // Carf // calcium response factor // 1 C2 // /// ENSMUST E-04 NM_ // Rnf138 // ring finger protein 138 // 18 A2 // /// NM_ / E-04 NM_ // Adamts12 // a disintegrin-like and metallopeptidase (reprolysin typ E-04 NM_ // Eml3 // echinoderm microtubule associated protein like 3 // 19 A // E-04 NM_ // Sash1 // SAM and SH3 domain containing 1 // 10 A1 // /// ENSM E-04 NM_ // Cdc2l6 // cell division cycle 2-like 6 (CDK8-like) // 10 B1 // E-04 NM_ // Ddr1 // discoidin domain receptor family, member 1 // 17 C E-04 NM_ // Bag3 // BCL2-associated athanogene 3 // 7 F3 // /// ENSMUST E-05 NM_ // Bcor // BCL6 interacting corepressor // X A1.2 // /// NM_ E-03 NM_ // Ppt2 // palmitoyl-protein thioesterase 2 // 17 B cm // E-04 NM_ // Tmem54 // transmembrane protein 54 // 4 D2.2 // /// ENSMUST E-04 NM_ // Fdxr // ferredoxin reductase // 11 E2 // /// ENSMUST E-04 NM_ // E11Rik // RIKEN cdna E11 gene // 9 A5.1 // /// E-05 NM_ // Slc10a7 // solute carrier family 10 (sodium/bile acid cotransporter E-06 NM_ // Dbc1 // deleted in bladder cancer 1 (human) // 4 C2 // /// EN E-06 NM_ // Rnf149 // ring finger protein 149 // 1 B // /// ENSMUST E-04 NM_ // Chpf2 // chondroitin polymerizing factor 2 // 5 A3 // /// EN E-04 NM_ // Purg // purine-rich element binding protein G // 8 A4 // / E-04 NM_ // Svep1 // sushi, von Willebrand factor type A, EGF and pentraxin dom E-04 NM_ // P08Rik // RIKEN cdna P08 gene // 13 B3 // /// N E-04

17 Synj1 Mras Rdx H24Rik Tmem173 Mknk2 Hdac5 Metrnl Pcnx Blzf1 Phlda3 Shroom G10Rik Kifap3 Trp53i11 Fstl1 Abcc1 Itfg3 Magmas Gpsm1 Stxbp1 Polk Gpd2 Zswim4 Kctd10 Hdac1 Mthfd2l Adrbk1 Timp2 Fam128b ENSMUST // Synj1 // synaptojanin 1 // 16 C3-C4 // /// AB E-04 NM_ // Mras // muscle and microspikes RAS // 9 E3.3 // E-04 NM_ // Rdx // radixin // 9 A5.3 // /// NM_ // Rdx // radixi E-03 BC // H24Rik // RIKEN cdna H24 gene // 2 F3 2 // /// E-04 BC // Tmem173 // transmembrane protein 173 // 18 B3 18 // /// DQ E-04 NM_ // Mknk2 // MAP kinase-interacting serine/threonine kinase 2 // 10 C E-04 NM_ // Hdac5 // histone deacetylase 5 // 11 D // /// NM_ // E-05 NM_ // Metrnl // meteorin, glial cell differentiation regulatorlike // E-04 NM_ // Pcnx // pecanex homolog (Drosophila) // 12 D1 // /// ENSMUST E-04 NM_ // Blzf1 // basic leucine zipper nuclear factor 1 // 1 H1 // /// E-05 NM_ // Phlda3 // pleckstrin homology-like domain, family A, member 3 // E-04 NM_ // Shroom4 // shroom family member 4 // X A1.1 // /// ENSMUS E-03 NM_ // G10Rik // RIKEN cdna G10 gene // 4 E2 // /// N E-04 NM_ // Kifap3 // kinesin-associated protein 3 // 1 H1 // /// ENSMUST E-04 NM_ // Trp53i11 // transformation related protein 53 inducible protein E-04 NM_ // Fstl1 // follistatin-like 1 // 16 B cm // /// ENSMUS E-04 NM_ // Abcc1 // ATP-binding cassette, sub-family C (CFTR/MRP), member 1 // E-05 NM_ // Itfg3 // integrin alpha FG-GAP repeat containing 3 // 17 A3.3 // E-04 NM_ // Magmas // mitochondria-associated protein involved in granulocyte-m E-04 NM_ // Gpsm1 // G-protein signalling modulator 1 (AGS3- like, C. elegans) / E-04 NM_ // Stxbp1 // syntaxin binding protein 1 // 2 B cm // / E-04 NM_ // Polk // polymerase (DNA directed), kappa // 13 D1 // /// ENSM E-03 NM_ // Gpd2 // glycerol phosphate dehydrogenase 2, mitochondrial // 2 C E-04 NM_ // Zswim4 // zinc finger, SWIM domain containing 4 // 8 C3 // / E-04 NM_ // Kctd10 // potassium channel tetramerisation domain containing E-04 NM_ // Hdac1 // histone deacetylase 1 // 4 D cm // /// EN E-04 NM_ // Mthfd2l // methylenetetrahydrofolate dehydrogenase (NADP+ dependent E-04 NM_ // Adrbk1 // adrenergic receptor kinase, beta 1 // 19 A cm // E-03 NM_ // Timp2 // tissue inhibitor of metalloproteinase 2 // 11 E c E-05 BC // Fam128b // family with sequence similarity 128, member B // 16 A2 // E-04

18 Tsc22d2 Ptpn9 Rnf160 Mtmr3 Wars2 Lims1 Zfp189 Gpr137 Cpt1c Cdc25a Smap1 Ube2m Prrc1 Gdf10 Taf5 Srgap2 Coro1b Eme2 Gm10398 NM_ // Tsc22d2 // TSC22 domain family, member 2 // 3 D // /// ENS E-04 NM_ // Ptpn9 // protein tyrosine phosphatase, nonreceptor type 9 // --- / E-04 NM_ // Rnf160 // ring finger protein 160 // 16 C3.3 // /// ENSMUS E-04 NM_ // Mtmr3 // myotubularin related protein 3 // 11 A1 // /// ENSMU E-04 NM_ // Wars2 // tryptophanyl trna synthetase 2 (mitochondrial) // 3 F3 // E-04 NM_ // Lims1 // LIM and senescent cell antigen-like domains 1 // 10 B E-05 NM_ // Zfp189 // zinc finger protein 189 // 4 B1 // /// ENSMUST E-04 NM_ // Gpr137 // G protein-coupled receptor 137 // 19 A // /// NM_ E-04 NM_ // Cpt1c // carnitine palmitoyltransferase 1c // 7 B2 // /// ENS E-03 NM_ // Cdc25a // cell division cycle 25 homolog A (S. pombe) // 9 F E-05 NM_ // Smap1 // stromal membrane-associated protein 1 // 1 A5 // /// E-04 NM_ // Ube2m // ubiquitin-conjugating enzyme E2M (UBC12 homolog, yeast) // E-04 NM_ // Prrc1 // proline-rich coiled-coil 1 // 18 D3 // /// ENSMUST E-04 NM_ // Gdf10 // growth differentiation factor 10 // 14 B cm // E-04 NM_ // Taf5 // TAF5 RNA polymerase II, TATA box binding protein (TBP)-asso E-04 NM_ // Srgap2 // SLIT-ROBO Rho GTPase activating protein 2 // 1 E4 // E-04 NM_ // Coro1b // coronin, actin binding protein 1B // 19 A cm // E-04 ENSMUST // Eme2 // essential meiotic endonuclease 1 homolog 2 (S. pom E-04 ENSMUST // Gm10398 // predicted gene // -- - // E-04

19 Table S3. Transcripts induced by BMP4 in both wild-type and MuSK -/- myoblasts. Fold-changes indicate the upregulation of the listed transcript by BMP4. Gene Symbol Sp7 Fabp7 Grem2 Id1 Dlx2 Ptgs2 Id3 Smad6 Alpl Foxq1 Unc5b Smad7 Serpinb8 Bambi Lgr6 Fgfr2 Atoh8 Id2 Smad9 Lxn Adamts9 Nkd2 Gcnt2 fold change (MuSK-/-) gene_assignment fold change (wt) p-value p-value NM_ // Sp7 // Sp7 transcription factor 7 // 15 F3 // /// ENSMUST E E-04 NM_ // Fabp7 // fatty acid binding protein 7, brain // 10 B4 // /// E E-06 NM_ // Grem2 // gremlin 2 homolog, cysteine knot superfamily (Xenopus laev E E-06 NM_ // Id1 // inhibitor of DNA binding 1 // 2 H cm // /// EN E E-05 NM_ // Dlx2 // distal-less homeobox 2 // 2 C cm // /// ENSMU E E-04 NM_ // Ptgs2 // prostaglandinendoperoxide synthase 2 // 1 H cm // E E-04 NM_ // Id3 // inhibitor of DNA binding 3 // 4 D cm // /// EN E E-04 NM_ // Smad6 // MAD homolog 6 (Drosophila) // 9 D // /// ENSMUST E E-05 NM_ // Alpl // alkaline phosphatase, liver/bone/kidney // 4 D cm / E E-04 NM_ // Foxq1 // forkhead box Q1 // 13 A cm // /// ENSMUST E E-05 NM_ // Unc5b // unc-5 homolog B (C. elegans) // 10 B cm // E E-04 NM_ // Smad7 // MAD homolog 7 (Drosophila) // --- // /// ENSMUST E E-05 NM_ // Serpinb8 // serine (or cysteine) peptidase inhibitor, clade B, memb E E-04 NM_ // Bambi // BMP and activin membrane-bound inhibitor, homolog (Xenopus E E-05 NM_ // Lgr6 // leucine-rich repeat-containing G protein-coupled recepto E E-05 NM_ // Fgfr2 // fibroblast growth factor receptor 2 // 7 F3 // /// N E E-05 NM_ // Atoh8 // atonal homolog 8 (Drosophila) // 6 C1 // /// ENSMUST E E-04 NM_ // Id2 // inhibitor of DNA binding 2 // 12 B cm // /// EN E E-04 NM_ // Smad9 // MAD homolog 9 (Drosophila) // 3 D // /// ENSMUST E E-05 NM_ // Lxn // latexin // 3 E cm // /// ENSMUST // E E-04 NM_ // Adamts9 // a disintegrin-like and metallopeptidase (reprolysin type E E-05 NM_ // Nkd2 // naked cuticle 2 homolog (Drosophila) // 13 C1 // /// E E-04 NM_ // Gcnt2 // glucosaminyl (Nacetyl) transferase 2, I-branching enzyme E E-05

20 I 06Rik Dlx1 Rspo3 Smoc2 Enc1 Pgf Lfng Baalc Ctgf Foxl1 Serpine1 Gnb4 Wnt2 Kif26b Kctd12 Myo1d Pde8a Fam84a Ahcyl2 Csrp2 Wnt4 Optn Fam19a5 Cspg4 Gas6 NM_ // I06Rik // RIKEN cdna I06 gene // 13 A4 13 // // E E-04 NM_ // Dlx1 // distal-less homeobox 1 // 2 C cm // /// ENSMU E E-05 NM_ // Rspo3 // R-spondin 3 homolog (Xenopus laevis) // 10 A4 // /// E E-04 NM_ // Smoc2 // SPARC related modular calcium binding 2 // cm // E E-07 NM_ // Enc1 // ectodermal-neural cortex 1 // 13 D1 // /// ENSMUST E E-05 NM_ // Pgf // placental growth factor // 12 D cm // /// ENSM E E-04 NM_ // Lfng // LFNG O- fucosylpeptide 3-beta-Nacetylglucosaminyltransferas E E-05 NM_ // Baalc // brain and acute leukemia, cytoplasmic // 15 C cm / E E-05 NM_ // Ctgf // connective tissue growth factor // 10 A3-B cm // E E-05 NM_ // Foxl1 // forkhead box L1 // 8 E cm // /// BC // E E-04 NM_ // Serpine1 // serine (or cysteine) peptidase inhibitor, clade E, memb E E-04 NM_ // Gnb4 // guanine nucleotide binding protein (G protein), beta 4 // E E-04 NM_ // Wnt2 // wingless-related MMTV integration site 2 // cm // E E-04 NM_ // Kif26b // kinesin family member 26B // 1 H4 // /// BC E E-06 NM_ // Kctd12 // potassium channel tetramerisation domain containing 12 // E E-04 NM_ // Myo1d // myosin ID // 11 B cm // /// ENSMUST E E-05 NM_ // Pde8a // phosphodiesterase 8A // 7 D3 // /// ENSMUST E E-06 NM_ // Fam84a // family with sequence similarity 84, member A // 12 A3 // E E-05 NM_ // Ahcyl2 // S- adenosylhomocysteine hydrolase-like 2 // 6 A3.3 // E E-05 NM_ // Csrp2 // cysteine and glycine-rich protein 2 // 10 D1 // /// E E-04 NM_ // Wnt4 // wingless-related MMTV integration site 4 // 4 D3 // / E E-06 NM_ // Optn // optineurin // 2 A cm // /// ENSMUST E E-05 NM_ // Fam19a5 // family with sequence similarity 19, member A5 // 15 E3 / E E-05 NM_ // Cspg4 // chondroitin sulfate proteoglycan 4 // 9 B // /// EN E E-04 NM_ // Gas6 // growth arrest specific 6 // 8 A cm // /// EN E E-07

21 Nfkbia Hoxa10 Prrx2 Slc7a11 Cxcl14 Dock5 Ank Samhd1 Npr3 Mmp11 Chmp2b Dpysl3 Pcdh18 Jag1 Cux E23Rik Relt Adamtsl3 Tpbg Fam38b2 Sox9 Epha2 Tnfrsf21 Ptprm NM_ // Nfkbia // nuclear factor of kappa light polypeptide gene enhancer i E E-05 NM_ // Hoxa10 // homeo box A10 // 6 B cm // /// NM_ E E-04 NM_ // Prrx2 // paired related homeobox 2 // 2 B cm // /// EN E E-04 NM_ // Slc7a11 // solute carrier family 7 (cationic amino acid transporter E E-04 NM_ // Cxcl14 // chemokine (C-X-C motif) ligand 14 // 13 B1 // /// E E E-04 NM_ // Dock5 // dedicator of cytokinesis 5 // 14 D1 // /// ENSMUST E E-05 NM_ // Ank // progressive ankylosis // 15 B cm // /// ENSMU E E-06 NM_ // Samhd1 // SAM domain and HD domain, 1 // 2 H2 // /// NM_ E E-04 NM_ // Npr3 // natriuretic peptide receptor 3 // 15 A cm // E E-05 NM_ // Mmp11 // matrix metallopeptidase 11 // 10 C cm // // E E-05 NM_ // Chmp2b // chromatin modifying protein 2B // 16 C1.3 // /// EN E E-08 NM_ // Dpysl3 // dihydropyrimidinase-like 3 // 18 B3 // /// NM_ E E-07 NM_ // Pcdh18 // protocadherin 18 // 3 C // /// ENSMUST / E E-05 NM_ // Jag1 // jagged 1 // 2 F cm // /// ENSMUST E E-05 NM_ // Cux1 // cut-like homeobox 1 // 5 G cm // /// NM_ E E-04 NM_ // E23Rik // RIKEN cdna E23 gene // 3 E3 // /// EN E E-04 NM_ // Relt // RELT tumor necrosis factor receptor // 7 E3 // /// E E E-04 ENSMUST // Adamtsl3 // ADAMTS-like 3 // 7 D3 // /// AK / E E-05 NM_ // Tpbg // trophoblast glycoprotein // 9 E3.1 // /// ENSMUST E E-04 ENSMUST // Fam38b2 // family with sequence similarity 38, member B2 / E E-04 NM_ // Sox9 // SRY-box containing gene 9 // 11 E cm // /// E E-04 NM_ // Epha2 // Eph receptor A2 // 4 D-E cm // /// ENSMUST E E-04 NM_ // Tnfrsf21 // tumor necrosis factor receptor superfamily, member 21 / E E-05 NM_ // Ptprm // protein tyrosine phosphatase, receptor type, M // 17 E E E-04

22 Crim1 Atp10d Man1a Lyst Fzd6 Ass1 Tmem2 Gclc Slc44a1 Slc5a3 Palld Atp2c1 Slc7a2 Kirrel Capn G13Rik Chst11 Peli2 Ahr Lrp6 Ednra Tln2 Acvr1 Galnt2 Dlst Fam65a NM_ // Crim1 // cysteine rich transmembrane BMP regulator 1 (chordin like) E E-05 NR_ // Atp10d // ATPase, class V, type 10D // 5 C3.2 // /// NM_ E E-04 NM_ // Man1a // mannosidase 1, alpha // 10 B3 // /// ENSMUST E E-04 NM_ // Lyst // lysosomal trafficking regulator // 13 A cm // E E-04 NM_ // Fzd6 // frizzled homolog 6 (Drosophila) // 15 B cm // E E-06 NM_ // Ass1 // argininosuccinate synthetase 1 // 2 B cm // // E E-05 NM_ // Tmem2 // transmembrane protein 2 // 19 B // /// NM_ E E-05 NM_ // Gclc // glutamate-cysteine ligase, catalytic subunit // 9 D-E E E-05 NM_ // Slc44a1 // solute carrier family 44, member 1 // 4 B2 // /// E E-04 NM_ // Slc5a3 // solute carrier family 5 (inositol transporters), member E E-05 NM_ // Palld // palladin, cytoskeletal associated protein // 8 B3.3 // E E-05 NM_ // Atp2c1 // ATPase, Ca++sequestering // 9 F1 // /// ENSMUST E E-04 NM_ // Slc7a2 // solute carrier family 7 (cationic amino acid transporter, E E-04 NM_ // Kirrel // kin of IRRE like (Drosophila) // 3 F1 // /// ENSMU E E-04 NM_ // Capn5 // calpain 5 // 7 E2 // /// ENSMUST // Capn E E-04 BC // G13Rik // RIKEN cdna G13 gene // 4 C1 // /// NM E E-04 NM_ // Chst11 // carbohydrate sulfotransferase 11 // 10 C1 // /// EN E E-06 NM_ // Peli2 // pellino 2 // 14 C cm // /// ENSMUST E E-05 NM_ // Ahr // aryl-hydrocarbon receptor // 12 A cm // /// E E E-05 NM_ // Lrp6 // low density lipoprotein receptor-related protein 6 // 6 G E E-04 NM_ // Ednra // endothelin receptor type A // --- // /// ENSMUST E E-05 NM_ // Tln2 // talin 2 // 9 C // /// ENSMUST // Tln2 / E E-05 NM_ // Acvr1 // activin A receptor, type 1 // 2 C1.1 // /// NM_ E E-04 NM_ // Galnt2 // UDP-N-acetylalpha-D-galactosamine:polypeptide N- acetylga E E-04 NM_ // Dlst // dihydrolipoamide S- succinyltransferase (E2 component of 2-o E E-04 NM_ // Fam65a // family with sequence similarity 65, member A // 8 D3 / E E-04

23 Csnk1g3 Fut8 Cdh11 Zfp287 Fryl NM_ // Csnk1g3 // casein kinase 1, gamma 3 // 18 D1-D2 // /// BC E E-04 NM_ // Fut8 // fucosyltransferase 8 // 12 C3 // /// ENSMUST E E-04 NM_ // Cdh11 // cadherin 11 // 8 D cm // /// ENSMUST E E-04 NM_ // Zfp287 // zinc finger protein 287 // 11 B2 // /// ENSMUST E E-04 NM_ // Fryl // furry homolog-like (Drosophila) // 5 C3.2 // /// ENSM E E-04

24 Table S4. Transcripts induced by BMP4 only in MuSK -/- myoblasts. Fold-changes indicate the upregulation of the listed transcript by BMP4. Gene Symbol gene_assignment fold change p-value Lin7a NM_ // Lin7a // lin-7 homolog A (C. elegans) // 10 D1 // /// NM_ E-04 Gm12824 NM_ // Gm12824 // predicted gene // 4 D1 4 // /// ENSMUST E-04 Hey1 NM_ // Hey1 // hairy/enhancer-of-split related with YRPW motif 1 // 3 A E-04 Selp NM_ // Selp // selectin, platelet // 1 H cm // /// ENSMUST E-06 Tbx1 NM_ // Tbx1 // T-box 1 // 16 A cm // /// ENSMUST E-04 Stc2 NM_ // Stc2 // stanniocalcin 2 // 11 A4 // /// ENSMUST // E-04 Slc1a3 NM_ // Slc1a3 // solute carrier family 1 (glial high affinity glutamate tr E-05 Irf5 NM_ // Irf5 // interferon regulatory factor 5 // 6 A cm // E-04 Emb NM_ // Emb // embigin // 13 D2.3 // /// ENSMUST // Emb // E-04 Klhl29 BC // Klhl29 // kelch-like 29 (Drosophila) // 12 A1.1 // /// ENSMUS E-04 Kcnh5 NM_ // Kcnh5 // potassium voltage-gated channel, subfamily H (eag-related) E-05 Gjb3 NM_ // Gjb3 // gap junction protein, beta 3 // 4 D cm // / E-05 Il15 NM_ // Il15 // interleukin 15 // 8 C cm // /// ENSMUST E-04 Adam12 NM_ // Adam12 // a disintegrin and metallopeptidase domain 12 (meltrin alp E-06 Fam55c NM_ // Fam55c // family with sequence similarity 55, member C // 16 C E-05 Fst NM_ // Fst // follistatin // 13 D2.2 // /// ENSMUST // Fs E-05 Ppp1r3c NM_ // Ppp1r3c // protein phosphatase 1, regulatory (inhibitor) subunit 3C E-05 Slc2a13 NM_ // Slc2a13 // solute carrier family 2 (facilitated glucose transpor E-04 Tbx20 NM_ // Tbx20 // T-box 20 // 9 A4 // /// NM_ // Tbx20 // T-box E-05 Ankrd44 NM_ // Ankrd44 // ankyrin repeat domain 44 // 1 C1.1 // /// ENSM E-05 Depdc6 NM_ // Depdc6 // DEP domain containing 6 // 15 D cm // // E-04 Hmgcll1 NM_ // Hmgcll1 // 3-hydroxymethyl-3-methylglutaryl- Coenzyme A lyase-like E-04 Krt19 NM_ // Krt19 // keratin 19 // 11 D cm // /// ENSMUST E-04 Adcy8 NM_ // Adcy8 // adenylate cyclase 8 // 15 D cm // /// ENSMU E-04 Adamtsl1 NM_ // Adamtsl1 // ADAMTS-like 1 // 4 C4 // /// ENSMUST / E-05 Bmp2k NM_ // Bmp2k // BMP2 inducible kinase // 5 E3 // /// ENSMUST E-04

25 Grem1 Pparg Fzd4 Pdgfrl Acss3 Osbpl6 A930038C07Rik Rims2 Iqgap2 Vegfc Asb4 Efna P16Rik Prrg1 Grhl1 Esyt3 Hoxb2 Sostdc1 Acsl1 Zbtb25 Cish Cd47 Pgam2 Il13ra1 Hoxa9 Chsy3 Nrp2 Trib2 Gramd2 Glis3 NM_ // Grem1 // gremlin 1 // 2 E cm // /// ENSMUST E-04 NM_ // Pparg // peroxisome proliferator activated receptor gamma // 6 E E-04 NM_ // Fzd4 // frizzled homolog 4 (Drosophila) // 7 E cm // E-05 NM_ // Pdgfrl // platelet-derived growth factor receptor-like // 8 A4 // E-06 NM_ // Acss3 // acyl-coa synthetase short-chain family member 3 // 10 D E-04 NM_ // Osbpl6 // oxysterol binding protein-like 6 // 2 C3 // /// ENS E-04 BC // A930038C07Rik // RIKEN cdna A930038C07 gene // 6 C1 // /// NM_ E-06 NM_ // Rims2 // regulating synaptic membrane exocytosis 2 // 15 C E-05 NM_ // Iqgap2 // IQ motif containing GTPase activating protein 2 // 13 D E-05 NM_ // Vegfc // vascular endothelial growth factor C // 8 B3 // /// E-04 NM_ // Asb4 // ankyrin repeat and SOCS box-containing 4 // 6 A cm / E-04 NM_ // Efna3 // ephrin A3 // 3 F cm // /// ENSMUST E-04 BC // P16Rik // RIKEN cdna P16 gene // 7 B1 // /// NM E-04 BC // Prrg1 // proline rich Gla (G-carboxyglutamic acid) 1 // X B // E-04 NM_ // Grhl1 // grainyhead-like 1 (Drosophila) // 12 A1.3 // /// E-04 NM_ // Esyt3 // extended synaptotagmin-like protein 3 // 9 E cm E-04 NM_ // Hoxb2 // homeo box B2 // 11 D cm // /// ENSMUST E-04 NM_ // Sostdc1 // sclerostin domain containing 1 // 12 B2 // /// ENS E-04 NM_ // Acsl1 // acyl-coa synthetase long-chain family member 1 // 8 B2 // E-05 NM_ // Zbtb25 // zinc finger and BTB domain containing 25 // cm // E-04 NM_ // Cish // cytokine inducible SH2-containing protein // 9 F cm E-04 NM_ // Cd47 // CD47 antigen (Rh-related antigen, integrinassociated signa E-04 NM_ // Pgam2 // phosphoglycerate mutase 2 // 11 A1 // /// ENSMUST E-04 NM_ // Il13ra1 // interleukin 13 receptor, alpha 1 // X A3.3 X 12.5 cm // E-04 NM_ // Hoxa9 // homeo box A9 // 6 B cm // /// ENSMUST E-04 NM_ // Chsy3 // chondroitin sulfate synthase 3 // 18 D3 // /// EN E-04 NM_ // Nrp2 // neuropilin 2 // 1 C2 // /// NM_ // Nrp2 / E-06 NM_ // Trib2 // tribbles homolog 2 (Drosophila) // 12 A1.1 // /// E E-06 NM_ // Gramd2 // GRAM domain containing 2 // 9 B // /// ENSMUST E-06 NM_ // Glis3 // GLIS family zinc finger 3 // 19 C1 // /// ENSMUST E-04