Table 1.
Protein binding identified at the Myod proximal regulatory region (PRR), distal regulatory region (DRR), core enhancer (CE) and adjacent regions
| Region | Interacting protein | Binding shown by | Binding sitea | References |
|---|---|---|---|---|
| PRR | MSC | ChIP-qPCR in mouse embryo branchial arch tissue | Not characterised | Moncaut et al. (2012) |
| TCF21 | ChIP-qPCR in mouse embryo branchial arch tissue | Not characterised. | Moncaut et al. (2012) | |
| RAD21 | ChIP-qPCR in Rhabdomyosarcoma cells | Not characterised | Taberlay et al. (2011) | |
| p300 | ChIP-qPCR in C2C12 cells | Not characterised | Hamed et al. (2013) | |
| MYOD | ChIP-seq in C2C12 cells and primary myoblasts | Not characterised | Mousavi et al. (2013) and Umansky et al. (2015) | |
| MYF5 | ChIP-seq in mouse embryonic fibroblasts transduced with MYF5 | Not characterised | Conerly et al. (2016) | |
| PITX2 | ChIP-PCR in C2C12 cells and extraocular eye muscle cell line | Not characterised | Zacharias et al. (2011) | |
| DELTEX2 | ChIP-qPCR in C2C12 cells | Not characterised | Luo et al. (2017) | |
| Inter PRR–DRR | PITX2 | ChIP-qPCR in hindlimb buds and myotome. EMSA with in vitro translated PITX2 | PITX2 binding site at − 615 bp | L’Honore et al. (2010) |
| MYOD | EMSA with nuclear extracts from hindlimb muscle, G8 myoblasts and C3H/lOT1/2 fibroblasts | Two E boxes at − 1750 and − 865 bp | Zingg et al. (1994) | |
| GLI2 | ChIP-pPCR in P19 cells | GLI consensus binding sites at − 1.6 kb and − 0.6 kb | Voronova et al. (2013) | |
| FOXO3 | ChIP-PCR antibody in C2C12 cells. EMSA with recombinant FOXO3 | Two Forkhead Regulatory Elements at − 940 bp and − 1598 bp | Hu et al. (2008) | |
| PAX3/7 | ChIP-PCR in C2C12 cells. EMSA with recombinant PAX3 and PAX7 | Paired binding site at − 1502 bp | Hu et al. (2008) | |
| CHOP | ChIP-PCR with C2C12 cells | Not characterised. Primers bind at − 3 kb and − 4 kb | Alter and Bengal (2011) | |
| DRR | SIX1/4 | ChIP-seq and -qPCR in C2C12 cells and satellite cell derived myoblasts. EMSA with in vitro translated SIX1 and SIX4 | MEF3 site in DRR | Le Grand et al. (2012), Liu et al. (2010) and Relaix et al. (2013) |
| EYA1/2 | ChIP-qPCR in mouse embryo trunk muscle precursor cells | Not characterised, likely to be via SIX binding at MEF3 site | Relaix et al. (2013) | |
| PITX2 | ChIP-qPCR in mouse embryo myotome | Not characterised | L’Honore et al. (2010) | |
| MSC | ChIP-qPCR in mouse embryo branchial arch tissue | Not characterised | Moncaut et al. (2012) | |
| TCF21 | ChIP-qPCR in mouse embryo branchial arch tissue | Not characterised | Moncaut et al. (2012) | |
| SRF | ChIP-qPCR in C2C12 cells. EMSA with nuclear extracts from C2.7 cells | Divergent CaRG box (a hybrid SRF/MEF2 binding site) | L’Honore et al. (2003) and L’Honore et al. (2007) | |
| MEF2 | ChIP-qPCR in C2C12 cells.. EMSA with nuclear extracts from C2C12 cells | Divergent CaRG box (a hybrid SRF/MEF2 binding site), and a canonical MEF2 binding site | L’Honore et al. (2007) and Mokalled et al. (2012) | |
| YY1 | EMSA with nuclear extracts from C2.7 cells | Divergent CaRG box (a hybrid SRF/MEF2 binding site) | L’Honore et al. (2003) | |
| MRTF-A | ChIP-qPCR in C2C12 cells | Divergent CaRG box (a hybrid SRF/MEF2 binding site) | Mokalled et al. (2012) | |
| MASTR | ChIP-qPCR in C2C12 cells | Divergent CaRG box (a hybrid SRF/MEF2 binding site), and a canonical MEF2 binding site | Mokalled et al. (2012) | |
| C/EBP | EMSA with nuclear extracts from C2.7 cells | Divergent CaRG box (a hybrid SRF/MEF2 binding site) | L’Honore et al. (2003) | |
| p300 | EMSA with nuclear extracts from C2.7 cells. ChIP-qPCR in C2C12 cells | Divergent CaRG box (a hybrid SRF/MEF2 binding site) | L’Honore et al. (2003) and Hamed et al. (2013) | |
| MYOD | ChIP-seq in C2C12 cells and primary myoblasts. | Not characterised | Mousavi et al. (2013) and Umansky et al. (2015) | |
| MYF5 | ChIP-seq in mouse embryonic fibroblasts transduced with MYF5 | Not characterised | Conerly et al. (2016) | |
| DELTEX2 | ChIP-qPCR in C2C12 cells. | Not characterised | Luo et al. (2017) | |
| Inter DRR–CE | MYOD | ChIP-seq in C2C12 cells and primary myoblasts | Not characterised. Chip-seq peaks map to region around − 10.5 kb and − 12 kb | Conerly et al. (2016), Cui et al. (2017) and Umansky et al. (2015) |
| MYF5 | ChIP-seq in mouse embryonic fibroblasts transduced with MYF5 | Not characterised. Chip-seq peaks map to region around − 10.5 kb | Conerly et al. (2016) | |
| CE | SIX1/4 | ChIP -seq and -qPCR in C2C12 cells. EMSA with in vitro translated SIX1 and SIX4 | Two MEF3 sites | Liu et al. (2010) and Relaix et al. (2013) |
| EYA1/2 | ChIP-qPCR in mouse embryo trunk muscle precursor cells | Not characterised, likely to be via SIX binding at MEF3 site | Relaix et al. (2013) | |
| PITX2 | ChIP-qPCR in hindlimb buds and myotome. EMSA with in vitro translated PITX2 | Two PITX2 binding sites | L’Honore et al. (2010) | |
| RAD21 | ChIP-qPCR in Rhabdomyosarcoma cells | Not characterised | Taberlay et al. (2011) | |
| LSD1 | ChIP-qPCR antibody in C2C12 cells | Not characterised | Scionti et al. (2017) | |
| CLOCK | ChIP-PCR in muscles from mice kept in a 12 h light–dark cycle. EMSA with extract from C2C12 cells overexpressing CLOCK and BMAL | Divergent E-box (CAGCTT) | Andrews et al. (2010) and Zhang et al. (2012) | |
| BMAL2 | ChIP-PCR in muscles from mice kept in a 12 h light–dark cycle. EMSA with extract from C2C12 cells overexpressing CLOCK and BMAL | Divergent E-box (CAGCTT) | Andrews et al. (2010) and Zhang et al. (2012) | |
| MYOD | ChIP-seq in mouse embryonic fibroblasts transduced with Myod, in C2C12 cells, and primary myoblasts | Not characterised | Conerly et al. (2016), Cui et al. (2017), Mousavi et al. (2013) and Umansky et al. (2015) | |
| MYF5 | ChIP-seq with in mouse embryonic fibroblasts transduced with MYF5 | Not characterised | Conerly et al. (2016) | |
| YB1 | ChIP-PCR and -qPCR in C2C12 cells expressing | Not characterised | Lee et al. (2004) and Song and Lee (2010) | |
| MSX1 | ChIP-PCR in C2C12 cells and mouse embryo limbs | Not characterised | Lee et al. (2004), Song and Lee (2010) and Wang et al. (2011) | |
| SIM2 | ChIP-PCR in mouse embryo limb buds | Not characterised | Havis et al. (2012) | |
| Upstream of CE | GLI2 | ChIP-pPCR in P19 cells overexpressing GLI2 | GLI consensus binding sites at − 32 kb and − 36 kb | Voronova et al. (2013) |
| PAX7 | Chromatin Tandem Affinity Purification (ChTAP) in satellite cell-derived myoblasts | Not characterised. Chip-seq peaks map to region around − 40 kb | Soleimani et al. (2012b) |
aCharacterized binding sites are those sites where physical binding and/or function had been validated via EMSA and/or luciferase assays, including mutation of the binding site. For some ChIP-seq studies binding was determined through analysis of files downloaded from the Gene Expression Omnibus (Conerly et al. 2016; GEO accession: GSE75370; Cui et al. 2017; GEO accession: GSE63716; Umansky et al. 2015, GEO accession: GSE56131)