Table 3.
Enriched transcription factor-binding site analysis
Binding site enrichment analysis was performed using the Genomatix software suite to determine enriched motifs adjacent (within 50 bp) of MEF2 consensus binding sites in the regulatory region 5 kb upstream of the putative transcriptional start site of antagonistically regulated genes (differentiation genes at the top, cell cycle/proliferation genes at the bottom). The table provides a description of each candidate co-regulator for each enriched motif with a Z-score (Z-scores > 2.0 were considered significantly enriched). The binding factors and their relevant binding domains are included when known. Finally, a brief summary of relevant regulatory function is provided.
| TF module | Module description | Z-Score | Known factor(s) | Binding domain | Function |
|---|---|---|---|---|---|
| Differentiation | |||||
| V$HAND V$MEF2 | Twist subfamily of class B bHLH transcription factors | 4.33 | Hand1, Hand2, Lyl1, Mesp1, Mesp2 Nhlh1, Nhlh2, Scx, Tal1, Tal2, Tcf3, Tcf4, Tcf12, Tcf15, Twist1, Twist2 | bHLH | Positive regulator of striated muscle differentiation, secondary heart field specification |
| V$EBOX V$MEF2 | E-box-binding factors | 4.22 | Atf6, Atf6b, Max, Mga, Mlx, Mlxip, Mlxipl, Mnt, Mxd3, Mxd4, Mxi1, Myc, Mycl, Mycn, Tcfl5, Usf1, Usf2 | bHLH-ZIP, bZIP | Wnt signaling pathway, positive regulator of apoptosis |
| V$MEF2 V$RXRF | RXR heterodimer-binding sites | 3.53 | Nr1h2, Nr1h3, Nr1i2, Nr1i3, Rara, Rarb, Rarg, Rxra, Rxrb, Rxrg, Thra, Thrb, Vdr | C4 zinc-finger domain | Cardiac muscle proliferation, canonical Wnt signaling, ventricular cardiac muscle differentiation |
| V$EGRF V$MEF2 | EGR/nerve growth factor-induced protein C and related factors | 3.41 | Egr1–4, Wt1 | C2H2 zinc-finger domain | Heart development, BMP signaling, positive regulation of cell proliferation |
| V$MEF2 V$RBPF | RBPJ-κ | 2.85 | Rbpj, Rbpjl | RHR | Notch-binding transcriptional regulator, cardiac differentiation |
| V$MEF2 V$SRFF | Serum-response element-binding factor | 2.84 | Srf | MADS box | Positive regulator of cell differentiation |
| V$HESF V$MEF2 | Vertebrate homologues of enhancer of split complex | 2.73 | Bhlhe40, Bhlhe41, Helt, Hes1, Hes2, Hes3, Hes5, Hes6, Hes7, Hey1, Hey2, Heyl, Itgb3bp, Sohlh1, Sohlh2 | bHLH | Notch signaling in cardiac development, cardiac hypertrophy in response to stress |
| V$HOXH V$MEF2 | HOX-MEIS1 heterodimers | 2.72 | Hoxa10, Hoxa11, Hoxa13, Hoxa9, Hoxa9l, Hoxb13, Hoxb9, Hoxc10, Hoxc12, Hoxd10, Hoxd12, Hoxd13, Hoxd9, Meis1–3, | TALE class homeodomain, homeodomain | Embryonic patterning, skeletal muscle tissue development |
| V$MEF2 V$PBXC | PBX-MEIS complexes | 2.14 | Meis1–3, Pbx1–4, Pknox1, Pknox2 | TALE class homeodomain | Heart development |
| Cell cycle | |||||
| V$HAND V$MEF2 | Twist subfamily of class B bHLH transcription factors | 4.33 | Hand1, Hand2, Lyl1, Mesp1, Mesp2 Nhlh1, Nhlh2, Scx, Tal1, Tal2, Tcf3, Tcf4, Tcf12, Tcf15, Twist1, Twist2 | bHLH | Positive regulator of striated muscle differentiation, secondary heart field specification |
| V$FKHD V$MEF2 | Forkhead domain factors | 4.1 | Foxa1–3, Foxb2, Foxc1-2, Foxd1–4, Foxe1, Foxe3, Foxf1, Foxg1, Foxj1-3, Foxk1-2, Foxl1-2, Foxm1, Foxn2-3, Foxo1, Fox3-4, Foxo6, Foxp1–5, Foxq1, Foxs1 | Forkhead domain (winged helix) | G2/M transition, anatomical structure morphogenesis, cardiac muscle proliferation, ventricular cardiac muscle morphogenesis |
| V$MEF2 V$RXRF | RXR heterodimer-binding sites | 3.53 | Nr1h2, Nr1h3, Nr1i2, Nr1i3, Rara, Rarb, Rarg, Rxra, Rxrb, Rxrg, Thra, Thrb, Vdr | C4 zinc-finger domain | Cardiac muscle proliferation, canonical Wnt signaling, ventricular cardiac muscle |
| V$AP1R V$MEF2 | MAF- and AP1-related factors | 3.06 | Bach1-2, Maf, Mafa, Mafb, Maff, Mafg, Mafk, Nfe2, Nfe2l1–3, Nrl, RGD1562865 | BTB-POZ bZIP, bZIP | Regulator of anatomical structure morphogenesis, embryonic development |
| V$MEF2 V$SRFF | Serum-response element-binding factor | 2.84 | Srf | MADS box | Positive regulator of cell differentiation |
| V$IRXF V$MEF2 | Iroquois homeobox factors | 2.63 | Irx1–6, Mkx | Homeodomain | Heart development, negative regulator of myoblast differentiation |
| V$MEF2 V$P53F | p53 tumor supressor | 2.47 | Tp53, Tp63, Tp73 | p53 domain | Cell-cycle arrest, DNA-damage response, regulator of mitotic cell cycle |
| V$GLIF V$MEF2 | GLI zinc finger family | 2.05 | Gli1–3, Glis1–3, Zic1–5 | C2H2 zinc-finger domain | Heart development/looping, cell proliferation, Hedgehog signaling |