Table 1. Chromatin accessibility study identifies driver candidates during EMT.
| Accessibility change Day 2 | Gene expression change | Gene | Gene full name | GO Function |
|---|---|---|---|---|
| Decreased (closed) | Down-regulated | KRT5 | keratin 5 | scaffold protein binding and structural constituent of cytoskeleton |
| IRF6 | interferon regulatory factor 6 | regulatory region DNA binding and sequence-specific DNA binding transcription factor activity | ||
| MAP7 | microtubule-associated protein 7 | structural molecule activity and receptor binding. | ||
| PTPN3 | protein tyrosine phosphatase, non-receptor type 3 | protein tyrosine phosphatase activityand ATPase binding | ||
| SNCA | synuclein, alpha | phospholipid binding and calcium ion binding. | ||
| MST1R | macrophage stimulating 1 receptor | macrophage colony-stimulating factor receptor activity andenzyme binding | ||
| CYP27B1 | cytochrome P450, family 27 | electron carrier activity and heme binding | ||
| EPHA1 | EPH receptor A1 | Trans membrane-ephrin receptor activity and protein kinase binding | ||
| CYP4F11 | cytochrome P450, subfamily 4F, polypeptide 11 | electron carrier activity and heme binding | ||
| GNAL | guanine nucleotide binding protein | GTP binding and GTPase activity | ||
| DDR1 | discoidin domain receptor tyrosine kinase 1 | collagen binding and protein tyrosine kinase collagen receptor activity | ||
| IL1RN | interleukin 1 receptor antagonist | interleukin-1 receptor binding and interleukin-1, Type I receptor binding | ||
| WWC1 | WW and C2 domain containing 1 | transcription coactivator activity and protein binding, bridging | ||
| TRIM29 | tripartite motif containing 29 | p53 binding and sequence-specific DNA binding transcription factor activity | ||
| Increased (opened) | Up-regulated | FADS1 | fatty acid desaturase 1 | oxidoreductase activity and iron ion binding |
| RGS4 | regulator of G-protein signaling 4 | calmodulin binding and GTPase activator activity | ||
| ACP1 | acid phosphatase 1 | SH3 domain binding and non-membrane spanning protein tyrosine phosphatase activity | ||
| VIM | vimentin | structural constituent of cytoskeleton and identical protein binding |
Intersection of genes that gain or lose accessibility on day 2 of TWIST-driven EMT with lists of genes getting upregulated or downregulated upon EMT induction with 5 different methods [33].