Table A4.
Putative TEAD binding sites in the promoter regions of the proneurogenic genes. A PSSM was generated from the JASPAR consensus sequence for binding of the four TEAD paralogs, and used to scan these genes according to a Phython 3.4-based bioinformatics program (available upon request). Putative sequences were then curated with the following criteria: (1) from the ENCODE data base, putative sites were selected on the basis of their location in DNAse I and H3K27Ac sensitive regions, indicative of being regulatory regions; (2) only one mismatch was allowed in the core consensus sequence CATTCC (underlined). The table shows chromosome location, putative TEAD2-binding sequence, maximal score (MS) and relative score (RS) (>80%) of each TEAD isoform according to the Python program. Blanc cells indicate that the program did not recognize a certain sequence for a certain TEAD isoform with a threshold >80%. The letters in brackets in the “Sequence” column correspond to the core of the fragments that were found by ChIP-pPCR with anti-TAZ antibody (See Table A2 of the Appendix A for ChIP primers and PCR fragment length). TEAD2 shows the most robust data and, as shown in Figure A2 of the Appendix A, this is the isoform preferentially expressed in ReNcells VM.
| GENE | LOCALIZATION | SEQUENCE (FROM TEAD2) |
TEAD2 | TEAD1 | TEAD3 | TEAD4 | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| MS | RS | MS | RS | MS | RS | MS | RS | |||
| SOX2 | Chr3: 181428844-181428831 | CCCCATTCCCATC (a) | 8.49 | 90.9 | - | - | - | |||
| chr3:181431413-181431401 | TCCATTCCCCCG (b) | 6.99 | 89.3 | 13.88 | 83 | 2.17 | 92.9 | - | ||
| chr3:181428382-181428394 | AAGATTCCTGAG (c) | 8.06 | 90.5 | 13.77 | 82.8 | 8.01 | 95.8 | 8.78 | 90.8 | |
| ASCL1 | chr12:103349820-103349833 | CCACATACCAAGA (a) | 9.6 | 92 | - | 12.2 | 97.8 | 12.62 | 94.6 | |
| chr12:103349554-103349542 | CACATCCCTGAC (b) | 9.57 | 92 | 13.99 | 83.1 | - | - | |||
| chr12:103354060-103354047 | CAACATTTCTATA (c) | 7.77 | 90.1 | - | - | - | ||||
| NEUROG2 | chr4:113435415-113435427 | TTGCATTCCCCCT (a) | 9.07 | 91.5 | 14.3 | 83.6 | 9.23 | 96.4 | 10.91 | 92.9 |
| chr4:113435345-113435358 | ATACATTTCTTTC (a) | 9.31 | 91.8 | - | - | - | ||||
| chr4:113435031-113435044 | TTGCATTCAATCA (b) | 5.56 | 87.9 | - | - | - | ||||
| NEUROD1 | chr2:182545564-182545577 | CTCCATTCCGGCC (a) | 9.07 | 91.5 | - | - | - | |||
| chr2:182543940-182543952 | TACATTTCAGCG (b) | 10.29 | 92.8 | 15.41 | 85.4 | - | 8.8 | 90.8 | ||
| chr2:182544023-182544035 | CACATTCTACTT (c) | 9.16 | 91.6 | 15.78 | 86 | - | 13.72 | 95.6 | ||