Table I. Core hexamers enriched in gene body sequences and intergenic sequences.
The hexamers found at >2σ abundance in OsMADS1-bound chromatin sequences (as in Fig. 5) were queried for match to consensus binding sequences for 92 known transcription factor classes in PLACE (http://www.dna.affrc.go.jp/PLACE/). We show the core hexamers (column 3), and their presence in the larger consensus binding sites of which they are a part are listed (column 2, underlined nucleotides). The sequences that contain the larger consensus motif, for the respective transcription factor, are given within parentheses in column 2. The transcription factor class that binds the consensus sequence is given below where it is known. The number of OsMADS1-bound sequences containing the core hexamer sequence and the CArG element is listed in column 5, while column 4 lists the numbers in all OsMADS1-bound data. Hexamers co-occurring with CArG motif, in statistically insignificant numbers, are indicated in boldface in column 5; these bound sites likely contain A-tracts.
| cis-Element | Consensus Binding Sequence and Transcription Factor Class |
Core Hexamer Motif |
No. of Sequences with Core Hexamer Motif |
No. of Sequences with CArG Element and Core Hexamer Motif |
|---|---|---|---|---|
| Core hexamers found in gene body sequences compared with the shuffled sequences | ||||
| GCrichrepeatII | CGCCGCGC (41) | CGCCGC | 274 (P < 0.0001) | 58 (P < 0.0001) |
| AGCBOXNPGLB | AGCCGCC (28) ERF-domain | GCCGCC | 243 (P < 0.0001) | 54 (P < 0.0001) |
| A-T rich binding motif for AP2R2 or GARE | TTTGTT/AACAAA (314) euAP2 with double Ap2 domain | TTTGTT | 314 (P < 0.0001) | 246 (P < 0.0001) |
| REGION1OSOSEM | CGGCGGCCTCGCCACG bZIP | CGGCGG/CTCGCC | 316 (P < 0.0001) | 63 (P = 0.6251) |
| GLUEBOX2/OSGT3 | CTTTTGTGTACCTA | TTTTGT | 283 (P = 0.0001) | 233 (P < 0.0001) |
| RGATAOS | CAGAAGATA (2) | AGAAGA | 192 (P < 0.0001) | 112 (P < 0.0001) |
| GCrichrepeatIV | GTCTCCCT (7) | CTCCCT | 152 (P < 0.0001) | 79 (P = 0.0002) |
| RYREPEATVFLE B4/ RYREPEAT4 | CATGCATG (21) B3 domain | CATGCA | 150 (P < 0.0001) | 109 (P < 0.0001) |
| PROLAMINBOXO SGLUB1 | TGCAAAG (37) | TGCAAA | 175 (P < 0.0001) | 133 (P < 0.0001) |
| TATAboxIV | TATATACA (23) | TATATA | 178 (P = 0.3517) | 132 (P = 0.0269) |
| GCAAmotif | SCAAAATGA (11) | AAAATG | 209 (P < 0.0001) | 170 (P < 0.0001) |
| Core hexamers found in intergenic sequences compared with the shuffled sequences | ||||
| TATAboxII | TATTTAAA (14) | TTTAAA | 223 (P = 0.004) | 184 (P = 0.5465) |
| GCrichrepeatII | CGCCGCGC (8) | CGCCGC | 61 (P = 0.0002) | 26 (P = 0.8415) |
| A-T rich binding motif for AP2R2 or GARE | TTTGTT/AACAAA (183) euAP2 with double Ap2 domain | AACAAA | 183 (P < 0.0001) | 145 (P < 0.0001) |
| REGION1OSOSEM | CGGCGGCCTCGCCACG bZIP | GGCGGC | 62 (P < 0.0001) | 29 (P = 0.2109) |
| RYREPEATVFLE B4/ RYREPEAT4 | CATGCATG (22) B3 domain | CATGCA | 106 (P < 0.0001) | 68 (P < 0.0001) |
| GLUEBOX2/OSGT3 | CTTTTGTGTACCTTA | TTTTGT | 182 (P < 0.0001) | 149 (P < 0.0043) |
| DirectRepeat | GGTTTTTAAGTT | GTTTTT | 173 (P < 0.0001) | 138 (P = 0.0001) |
| GCAAmotif | SCAAAATGA (1) | CAAAAT | 172 (P < 0.0001) | 147 (P < 0.0001) |
| PROLAMINBOX | CACATGTGTAAAGGT | ACATGT | 119 (P < 0.0001) | 96 (P < 0.0001) |
| MYCATERD1 | CATGTG (109) Myc domain | CATGTG | 109 (P < 0.0001) | 76 (P < 0.0001) |
| GLUTEBP1OS | AAGCAACACACAAC | ACACAC | 77 (P < 0.0001) | 55 (P = 0.0003) |
| Element II Os region Element II OsPCNA-2 | TGGGCCCGT Class II TCP domain | TGGGCC | 74 (P < 0.0001) | 48 (P < 0.0001) |
| PYRIMIDINEBOXOSRAMY1A | CCTTTT (121) | CCTTTT | 121 (P < 0.0001) | 99 (P < 0.0001) |