Table 1.
Nucleic acid binding domains. The domain, protein, and histone substrate is indicated. Dissociation constants for nucleic acids are shown if known, or indicated as (+) for detected binding with no determined affinity. Lack of binding is indicated by (−). NT indicates not tested. Nucleic acid substrates include single stranded (ss) or double-stranded (ds) RNA or DNA or nucleosomes.
| Reader Domain | Protein | Organism | Histone Substrate | ssRNA | dsRNA | ssDNA | dsDNA | Nucleosome |
|---|---|---|---|---|---|---|---|---|
| BD | BRM [23] | H. sapiens | H3K14ac | NT | NT | NT | 600 μM (10 bp) | NT |
| BRG1 [23,24,25] | H. sapiens | H3K14ac | NT | NT | NT | + | NT | |
| BRDT1 BD1 [17] | H. sapiens | H4K5acK8ac | NT | NT | NT | 52 μM (25 bp) | 2 μM | |
| PHD finger | BRPF2 PHD2 [26] | H. sapiens | none | NT | NT | 9 μM (14 nt) | 4 μM (14 bp) | NT |
| PHF6 ePHD2 [27] | H. sapiens | none | NT | NT | NT | 13 μM (14 bp) | NT | |
| PWWP | DNMT3b [28] | H. sapiens | H3K36me3 | NT | NT | NT | 0.23 μM (30 bp) | NT |
| Pdp1 [29] | S. pombe | H4K20me3 | NT | NT | NT | 4.9–5.3 μM (33 bp) | + | |
| HDGF [30,31] | H. sapiens | none | NT | NT | − | + | NT | |
| MSH6 [32,33] | H. sapiens | H3K36me3 | NT | NT | 2.5 μM (35nt) | 0.13 μM (35 bp) | NT | |
| PSIP1/LEDGF [34,35] | H. sapiens | H3K36me3 | NT | NT | NT | 150 μM (10 bp), 1.6 μM (40 bp) | 1.5 μM, 48 nM | |
| CD/ Chromobarrel |
MOF [36] | D. melanogaster | none | + | NT | NT | NT | NT |
| MSL-3 [37,38] | D. melanogaster | H4K20me1 | + | + | NT | 0.4 μM (18 bp) | NT | |
| MSL-3 [37,38] | H. sapiens | H4K20me1 | − | − | + | 0.3 μM (18 bp) | NT | |
| CBX2 [18,39] | H. sapiens | H3K27me3 | 3.5 μM (130 nt) | NT | NT | 8.1 μM (130 bp) | NT | |
| CBX4 [19] | M. musculus | H3K9me3 | + | NT | NT | NT | NT | |
| CBX6 [19] | M. musculus | H3K27me3 | + | NT | NT | NT | NT | |
| CBX7 [19] | M. musculus | H3K9me3 | 100 μM (500 nt) | + | NT | + | NT | |
| CBX7 [18,40,41] | H. sapiens | H3K9me3 | 51 μM (13 nt) | NT | NT | − | NT | |
| CBX8 [19] | M. musculus | H3K27me3 | + | NT | NT | NT | NT | |
| SUV39H1 [42,43] | M. musculus | H3K9me3 | 0.35 μM (130 nt) | NT | NT | + | NT | |
| SUV39H1 [42,44] | H. sapiens | H3K9me3 | 2.3 μM (19 nt) | + | + | + | NT | |
| Clr4 [45,46] | S. pombe | H3K9me3 | + | NT | + | + | NT | |
| Chp1 [45,46] | S. pombe | H3K9me3 | 3.9 μM (75 nt) | NT | + | + | NT | |
| MI-2 [47] | D. melanogaster | none | NT | NT | NT | + | + | |
| Tudor | PHF1 [20,48] | H. sapiens | H3K36me3 | NT | NT | − | 201 μM (10 bp) | + |
| 53BP1 [21,49] | M. musculus | H4K20me2 | NT | NT | NT | + | NT | |
| 53BP1 [22,49] | H. sapiens | H4K20me2 | NT | NT | + | + | NT | |
| Esa1 [50] | S. cerevisiae | none | NT | 21–112 μM (varying) | NT | 70–241 μM (varying) | NT | |
| SANT/Myb | c-Myb R2R3 [51,52,53,54] | H. sapiens | unmod H3, unmod H4 | NT | NT | NT | 3.8 nM (16 bp) | + |
| ISW1a [55] | S. cerevisiae | none | NT | NT | NT | + | + | |
| ISWI [56] | D. melanogaster | none | NT | NT | NT | + | + | |
| Chd1 [57,58,59] | S. cerevisiae | none | − | NT | − | + | + | |
| CoRest1 [60,61] | H. sapiens | none | NT | NT | NT | 81 μM (18 bp) | + | |
| Integrated Domains | ZMYND11 | H. sapiens | H3K36me3 | NT | NT | NT | 31 μM (33 bp), 4.6 μM (22 bp) | 0.95 μM (unmod), 0.16 μM (H3K36me3) |
| ZMYND8 [62] | H. sapiens | H3K4me0, H3K14ac, H3K36me0 | NT | NT | NT | + | NT |