Table 3 Summary of histones and histone modifying enzymes annotation
Type | Family | Lineage | Model species | RKN | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Ce | Hs | Mi | Mj | Ma | Mh | ||||||
Number | Sequences | Number | Sequences | Number | Transcriptional Support | Number | Number | Number | |||
Histone | Linker | H1 | 9 | HIL-1/2/3/4/5/6/7/8/, HIS-24 | 11 | H1, H1.0/1/2/3/4/5, H1F0, H1t, H1oo, H1x | 2 | X | 7 | 10 | 2 |
Core | H2A | 5 | HIS-3/35, HTAS-1, HTZ-1, ZC155.2 | 18 | H2A.1, H2A.J, H2A.V, H2A.Z, H2A1A/B/D/H/J, H2A2A/B/C, H2A3, H2AB1, H2AFB1, H2AG, H2AX, H2AW | 21 | X | 28 | 23 | 5 | |
H2B | 5 | HIS-4/11/39/41/48 | 22 | H2B1A/B/C/D/E/F/G/H/I/K/L/M/N/O, H2B2C/D/E/F, H2B3B, H2BFM, H2BFS, H2BWT | 10 | X | 12 | 16 | 1 | ||
H3 | 11 | CPAR-1, HCP-3, HIS-2/40/69/70/71/72/73/74, F20D6.9 | 6 | H3, H3.1/2/3, H3.1 t, H3.3C | 19 | X | 22 | 23 | 7 | ||
H4 | 1 | HIS-1 | 2 | H4, H4G | 9 | X | 11 | 9 | 0 | ||
Histone acetyltransferase | GNAT | ELP3 | 1 | ELPC-3 | 1 | ELP3 | 0 | 0 | 0 | 0 | |
F08F8.4 | 1 | F08F8.4 | 2 | ESCO1/2 | 2 | X | 4 | 4 | 1 | ||
HAT1 | 1 | HAT-1 | 1 | HAT1 | 3 | X | 4 | 4 | 1 | ||
NAA40 | 1 | Y38A10A.7 | 1 | NAA40 | 2 | X | 2 | 3 | 1 | ||
NAA50 | 1 | F40F4.7 | 1 | NAA50 | 2 | X | 3 | 3 | 1 | ||
NAA60 | 1 | F30F8.10 | 1 | NAA60 | 1 | 2 | 4 | 1 | |||
NAT10 | 1 | NATH-10 | 1 | NAT10 | 6 | X | 3 | 5 | 1 | ||
PCAF1 | 1 | PCAF-1 | 1 | KAT2A/B | 3 | 4 | 4 | 1 | |||
MYST | MYS1 | 1 | MYS-1 | 1 | KAT5 | 2 | X | 2 | 5 | 1 | |
MYS2 | 1 | MYS-2 | 1 | KAT8 | 3 | X | 5 | 4 | 1 | ||
MYS4/LSY12 (LSY12) | 1 | LSY-12 | 2 | KAT6A/B | 3 | X | 6 | 3 | 1 | ||
MYS4/LSY12 (MYS4) | 1 | MYS-4 | 0 | – | 2 | X | 3 | 8 | 1 | ||
TF/NF | TAF1 | 1 | TAF-1 | 2 | TAF1/1 L | 13 | X | 14 | 12 | 1 | |
Histone deacetylase | Class I | Class1 (HDA1/3) | 2 | HDA-1/3 | 2 | HDAC1/2 | 8 | X | 8 | 9 | 2 |
Class1 (HDA2) | 1 | HDA-2 | 1 | HDAC3 | 4 | X | 3 | 3 | 1 | ||
Class II | Class II (HDA4) | 1 | HDA-4 | 4 | HDAC4/5/7/9 | 4 | X | 3 | 4 | 1 | |
Class II (HDA5/6/10) | 1 | HDA-6 | 0 | – | 0 | 0 | 0 | 0 | |||
Class II (HDA5/6/10) | 3 | HDA-5/10, F43G6.17 | 2 | HDAC6/10 | 3 | X | 5 | 2 | 1 | ||
Class III | Class III (SIR2.1) | 1 | SIR-2.1 | 1 | SIRT1 | 3 | 3 | 3 | 1 | ||
Class III (SIR2.2/2.3) | 2 | SIR-2.2/2.3 | 1 | SIRT4 | 0 | 0 | 0 | 0 | |||
Class III (SIR2.4) | 1 | SIR-2.4 | 1 | SIRT6 | 2 | X | 1 | 2 | 1 | ||
Class IV | HDA11 | 1 | HDA-11 | 1 | HDAC11 | 2 | X | 5 | 4 | 1 | |
Histone methyltransferase | DOT1 | DOT1 | 6 | DOT-1.1-1.5, D1053.2 | 1 | DOT1M | 2 | X | 9 | 7 | 1 |
PRMT | CARM1 | 0 | – | 1 | CARM1 | 3 | X | 4 | 5 | 1 | |
PRMT1 | 1 | PRMT-1 | 2 | PRMT1/8 | 2 | X | 3 | 5 | 1 | ||
PRMT3/7 | 1 | PRMT-3 | 1 | PRMT7 | 3 | X | 5 | 4 | 1 | ||
PRMT3/7 | 1 | PRMT-7 | 1 | PRMT9 | 0 | 0 | 0 | 0 | |||
PRMT5 | 1 | PRMT-5 | 1 | PRMT5 | 6 | 4 | 5 | 2 | |||
SET eu1 | SET30 | 1 | SET-30 | 2 | SMYD2/3 | 2 | X | 5 | 4 | 1 | |
SET3 | 1 | SET-3 | 1 | SETD7 | 0 | 0 | 0 | 0 | |||
SET27 | 1 | SET-27 | 0 | – | 0 | 0 | 0 | 0 | |||
SET29 | 1 | SET-29 | 0 | – | 3 | 4 | 4 | 1 | |||
SET eu2 | SET1 | 1 | SET-1 | 0 | – | 5 | 7 | 7 | 2 | ||
MES4 | 1 | MES-4 | 2 | NSD1, WHSC1L1 | 4 | X | 5 | 4 | 1 | ||
SET16 | 1 | SET-16 | 2 | KMT2C/D | 10 | X | 10 | 9 | 1 | ||
SET2 | 1 | SET-2 | 2 | SETD1A/B | 4 | X | 7 | 7 | 1 | ||
Y73B3A.1 | 1 | Y73B3A.1 | 1 | KMT2E | 2 | X | 3 | 3 | 0 | ||
– | 1 | SET-8 | 0 | – | 0 | 0 | 0 | 0 | |||
MET-1/LIN-59 | 1 | MET-1 | 1 | SETD2 | 0 | 0 | 0 | 0 | |||
MET-1/LIN-59 | 1 | LIN-59 | 1 | ASH1L | 0 | 0 | 0 | 0 | |||
SET hetero | DNMT1/CMT (DNMT1) | 0 | – | 2 | SUV39H1/2 | 2 | 2 | 5 | 1 | ||
MET2 | 1 | MET-2 | 2 | SETDB1/2 | 3 | X | 7 | 7 | 1 | ||
SET23 | 1 | SET-23 | 0 | – | 2 | X | 4 | 4 | 1 | ||
MES2/SET12 | 1 | MES-2 | 2 | EZH1/2 | 3 | X | 5 | 5 | 1 | ||
MES2/SET12 | 1 | SET-12 | 1 | WHSC1 | 0 | 0 | 0 | 0 | |||
SET4 | 1 | SET-4 | 2 | KMT5B/C, Dm|Hmt4–2 | 2 | X | 5 | 6 | 1 | ||
SET-11 | 1 | SET-11 | 2 | EHMT1/2 | 0 | 0 | 0 | 0 | |||
SET-6 family | 8 | SET-6/13/15/19/20/21/32/33 | 0 | – | 0 | 0 | 0 | 0 | |||
no | 1 | SET-25 | 0 | – | 0 | 0 | 0 | 0 | |||
no | 1 | SET-9 | 0 | – | 0 | 0 | 0 | 0 | |||
SET - PPN | Cons07 | 0 | – | 0 | – | 3 | X | 3 | 4 | 1 | |
Cons12 | 0 | – | 0 | – | 2 | X | 3 | 4 | 1 | ||
Cons18 | 0 | – | 0 | – | 0 | 1 | 0 | 0 | |||
Histone deacetylase | LSD | AMX1 | 1 | AMX-1 | 1 | KDM1B | 0 | 0 | 0 | 0 | |
LSD1/SPR5 | 2 | LSD-1, SPR-5 | 1 | KDM1A | 4 | X | 6 | 6 | 2 | ||
JMJ | JMJC1 | 1 | JMJC-1 | 1 | NO66 | 6 | X | 7 | 8 | 2 | |
JMJD1/JHDM1 (JHDM1) | 1 | JHDM-1 | 2 | KDM2A/B | 3 | X | 3 | 5 | 0 | ||
JMJD1/JHDM1 (JMJD1) | 2 | JMJD-1.1/1.2 | 3 | KDMT7A, PHF2, PHF8 | 2 | X | 3 | 5 | 0 | ||
JMJD2 | 1 | JMJD-2 | 5 | KDM4A/B/C/D/E | 3 | X | 9 | 10 | 1 | ||
RBR2 | 1 | RBR-2 | 4 | KDM5A/B/C/D | 4 | 6 | 5 | 1 | |||
JMJD3/UTX1 (JMJD3) | 3 | JMJD-3.1/3.2/3.3 | 0 | – | 0 | 0 | 0 | 0 | |||
JMJD3/UTX1 (UTX1) | 1 | UTX-1 | 3 | KDM6A/B, UTY | 2 | X | 2 | 4 | 1 | ||
JMJD4/PSR1 (JMJD4) | 1 | JMJD-4 | 0 | – | 0 | 0 | 0 | 0 | |||
JMJD5 | 1 | JMJD-5 | 1 | KDM8 | 2 | X | 2 | 2 | 1 | ||
JMJD4/PSR1 (PSR1) | 1 | PSR-1 | 1 | JMJD6 | 2 | X | 2 | 3 | 1 | ||