Epigenetic Machinery Explorer
Predicted epi-miRNAs — miRNAs targeting the enzymes and cofactors that deposit, remove, read, and process epigenetic marks — organized by the manuscript's functional categories. This is, to the authors' knowledge, the first description of epi-miRNAs in cnidarians. 66 unique miRNA–epimachinery target pairs were recovered across the three species.
Roughly half of these pairs are positively coexpressed — which does not match canonical
miRNA repression. The exception is DNA-methylation machinery (TET3, MBD, PRDM14), where all
observed targets are negatively coexpressed. All relationships are predicted.
Targets by category
negative coexpression (canonical repression) positive coexpression
DNA methylation & reading
Histone modification & variants
Chromatin signaling
Ubiquitin signaling
RNA modification
ncRNA biogenesis & silencing
ADP-ribosylation
Bar length is total target pairs; split shows negative (left) vs positive (right) coexpression. Compare with manuscript Figure 3.
Browse targets
| Target (gene) | Category | Species | Targeting miRNA | Direction | Pearson r | p-value | Network |
|---|---|---|---|---|---|---|---|
| USP19 USP19-205 | Ubiquitin signaling | A. pulchra | apul-mir-novel-19 | ＋ positive | 0.890 | 4.3e-2 | view → |
| USP7 USP7-201 | Ubiquitin signaling | A. pulchra | apul-mir-novel-15 | ＋ positive | 0.957 | 1.1e-2 | view → |
| USP31 USP31-201; USP43-201 | Ubiquitin signaling | A. pulchra | apul-mir-100 ★ | － negative | -0.895 | 4.0e-2 | view → |
| PAN2 PAN2-201 | ncRNA biogenesis & silencing | A. pulchra | apul-mir-novel-15 | ＋ positive | 0.965 | 8.0e-3 | view → |
| JOSD1 JOSD1-210; JOSD2-204 | Ubiquitin signaling | A. pulchra | apul-mir-novel-8a; apul-mir-novel-8b | － negative | -0.965 | 7.8e-3 | view → |
| PSMD14 PSMD14-201 | Ubiquitin signaling | A. pulchra | apul-mir-2022 ★ | － negative | -0.976 | 4.5e-3 | view → |
| COPS6 COPS6-201 | Ubiquitin signaling | A. pulchra | apul-mir-novel-31 | ＋ positive | 0.889 | 4.4e-2 | view → |
| Parp5a-Tnks Parp5a-Tnks-201; Parp5b-Tnks2-201 | ADP-ribosylation | A. pulchra | apul-mir-novel-23 | ＋ positive | 0.901 | 3.7e-2 | view → |
| Parp7-Tiparp Parp7-Tiparp-201 | ADP-ribosylation | A. pulchra | apul-mir-novel-17 | ＋ positive | 0.913 | 3.0e-2 | view → |
| Parp9 Parp9-203; Parp14-201; PARP15-202 | ADP-ribosylation | A. pulchra | apul-mir-novel-13 | ＋ positive | 0.950 | 1.3e-2 | view → |
| Arh1-Adprh Arh1-Adprh-201 | ADP-ribosylation | A. pulchra | apul-mir-novel-9 | ＋ positive | 0.949 | 1.4e-2 | view → |
| Kat14 Kat14-201 | Histone modification & variants | A. pulchra | apul-mir-novel-31 | ＋ positive | 0.895 | 4.0e-2 | view → |
| Kdm3a Kdm3a-201; Kdm3b-201; Kdm3c-Jmjd1c-211 | Histone modification & variants | A. pulchra | apul-mir-novel-23 | ＋ positive | 0.980 | 3.4e-3 | view → |
| Kdm6a Kdm6a-202; Uty-201 | Histone modification & variants | A. pulchra | apul-mir-novel-23 | ＋ positive | 0.925 | 2.5e-2 | view → |
| MAP3K12 MAP3K12-205 | Chromatin signaling | A. pulchra | apul-mir-2030 ★ | － negative | -0.890 | 4.3e-2 | view → |
| Chuk Chuk-201 | Chromatin signaling | A. pulchra | apul-mir-2023 ★ | ＋ positive | 0.899 | 3.8e-2 | view → |
| Kmt5a—Setd8 Kmt5a—Setd8-202 | Histone modification & variants | A. pulchra | apul-mir-novel-9 | ＋ positive | 0.965 | 7.8e-3 | view → |
| Mbd2 Mbd2-201; Mbd3-201 | DNA methylation & reading | A. pulchra | apul-mir-novel-27 | － negative | -0.951 | 1.3e-2 | view → |
| DUS1L DUS1L-201 | RNA modification | A. pulchra | apul-mir-novel-30 | ＋ positive | 0.908 | 3.3e-2 | view → |
| PPP1CB PPP1CB-203 | Chromatin signaling | A. pulchra | apul-mir-novel-4 | － negative | -0.970 | 6.2e-3 | view → |
| Prmt7 Prmt7-201 | Histone modification & variants | A. pulchra | apul-mir-novel-28 | ＋ positive | 0.881 | 4.8e-2 | view → |
| PPP1R7 PPP1R7-201 | Chromatin signaling | A. pulchra | apul-mir-novel-29 | － negative | -0.947 | 1.4e-2 | view → |
| TRMT1 TRMT1-202 | RNA modification | A. pulchra | apul-mir-100 ★ | － negative | -0.906 | 3.4e-2 | view → |
| TRMT61A TRMT61A-202 | RNA modification | A. pulchra | apul-mir-novel-34 | － negative | -0.894 | 4.1e-2 | view → |
| PUS7L PUS7L-201 | RNA modification | A. pulchra | apul-mir-novel-7 | ＋ positive | 0.879 | 4.9e-2 | view → |
| PUS7L PUS7L-201 | RNA modification | A. pulchra | apul-mir-novel-9 | ＋ positive | 0.930 | 2.2e-2 | view → |
| ADAR ADAR-202 | RNA modification | A. pulchra | apul-mir-novel-5 | ＋ positive | 0.919 | 2.7e-2 | view → |
| Tet3 Tet3-203 | DNA methylation & reading | A. pulchra | apul-mir-novel-14 | － negative | -0.879 | 5.0e-2 | view → |
| UBE4A UBE4A-201 | Ubiquitin signaling | A. pulchra | apul-mir-novel-10 | － negative | -0.922 | 2.6e-2 | view → |
| DDB1 DDB1-201 | Ubiquitin signaling | A. pulchra | apul-mir-novel-15 | ＋ positive | 0.985 | 2.1e-3 | view → |
| EXOSC6 | ncRNA biogenesis & silencing | A. pulchra | apul-mir-2050 ★ | － negative | -0.883 | 4.7e-2 | view → |
| INTS6 | ncRNA biogenesis & silencing | A. pulchra | apul-mir-2023 ★ | ＋ positive | 1.000 | 8.0e-6 | view → |
| RDRP | ncRNA biogenesis & silencing | A. pulchra | apul-mir-novel-28 | － negative | -0.961 | 9.3e-3 | view → |
| AGO3 AGO3; AGO4; AGO1; AGO2 | ncRNA biogenesis & silencing | A. pulchra | apul-mir-novel-32 | ＋ positive | 0.966 | 7.5e-3 | view → |
| PQBP1 | ncRNA biogenesis & silencing | A. pulchra | apul-mir-novel-31 | ＋ positive | 0.881 | 4.8e-2 | view → |
| VCPIP1 VCPIP1-201 | Ubiquitin signaling | P. evermanni | peve-mir-novel-39 | ＋ positive | 1.000 | 5.5e-3 | view → |
| PSMD14 PSMD14-201 | Ubiquitin signaling | P. evermanni | peve-mir-novel-39 | ＋ positive | 0.999 | 3.4e-2 | view → |
| Kat6a Kat6a-201; Kat6b-214 | Histone modification & variants | P. evermanni | peve-mir-novel-39 | ＋ positive | 0.997 | 4.8e-2 | view → |
| MCM3AP MCM3AP-201 | ncRNA biogenesis & silencing | P. evermanni | peve-mir-novel-2 | － negative | -0.999 | 2.5e-2 | view → |
| MCM3AP MCM3AP-201 | ncRNA biogenesis & silencing | P. evermanni | peve-mir-novel-3 | ＋ positive | 0.999 | 3.2e-2 | view → |
| Riox1 Riox1-201 | Histone modification & variants | P. evermanni | peve-mir-novel-6 | － negative | -1.000 | 2.3e-4 | view → |
| MAP2K1 MAP2K1-201 | Chromatin signaling | P. evermanni | peve-mir-novel-40 | － negative | -0.998 | 4.2e-2 | view → |
| Prdm14 Prdm14-201 | DNA methylation & reading | P. evermanni | peve-mir-novel-25 | － negative | -1.000 | 1.2e-2 | view → |
| UBE2D1 UBE2D1-201; UBE2D2-202; UBE2D3-210 | Ubiquitin signaling | P. evermanni | peve-mir-novel-2 | － negative | -0.999 | 3.3e-2 | view → |
| UBE3A UBE3A-226 | Ubiquitin signaling | P. evermanni | peve-mir-100 ★ | ＋ positive | 0.998 | 3.9e-2 | view → |
| UBR2 UBR2-202 | Ubiquitin signaling | P. evermanni | peve-mir-novel-6 | － negative | -0.999 | 3.2e-2 | view → |
| CUL4A CUL4A-202 | Ubiquitin signaling | P. evermanni | peve-mir-novel-2 | － negative | -0.998 | 3.7e-2 | view → |
| ZFC3H1 | ncRNA biogenesis & silencing | P. evermanni | peve-mir-novel-2 | － negative | -1.000 | 9.7e-3 | view → |
| INTS4 | ncRNA biogenesis & silencing | P. evermanni | peve-mir-novel-7 | － negative | -0.998 | 3.7e-2 | view → |
| SRRT | ncRNA biogenesis & silencing | P. evermanni | peve-mir-novel-2 | － negative | -0.998 | 4.3e-2 | view → |
| USP48 USP48-201 | Ubiquitin signaling | P. tuahiniensis | ptuh-mir-novel-7 | ＋ positive | 0.959 | 9.8e-3 | view → |
| BAP1 BAP1-202 | Ubiquitin signaling | P. tuahiniensis | ptuh-mir-novel-3 | ＋ positive | 0.928 | 2.3e-2 | view → |
| Hdac4 Hdac4-201; Hdac5-201; Hdac7-204; Hdac9-204 | Histone modification & variants | P. tuahiniensis | ptuh-mir-novel-32 | － negative | -0.882 | 4.8e-2 | view → |
| Sirt7 Sirt7-201 | Histone modification & variants | P. tuahiniensis | ptuh-mir-novel-33 | － negative | -0.920 | 2.7e-2 | view → |
| Kat2a Kat2a-202; Kat2b-201 | Histone modification & variants | P. tuahiniensis | ptuh-mir-novel-26 | ＋ positive | 0.879 | 5.0e-2 | view → |
| MCM3AP MCM3AP-201 | ncRNA biogenesis & silencing | P. tuahiniensis | ptuh-mir-novel-16 | ＋ positive | 0.884 | 4.7e-2 | view → |
| Hspbap1 Hspbap1-202 | Histone modification & variants | P. tuahiniensis | ptuh-mir-novel-6 | ＋ positive | 0.907 | 3.4e-2 | view → |
| PKN1 PKN1-201 | Histone modification & variants | P. tuahiniensis | ptuh-mir-novel-33 | － negative | -0.893 | 4.1e-2 | view → |
| HNRNPA2B1 HNRNPA2B1-201 | RNA modification | P. tuahiniensis | ptuh-mir-novel-24 | ＋ positive | 0.896 | 4.0e-2 | view → |
| UBR2 UBR2-202 | Ubiquitin signaling | P. tuahiniensis | ptuh-mir-novel-10 | － negative | -0.967 | 7.3e-3 | view → |
| DIS3L | ncRNA biogenesis & silencing | P. tuahiniensis | ptuh-mir-novel-24 | ＋ positive | 0.926 | 2.4e-2 | view → |
| TNRC6 | ncRNA biogenesis & silencing | P. tuahiniensis | ptuh-mir-novel-4 | － negative | -0.905 | 3.5e-2 | view → |
| MTREX | ncRNA biogenesis & silencing | P. tuahiniensis | ptuh-mir-novel-5 | ＋ positive | 0.965 | 7.9e-3 | view → |
| AGO3 AGO3; AGO4; AGO1; AGO2 | ncRNA biogenesis & silencing | P. tuahiniensis | ptuh-mir-novel-6 | ＋ positive | 0.897 | 3.9e-2 | view → |
| KHSRP | ncRNA biogenesis & silencing | P. tuahiniensis | ptuh-mir-novel-6 | － negative | -0.923 | 2.6e-2 | view → |
| LIN28A | ncRNA biogenesis & silencing | P. tuahiniensis | ptuh-mir-novel-7 | ＋ positive | 0.959 | 9.9e-3 | view → |
★ = conserved/known miRNA family. Source: 12-miRNA-epimachinery/miRNAtargets_mach.csv and manuscript Table 2. All predicted.