Table 3.
Confirmed HDA9-interacting proteins
| Interacting protein | Reference | Technique(s) used for interaction study | Target gene identification/ confirmation method(s)a |
|---|---|---|---|
| WRKY53 | Zheng, 2020 | Y2H, Co-IP, BiFC | qRT-PCR, ChIP-PCR, transient expression assays |
| PWR, WRKY53, AHL22 | Chen, 2016 | Co-IP, in vitro IP | qRT-PCR, RNA-seq, ChIP-PCR, ChIP-seq |
| PWR | Kim, 2016 | Co-IP, Y2H | qRT-PCR, RNA-seq, ChIP-PCR, ChIP-seq |
| HOS15, PWR | Suzuki, 2018 | Y2H | qRT-PCR |
| HOS15, PWR | Mayer 2019 | IP-MS, IP, BiFC | qRT-PCR, RNA-seq, ChIP-PCR, ChIP-seq |
| HOS15 | Yang, 2019 | Co-IP | qRT-PCR, RNA-seq, ChIP-PCR |
| HOS15 | Park 2018a | Split-LUC | qRT-PCR, ChIP-PCR |
| HOS15 | Park 2018b | IP-MS, Co-IP, Y2H, LCI | NA |
| HOS15, ELF3, LUX | Park 2019 | Co-IPb | qRT-PCR, RNA-seq, ChIP-PCR |
| ELF3 | Lee, 2019 | Y2H, Co-IP, BiFC | qRT-PCR, ChIP-PCR, transient expression assays. |
| AHL22 | Yun, 2012 | BiFC, in vitro pulldown | qRT-PCR, ChIP-PCR, EMSA, MAR binding assay |
| AFR1, AFR2 | Gu, 2013 | Y2H | qRT-PCR, ChIP-PCR |
| HOS1, FVE/MSI4 | Jung, 2013 | Y2H | qRT-PCR, ChIP-PCR |
| CYP1-1. HDA6, HDA19 c | Zheng, 2016 | Y2H | qRT-PCR, RNA-seq, ChIP-PCR |
| ASG2 | Ducos, 2017 | BiFC | NA |
| VAL1, VAL2 | Zeng, 2020 | Co-IP, Y2H | qRT-PCR, ChIP-PCR |
| HY5 | Yang, 2020 | Co-IP, BiFC | qRT-PCR, ChIP-PCR, dual-luciferase reporter assay |
| ABI4 | Baek, 2020 | Co-IP, Y2H | qRT-PCR, ChIP-PCR |
| ABI4, ABI3 | Khan, 2020 | Co-IP, Y2H | qRT-PCR, ChIP-PCR |
a The indicated techniques were used to identify target genes of either HDA9 and/or of the specified HDA9-interacting protein.
b Co-IP data by Park et al. (2019) suggest HDA9–LUX interaction, but a yeast two-hybrid assay did not confirm this interaction (Lee et al., 2019).
c These proposed interactions (yeast two-hybrid-based) should be considered with care, as Yuan et al. (2019) did not detect interaction between HDA9 and HDA6.
Abbreviations; Y2H, yeast two-hybrid; Co-IP, co-immunoprecipitation; IP-MS, immunoprecipitation followed by MS; BiFC, bimolecular fluorescence complementation; LCI, luciferase complementation imaging, qRT-PCR, quantitative real-time PCR; ChIP-PCR, chromatin immunoprecipitation-PCR; ChIP-seq, ChIP sequencing; RNA-seq, RNA sequencing (whole-transcriptome sequencing); MAR, matrix-attachment region; NA, not applicable.