TABLE 1.
List of known protein-cccDNA interactions associated with increased or decreased transcriptional regulation.
| cccDNA minichromosome partner | Process | References |
| Associated with Enhanced Replication – Verified Interactions | ||
| HBx | Required for replication and transcription. | Belloni et al., 2009 |
| HBc | HBc binds to the CpG islands of HBV cccDNA. | Guo et al., 2011 |
| CBP | HBx interacts and cooperates with CBP to modify chromatin dynamics and enhances CREB activity. | Pollicino et al., 2006; Belloni et al., 2009 |
| P300 | HBx increases amount of P300 recruited to promotors. | Belloni et al., 2009 |
| PCAF | Recruited to the cccDNA after HBx binding to the minichromosome. | Belloni et al., 2009 |
| LSD1/KDM1A | Recruited in an HBx-dependent manner, induces HBV replication and HBV transcription involves the demethylation of histone 3 lysine 9 (H3K9). | Alarcon et al., 2016 |
| CREB/CREB1 | Essential for HBV replication. It binds to the cAMP response elements (CREs) located at the X and preS2 promoters. Interaction with cccDNA dependent on CRTC1. | Tacke et al., 2005; Kim B.K. et al., 2008; Tang et al., 2014) |
| STAT1 | Binds to cccDNA, binding impaired upon IFN treatment. | Belloni et al., 2012 |
| STAT2 | Binds to cccDNA, binding impaired upon IFN treatment. | Belloni et al., 2012 |
| STAT3 | May bind to enhancer I (ENI) and increase function. | Quarleri, 2014 |
| Set1A/SETD1A | Recruited via a HBx-dependent manner, stimulates an active cccDNA epigenetic state by methylating histone 3 lysine 4 (H3K4) in viral HBV promoters. | Alarcon et al., 2016 |
| CRTC1 | Recruited to the preS2/S promotor for the activation of replication. Interaction with cccDNA dependent on CREB/CREB1. | Tang et al., 2014 |
| KLF15 | Activates S and HBc promotors and enhances replication when overexpressed. | Zhou et al., 2011 |
| SIRT1 | SIRT1 interacts with HBx and promotes the recruitment of HBx and other transcriptional factors to the cccDNA (specifically to the precore promoter), promoting the activation of HBV transcription (Deng et al., 2017). However, after IFNα treatment, SIRT1 is recruited to the cccDNA to repress transcription. | Belloni et al., 2012 |
| RFX1 | Binds the enhancer region upon doxorubicin treatment to promote replication. | Wang et al., 2018 |
| RXRα | RXRα recruitment to the cccDNA in parallel with P300 recruitment | Zhang Y. et al., 2017 |
| SP1 | Several binding sites, depending on the site, the activity of SP1 is enhancing or inhibitory. | Quasdorff and Protzer, 2010 |
| TBP | Binds the TATA box. | Quasdorff and Protzer, 2010 |
| NRF1 | Binds to the HBx promotor and positively regulates HBx transcription | Quasdorff and Protzer, 2010 |
| C/EBP | Binds enhancer II (EnhII) and the HBc promotor. Low concentrations have a positive effect on replication while high concentrations evoke inhibition. Potentially also a repressor role. | Pei and Shih, 1990; Quasdorff and Protzer, 2010 |
| PPAR | Increases transcription from several promotors. | Quasdorff and Protzer, 2010 |
| FXR/NR1H4 | Can bind EnhII and HBc regions to have a stimulating effect on transcription. | Quasdorff and Protzer, 2010 |
| AP1 | Binding to HBc promotor and shown to work in synergy with SIRT and HBx. | Quasdorff and Protzer, 2010; Ren et al., 2014 |
| HNF1/HNF1A | Binding sites on the preS promotor. HNF1/HNF1A synergistically works with Oct1 and LRH-1/NR5A2 to enhance replication. | Zhou and Yen, 1991; Cai et al., 2003 |
| LRH-1 (NR5A2)/hB1F | Transactivator of the EnhII and HBc regions. Synergy with HNF1/HNF1A. | Cai et al., 2003; Quasdorff and Protzer, 2010 |
| HNF3 | Several binding sites identified, binding seems to be associated with a stimulating effect. | Cai et al., 2003; Quasdorff and Protzer, 2010 |
| HNF4/HNF4A | Stimulation of transcription from several promotors. | Cai et al., 2003; Quasdorff and Protzer, 2010 |
| HLF | Stimulatory effect on the HBc regulatory region. | Ishida et al., 2000 |
| FTF | Stimulatory effect on EnhII. | Ishida et al., 2000 |
| Parvulin 14 | Recruited to cccDNA in the presence of HBx to promote transcriptional activation. | Saeed et al., 2018 |
| Parvulin 17 | Recruited to cccDNA in the presence of HBx to promote transcriptional activation. | Saeed et al., 2018 |
| Activation-induced cytidine deaminase (AID) | Interaction enhances cccDNA transcription. | Qiao et al., 2016 |
| P19 | Interaction enhances cccDNA transcription. | Qiao et al., 2016 |
| Associated with enhanced Replication – Potential Interactions | ||
| CRTC2 | Enhances HBV transcription and replication by inducing PGC1α expression. | Tian et al., 2014 |
| PGC1α | Induction of HBV transcription, potentially via FOXO1. | Quasdorff and Protzer, 2010; Tian et al., 2014 |
| NF1 | Three binding sites on HBV genome. | Ori et al., 1994; Quasdorff and Protzer, 2010 |
| Oct1 | Oct-1 and HNF-1 sites are necessary for liver-specific transcription of the preS1 promoter. | Zhou and Yen, 1991 |
| EFC | Binding site identified in central HBc promotor. | Quarleri, 2014 |
| Associated with supressed Replication – Verified Interactions | ||
| HDAC1 | Correlated with decline in replication. | Belloni et al., 2009; Levrero et al., 2009 |
| Actively recruited to the cccDNA under IFNα-treatment to repress transcription. | Belloni et al., 2012 | |
| YY1 | Part of the transcriptional repressor complex PRC2. Actively recruited to the cccDNA under IFNα treatment to repress transcription. | Belloni et al., 2012 |
| SETDB1 | Repressing histone deacetylase. | Riviere et al., 2015; Alarcon et al., 2016 |
| EZH2 | Repression of cccDNA. | Salerno et al., 2020 |
| HP1/CBX1 | HP1/CBX1 proteins are recruited to the cccDNA through interaction with H3K9me3 and contribute to transcriptional repression. | Riviere et al., 2015 |
| Spindlin 1/SPIN1 | Inhibition of transcription from the cccDNA via epigenetic modulation. | Ducroux et al., 2014 |
| APOBEC3G | May contribute to cccDNA editing. Antiviral effect through DNA and RNA packaging. | Nguyen et al., 2007; Luo et al., 2016 |
| SP1 | Several binding sites, depending on the site the activity of SP1 is enhancing or inhibitory. | Quasdorff and Protzer, 2010 |
| TR4 | Repressing function by inhibition of HNF4A mediated transactivation. Binds the HBc promotor. | Quasdorff and Protzer, 2010 |
| HNF1/HNF1A | Binding site identified on EnhII. Binding associated with a decline in replication by induction of NF-κB/NFKB1. | Cai et al., 2003; Dai X. et al., 2014; Lin et al., 2017 |
| HNF6 | Inhibits gene expression and replication. | Hao et al., 2015 |
| COUP-TF/NH2F1 | Overexpression of COUP-TF/NH2F1 led to a decrease in replication via binding on NRRE in the enhancer and HBc regions. | Yu and Mertz, 2003 |
| PRMT5 | PRMT5-mediated histone H4 dimethyl Arg3 (H4R3me2) repressed cccDNA transcription. PRMT5-H4R3me2 interacted with HBc and the Brg1-based hSWI/SNF chromatin remodeler, which accounted for the reduced binding of RNA polymerase II to cccDNA. | Zhang W. et al., 2017 |
| E4BP4/NFIL3 | Associated with suppression of EnhII. | Ishida et al., 2000 |
| NREBP | Inhibits core promotor activity by binding the NRE. Binding is inhibited by HBx. | Lee et al., 2019 |
| ZHX2 | Restriction factor that regulates HBV promoter activities and cccDNA modifications. | Xu et al., 2018 |
| Associated with supressed Replication – Potential Interactions | ||
| Prox1 | Interacts with LRH-1/NR5A2 and downregulates LRH-1/NR5A2 mediated activation. | Quasdorff and Protzer, 2010 |
| APOBEC3A | Upregulation by IFNα and lymphotoxin-β receptor resulted in cytidine deamination, | Lucifora et al., 2014 |
| apurinic/apyrimidinic site formation and finally cccDNA degradation. | ||
| APOBEC3B | Upregulation by IFNα and lymphotoxin-β receptor resulted in cytidine deamination, | Lucifora et al., 2014 |
| apurinic/apyrimidinic site formation and finally cccDNA degradation. | ||
| SIRT 3 | Mediates cccDNA transcription. Repression lifted by HBx. | Ren et al., 2018 |
Verified interactions are those protein-protein interactions that were identified using proteomics methods such as pull downs or yeast-2-hybrid. Potential interactions are those which have been shown using methods that strongly suggest an interaction (e.g., co-localization) but were not verified using pull-down methods.