ZNF638 represses HBV covalently closed circular DNA transcription involving HUSH complex epigenetic silencing

Hepatitis B virus (HBV) infection represents a significant public health burden worldwide. Covalently closed circular DNA (cccDNA) is the transcriptional template of HBV, which interacts with both host and viral proteins to form minichromosome in the nucleus and exhibits resistance to antiviral agents. Here, we provide evidence that ZNF638 mediates transcriptional silencing of HBV cccDNA. Mechanically, ZNF638 bound to HBV cccDNA, increasing the occupancy of HUSH complex to target loci, which subsequently recruited SETDB1, leading to enhanced H3K9me3 modification, thereby repressing cccDNA transcription. Our research findings improved the existing understanding of ZNF638- and HUSH-mediated epigenetic silencing on viral DNA, that (1) ZNF638 and HUSH complex inhibited HBV transcription, not only by epigenetic silencing extrachromosome cccDNA but also silencing the integrate viral DNA, and (2) ZNF638- and HUSH-mediated repression appeared to function as an epigenetic rheostat: occupancy of HUSH components at the locus inhibited transcription; release from the target locus activated transcription. In summary, the study demonstrates a novel epigenetic role of ZNF638 and HUSH complex in negatively regulating HBV cccDNA transcription by deposit repressive H3K9me3 histone marks and highlights the importance of epigenetic therapy targeting cccDNA, suggesting that ZNF638 could be a potential target for epigenetic therapy of viral diseases.