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Journal of General Virology header logo Journal of General Virology

Volume 105, Issue 1

CTCF regulates hepatitis B virus cccDNA chromatin topology Open Access

Abstract

Hepatitis B Virus (HBV) is a small DNA virus that replicates via an episomal covalently closed circular DNA (cccDNA) that serves as the transcriptional template for viral mRNAs. The host protein, CCCTC-binding factor (CTCF), is a key regulator of cellular transcription by maintaining epigenetic boundaries, nucleosome phasing, stabilisation of long-range chromatin loops and directing alternative exon splicing. We previously reported that CTCF binds two conserved motifs within Enhancer I of the HBV genome and represses viral transcription, however, the underlying mechanisms were not identified. We show that CTCF depletion in cells harbouring cccDNA-like HBV molecules and in infected cells resulted in an increase in spliced transcripts, which was most notable in the abundant SP1 spliced transcript. In contrast, depletion of CTCF in cell lines with integrated HBV DNA had no effect on the abundance of viral transcripts and in line with this observation there was limited evidence for CTCF binding to viral integrants, suggesting that CTCF-regulation of HBV transcription is specific to episomal cccDNA. Analysis of HBV chromatin topology by Assay for Transposase Accessible Chromatin Sequencing (ATAC-Seq) revealed an accessible region spanning Enhancers I and II and the basal core promoter (BCP). Mutating the CTCF binding sites within Enhancer I resulted in a dramatic rearrangement of chromatin accessibility where the open chromatin region was no longer detected, indicating loss of the phased nucleosome up- and down-stream of the HBV enhancer/BCP. These data demonstrate that CTCF functions to regulate HBV chromatin conformation and nucleosomal positioning in episomal maintained cccDNA, which has important consequences for HBV transcription regulation.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): chromatin , CTCF , HBV , viral integrants and viral transcription
Funding
This study was supported by the:
  • Chinese Academy of Medical Sciences (Award 0005025)
    • Principle Award Recipient: JaneA McKeating
  • Medical Research Council (Award MR/R022011/1)
    • Principle Award Recipient: JaneA McKeating
  • Wellcome Trust (Award 225198/Z/22/Z)
    • Principle Award Recipient: JaneA McKeating
  • Wellcome Trust (Award 200838/Z/16/Z)
    • Principle Award Recipient: JaneA McKeating
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-01-04
2025-01-21
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CTCF regulates hepatitis B virus cccDNA chromatin topology
J. Gen. Virol. 105, 001939 (2024); https://doi.org/10.1099/jgv.0.001939
/content/journal/jgv/10.1099/jgv.0.001939
/content/journal/jgv/10.1099/jgv.0.001939
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