Cargando…

The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression

The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons. We have previously demonstrated that CTCF binds to the E2 open reading...

Descripción completa

Detalles Bibliográficos
Autores principales: Ferguson, Jack, Campos-León, Karen, Pentland, Ieisha, Stockton, Joanne D., Günther, Thomas, Beggs, Andrew D., Grundhoff, Adam, Roberts, Sally, Noyvert, Boris, Parish, Joanna L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594839/
https://www.ncbi.nlm.nih.gov/pubmed/34735550
http://dx.doi.org/10.1371/journal.ppat.1010032
_version_ 1784600068819517440
author Ferguson, Jack
Campos-León, Karen
Pentland, Ieisha
Stockton, Joanne D.
Günther, Thomas
Beggs, Andrew D.
Grundhoff, Adam
Roberts, Sally
Noyvert, Boris
Parish, Joanna L.
author_facet Ferguson, Jack
Campos-León, Karen
Pentland, Ieisha
Stockton, Joanne D.
Günther, Thomas
Beggs, Andrew D.
Grundhoff, Adam
Roberts, Sally
Noyvert, Boris
Parish, Joanna L.
author_sort Ferguson, Jack
collection PubMed
description The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons. We have previously demonstrated that CTCF binds to the E2 open reading frame (ORF) of human papillomavirus (HPV) 18 and functions to repress viral oncogene expression in undifferentiated keratinocytes by co-ordinating an epigenetically repressed chromatin loop within HPV episomes. Keratinocyte differentiation disrupts CTCF-dependent chromatin looping of HPV18 episomes promoting induction of enhanced viral oncogene expression. To further characterise CTCF function in HPV transcription control we utilised direct, long-read Nanopore RNA-sequencing which provides information on the structure and abundance of full-length transcripts. Nanopore analysis of primary human keratinocytes containing HPV18 episomes before and after synchronous differentiation allowed quantification of viral transcript species, including the identification of low abundance novel transcripts. Comparison of transcripts produced in wild type HPV18 genome-containing cells to those identified in CTCF-binding deficient genome-containing cells identifies CTCF as a key regulator of differentiation-dependent late promoter activation, required for efficient E1^E4 and L1 protein expression. Furthermore, our data show that CTCF binding at the E2 ORF promotes usage of the downstream weak splice donor (SD) sites SD3165 and SD3284, to the dominant E4 splice acceptor site at nucleotide 3434. These findings demonstrate that in the HPV life cycle both early and late virus transcription programmes are facilitated by recruitment of CTCF to the E2 ORF.
format Online
Article
Text
id pubmed-8594839
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-85948392021-11-17 The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression Ferguson, Jack Campos-León, Karen Pentland, Ieisha Stockton, Joanne D. Günther, Thomas Beggs, Andrew D. Grundhoff, Adam Roberts, Sally Noyvert, Boris Parish, Joanna L. PLoS Pathog Research Article The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons. We have previously demonstrated that CTCF binds to the E2 open reading frame (ORF) of human papillomavirus (HPV) 18 and functions to repress viral oncogene expression in undifferentiated keratinocytes by co-ordinating an epigenetically repressed chromatin loop within HPV episomes. Keratinocyte differentiation disrupts CTCF-dependent chromatin looping of HPV18 episomes promoting induction of enhanced viral oncogene expression. To further characterise CTCF function in HPV transcription control we utilised direct, long-read Nanopore RNA-sequencing which provides information on the structure and abundance of full-length transcripts. Nanopore analysis of primary human keratinocytes containing HPV18 episomes before and after synchronous differentiation allowed quantification of viral transcript species, including the identification of low abundance novel transcripts. Comparison of transcripts produced in wild type HPV18 genome-containing cells to those identified in CTCF-binding deficient genome-containing cells identifies CTCF as a key regulator of differentiation-dependent late promoter activation, required for efficient E1^E4 and L1 protein expression. Furthermore, our data show that CTCF binding at the E2 ORF promotes usage of the downstream weak splice donor (SD) sites SD3165 and SD3284, to the dominant E4 splice acceptor site at nucleotide 3434. These findings demonstrate that in the HPV life cycle both early and late virus transcription programmes are facilitated by recruitment of CTCF to the E2 ORF. Public Library of Science 2021-11-04 /pmc/articles/PMC8594839/ /pubmed/34735550 http://dx.doi.org/10.1371/journal.ppat.1010032 Text en © 2021 Ferguson et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Ferguson, Jack
Campos-León, Karen
Pentland, Ieisha
Stockton, Joanne D.
Günther, Thomas
Beggs, Andrew D.
Grundhoff, Adam
Roberts, Sally
Noyvert, Boris
Parish, Joanna L.
The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression
title The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression
title_full The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression
title_fullStr The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression
title_full_unstemmed The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression
title_short The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression
title_sort chromatin insulator ctcf regulates hpv18 transcript splicing and differentiation-dependent late gene expression
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594839/
https://www.ncbi.nlm.nih.gov/pubmed/34735550
http://dx.doi.org/10.1371/journal.ppat.1010032
work_keys_str_mv AT fergusonjack thechromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT camposleonkaren thechromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT pentlandieisha thechromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT stocktonjoanned thechromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT guntherthomas thechromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT beggsandrewd thechromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT grundhoffadam thechromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT robertssally thechromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT noyvertboris thechromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT parishjoannal thechromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT fergusonjack chromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT camposleonkaren chromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT pentlandieisha chromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT stocktonjoanned chromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT guntherthomas chromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT beggsandrewd chromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT grundhoffadam chromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT robertssally chromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT noyvertboris chromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression
AT parishjoannal chromatininsulatorctcfregulateshpv18transcriptsplicinganddifferentiationdependentlategeneexpression