The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression.
The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression.
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DOI：
10.1371/journal.ppat.1010032
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发表时间：
2021-11
期刊：
影响因子：
6.7
通讯作者：
Parish JL
中科院分区：
文献类型：
--
作者：
Ferguson J;Campos-León K;Pentland I;Stockton JD;Günther T;Beggs AD;Grundhoff A;Roberts S;Noyvert B;Parish JL
普遍存在的宿主蛋白CCCTC结合因子（CTCF）是细胞转录的重要调节因子，其功能是维持表观遗传边界、稳定染色质环和调节可变外显子的剪接。我们以前已经证明，CTCF结合到E2开放阅读框（ORF）的人乳头瘤病毒（HPV）18和功能抑制病毒癌基因的表达在未分化的角质形成细胞通过协调HPV附加体内的表观遗传抑制染色质环。角质形成细胞分化破坏HPV18附加体的CTCF依赖性染色质环，促进病毒癌基因表达增强的诱导。为了进一步研究HPV转录控制中的CTCF功能，我们使用了直接的长读段纳米孔RNA测序，其提供了关于全长转录物的结构和丰度的信息。在同步分化之前和之后对含有HPV 18附加体的原代人角质形成细胞的纳米孔分析允许定量病毒转录物种类，包括鉴定低丰度的新转录物。将野生型HPV18基因组细胞中产生的转录物与CTCF结合缺陷基因组细胞中鉴定的转录物进行比较，确定CTCF是分化依赖性晚期启动子激活的关键调节因子，这是E1、E4和L1蛋白有效表达所必需的。此外，我们的数据表明，CTCF结合在E2 ORF促进下游弱剪接供体（SD）位点SD3165和SD3284的使用，在核苷酸3434处的优势E4剪接受体位点。这些发现表明，在HPV生命周期中，早期和晚期病毒转录程序都通过将CTCF募集到E2 ORF来促进。致癌性人乳头瘤病毒（HPV）感染是子宫颈、其他肛门生殖器区域和口咽部上皮癌的一个子集的原因。HPV感染在上皮的基底细胞中建立，其中病毒基因表达的受限程序是病毒附加体的复制和维持所必需的。HPV生命周期的完成取决于感染细胞的成熟（分化），其诱导增强的病毒基因表达和诱导衣壳产生。我们以前报道过宿主细胞转录调节因子CTCF被HPV劫持来控制病毒基因表达。在这项研究中，我们使用长读mRNA测序来定量绘制HPV生命周期早期和晚期产生的HPV转录物的种类和丰度，并剖析CTCF在控制HPV基因表达和转录加工中的功能。
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. Oncogenic human papillomavirus (HPV) infection is the cause of a subset of epithelial cancers of the uterine cervix, other anogenital areas and the oropharynx. HPV infection is established in the basal cells of epithelia where a restricted programme of viral gene expression is required for replication and maintenance of the viral episome. Completion of the HPV life cycle is dependent on the maturation (differentiation) of infected cells which induces enhanced viral gene expression and induction of capsid production. We previously reported that the host cell transcriptional regulator, CTCF, is hijacked by HPV to control viral gene expression. In this study, we use long-read mRNA sequencing to quantitatively map the variety and abundance of HPV transcripts produced in early and late stages of the HPV life cycle and to dissect the function of CTCF in controlling HPV gene expression and transcript processing.
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影响因子：
6.7
作者：
Günther T;Grundhoff A
通讯作者：
Grundhoff A
影响因子：
5.4
作者：
Agirre E;Bellora N;Alló M;Pagès A;Bertucci P;Kornblihtt AR;Eyras E
通讯作者：
Eyras E
DOI：
10.1002/path.2608
发表时间：
2009-11
期刊：
The Journal of pathology
影响因子：
--
作者：
Mole S;McFarlane M;Chuen-Im T;Milligan SG;Millan D;Graham SV
通讯作者：
Graham SV
影响因子：
5.9
作者：
Donovan-Banfield, I'ah;Turnell, Andrew S.;Matthews, David A.
通讯作者：
Matthews, David A.
影响因子：
7
作者：
Beagan JA;Duong MT;Titus KR;Zhou L;Cao Z;Ma J;Lachanski CV;Gillis DR;Phillips-Cremins JE
通讯作者：
Phillips-Cremins JE