Genome-Wide Mapping of the Binding Sites and Structural Analysis of Kaposi's Sarcoma-Associated Herpesvirus Viral Interferon Regulatory Factor 2 Reveal that It Is a DNA-Binding Transcription Factor
Genome-Wide Mapping of the Binding Sites and Structural Analysis of Kaposi's Sarcoma-Associated Herpesvirus Viral Interferon Regulatory Factor 2 Reveal that It Is a DNA-Binding Transcription Factor
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卡波西肉瘤相关疱疹病毒病毒干扰素调节因子 2 的结合位点全基因组图谱和结构分析表明它是一种 DNA 结合转录因子
DOI：
10.1128/jvi.01392-15
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发表时间：
2016-02-01
影响因子：
5.4
通讯作者：
Lan, Ke
中科院分区：
文献类型：
--
作者：
Hu, Haidai;Dong, Jiazhen;Lan, Ke
摘要致癌疱疹病毒卡波济肉瘤相关疱疹病毒（KSHV）编码4种干扰素调节因子（vIRF 1 ~-4），可破坏宿主的抗病毒免疫应答，但它们作为转录因子在宿主体内的DNA结合特征尚不清楚。在这里，我们首先使用染色质免疫沉淀结合高通量测序（ChIP-seq）在人类基因组中进行全基因组vIRF 2结合位点定位。vIRF 2能够结合100个推定的靶基因的启动子区。重要的是，我们证实了vIRF 2可以特异性地与编码PIK 3C 3、HMGCR和HMGCL的基因的启动子相互作用，这些基因与自噬体形成或肿瘤进展和转移相关，并在体内调节它们的转录。vIRF 2 DNA结合结构域（DBD）（此处称为vIRF 2DBD）的晶体结构显示与DNA结合特异性相关的vIRF 1和细胞IRFs不同的可变环构象和正电荷分布。基于结构的突变显示Arg 82和Arg 85是vIRF 2DBD体外DNA结合活性所必需的，并且可以消除vIRF 2对PIK 3C 3、HMGCR和HMGCL的启动子报告活性的转录调节功能。总的来说，我们的研究提供了独特的见解vIRF 2的DNA结合效力，并建议vIRF 2可以作为其靶基因在宿主抗病毒免疫反应的转录因子。致癌疱疹病毒KSHV是卡波西肉瘤、原发性渗出性淋巴瘤和多中心Castleman病的病原体。KSHV通过编码4个细胞干扰素调节因子（vIRF 1 ~-4）的同源物，形成了破坏宿主抗病毒免疫应答的独特机制。然而，到目前为止，它们在人类基因组中的DNA结合谱还没有被表征，并且它们不同的DNA结合特性的结构基础仍然知之甚少。在本研究中，我们在人类基因组中进行了第一次全基因组vIRF 2结合位点定位，发现vIRF 2可以结合100个靶细胞基因的启动子区域。X射线结构分析和功能研究提供了独特的见解，其DNA结合效力和调节靶基因的表达。我们的研究表明，vIRF 2可能作为其靶基因的转录因子，通过多种功能参与KSHV的感染和致病。
ABSTRACT The oncogenic herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) is known to encode four viral interferon regulatory factors (vIRF1 to -4) to subvert the host antiviral immune response, but their detailed DNA-binding profiles as transcription factors in the host remain uncharacterized. Here, we first performed genome-wide vIRF2-binding site mapping in the human genome using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq). vIRF2 was capable of binding to the promoter regions of 100 putative target genes. Importantly, we confirmed that vIRF2 can specifically interact with the promoters of the genes encoding PIK3C3, HMGCR, and HMGCL, which are associated with autophagosome formation or tumor progression and metastasis, and regulate their transcription in vivo. The crystal structure of the vIRF2 DNA-binding domain (DBD) (referred to here as vIRF2DBD) showed variable loop conformations and positive-charge distributions different from those of vIRF1 and cellular IRFs that are associated with DNA-binding specificities. Structure-based mutagenesis revealed that Arg82 and Arg85 are required for the in vitro DNA-binding activity of vIRF2DBD and can abolish the transcription regulation function of vIRF2 on the promoter reporter activity of PIK3C3, HMGCR, and HMGCL. Collectively, our study provided unique insights into the DNA-binding potency of vIRF2 and suggested that vIRF2 could act as a transcription factor of its target genes in the host antiviral immune response. IMPORTANCE The oncogenic herpesvirus KSHV is the etiological agent of Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. KSHV has developed a unique mechanism to subvert the host antiviral immune responses by encoding four homologues of cellular interferon regulatory factors (vIRF1 to -4). However, none of their DNA-binding profiles in the human genome have been characterized until now, and the structural basis for their diverse DNA-binding properties remain poorly understood. In this study, we performed the first genome-wide vIRF2-binding site mapping in the human genome and found vIRF2 can bind to the promoter regions of 100 target cellular genes. X-ray structure analysis and functional studies provided unique insights into its DNA-binding potency and regulation of target gene expression. Our study suggested that vIRF2 could act as a transcription factor of its target genes and contribute to KSHV infection and pathogenesis through versatile functions.