The chromatin modification by SUMO-2/3 but not SUMO-1 prevents the epigenetic activation of key immune-related genes during Kaposi’s sarcoma associated herpesvirus reactivation

Abstract

BackgroundSUMOylation, as part of the epigenetic regulation of transcription, has been intensively studied in lower eukaryotes that contain only a single SUMO protein; however, the functions of SUMOylation during mammalian epigenetic transcriptional regulation are largely uncharacterized. Mammals express three major SUMO paralogues: SUMO-1, SUMO-2, and SUMO-3 (normally referred to as SUMO-1 and SUMO-2/3). Herpesviruses, including Kaposi’s sarcoma associated herpesvirus (KSHV), seem to have evolved mechanisms that directly or indirectly modulate the SUMO machinery in order to evade host immune surveillance, thus advancing their survival. Interestingly, KSHV encodes a SUMO E3 ligase, K-bZIP, with specificity toward SUMO-2/3 and is an excellent model for investigating the global functional differences between SUMO paralogues.ResultsWe investigated the effect of experimental herpesvirus reactivation in a KSHV infected B lymphoma cell line on genomic SUMO-1 and SUMO-2/3 binding profiles together with the potential role of chromatin SUMOylation in transcription regulation. This was carried out via high-throughput sequencing analysis. Interestingly, chromatin immunoprecipitation sequencing (ChIP-seq) experiments showed that KSHV reactivation is accompanied by a significant increase in SUMO-2/3 modification around promoter regions, but SUMO-1 enrichment was absent. Expression profiling revealed that the SUMO-2/3 targeted genes are primarily highly transcribed genes that show no expression changes during viral reactivation. Gene ontology analysis further showed that these genes are involved in cellular immune responses and cytokine signaling. High-throughput annotation of SUMO occupancy of transcription factor binding sites (TFBS) pinpointed the presence of three master regulators of immune responses, IRF-1, IRF-2, and IRF-7, as potential SUMO-2/3 targeted transcriptional factors after KSHV reactivation.ConclusionOur study is the first to identify differential genome-wide SUMO modifications between SUMO paralogues during herpesvirus reactivation. Our findings indicate that SUMO-2/3 modification near protein-coding gene promoters occurs in order to maintain host immune-related gene unaltered during viral reactivation.

SUMO modification of a heterochromatin histone demethylase JMJD2A enables viral gene transactivation and viral replication

“…RNA-seq was performed at the Sequencing Core of National Research Program for Genomic Medicine at the National Yang-Ming University using Illumina HiSeq 2000. Sequencing reads were processed as described previously [21]. In this study, the sequence reads that did not map to hg19 were aligned to the KSHV genome.…”

“…Genome-wide studies have shown that SUMO modification may associate with either positive regulation [19,20] or negative restraint of gene transcription [20–22]. By using Kaposi’s sarcoma associated herpesvirus (KSHV) as a model, we recently showed that SUMO-2/3 specific chromatin modification restrains the transactivation of genes in the KSHV genomic euchromatin region [21,23]. This suggests that SUMO-paralog specific chromatin modifications may be involved in the observed variation in the role of SUMO in epigenetic regulation of transcription.…”

Modulation of global SUMOylation by Kaposi's sarcoma-associated herpesvirus and its effects on viral gene expression

“…K‐bZIP is SUMOylated at K158, and SUMOylation is essential for its function as a transcriptional repressor . K‐bZIP is a SUMO E3 ligase, catalyzing the SUMOylation of p53, Rb, IRF‐1, IRF‐2, and itself . K‐bZIP also catalyzes the SUMOylation of heterochromatin histone demethylase JMJD2A .…”

“…27 K-bZIP is a SUMO E3 ligase, catalyzing the SUMOylation of p53, Rb, IRF-1, IRF-2, and itself. 31,32 K-bZIP also catalyzes the SUMOylation of heterochromatin histone demethylase JMJD2A. 33 During viral reactivation, higher K-bZIP binding on the SUMO2/3-enriched chromatin region is observed.…”

“…34 Among viral promoters we analyzed whose activities were significantly enhanced by the SUMO2 transfection, k8, orf45, orf50, and orf57 were located in the high SUMO2/3 chromatin area, and the depositions of SUMO2/3 modification were also high on k2, orf8, and orf73 promoters, demonstrating that our results are in agreement with the report by Yang et al 34 In addition, SUMO2/3 enrichment within the host promoter regions was also reported to maintain the host immune response genes unaltered during viral reactivation. 32 The complexity of the interaction between KSHV and the SUMOylation system indicates its functional importance, and its inhibition may represent a potential therapeutic strategy to treat KSHV and other oncogenic herpesviruses.…”