EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells

Glaser, Laura V.; Rieger, Simone; Thumann, Sybille; Beer, Sophie; Kuklik-Roos, Cornelia; Martin, Dietmar E.; Maier, Kerstin; Harth-Hertle, Marie L.; Grüning, Björn; Backofen, Rolf; Krebs, Stefan; Blum, Helmut; Zimmer, Ralf; Erhard, Florian; Kempkes, Bettina

doi:10.1371/journal.ppat.1006664

Cited by 29 publications

(42 citation statements)

References 80 publications

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“…In addition to the presence of an EBNA2-bound super-enhancer upstream of the neighboring DUSP22 gene ( 27 ), we found that EBNA2 can also upregulate IRF4 transcription through an RBPJ-dependent enhancer located in an intergenic region 13 kb upstream from IRF4 . This is consistent with recent reports of IRF4 as an RBPJ-dependent EBNA2 target gene ( 40 ). At IRF4 and DUSP22 , EBNA2 therefore likely targets multiple enhancers and super-enhancers.…”

Section: Discussionsupporting

confidence: 94%

Enhancer Control of MicroRNA miR-155 Expression in Epstein-Barr Virus-Infected B Cells

Wood

Carvell

Gunnell

et al. 2018

J Virol

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MicroRNA miR-155 is expressed at high levels in many human cancers, particularly lymphomas. Epstein-Barr virus (EBV) infects human B cells and drives the development of numerous lymphomas. Two genes carried by EBV (LMP1 and EBNA2) upregulate miR-155 expression, and miR-155 expression is required for the growth of EBV-infected B cells. We show that the EBV transcription factor EBNA2 upregulates miR-155 expression by activating an enhancer upstream from the miR-155 host gene (miR-155HG) from which miR-155 is derived. We show that EBNA2 also indirectly activates miR-155 expression through enhancer-mediated activation of IRF4. IRF4 then activates both the miR-155HG promoter and the upstream enhancer, independently of EBNA2. Gene editing to remove the miR-155HG enhancer leads to a reduction in miR-155HG expression. We therefore identify enhancer-mediated activation of miR-155HG as a critical step in promoting B cell growth and a likely contributor to lymphoma development.

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Section: Discussionsupporting

confidence: 94%

Enhancer Control of MicroRNA miR-155 Expression in Epstein-Barr Virus-Infected B Cells

Wood

Carvell

Gunnell

et al. 2018

J Virol

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“…We found that miR-34a downregulation by EBNA2 likely involves recruitment of EBF1 at the miR-34a promoter. Glaser et al have recently shown that EBF1 interacts with the N-terminal portion of EBNA2 in a B-cell specific manner and this interaction promotes EBNA2 access to chromatin, without involving RBPJk, a known EBNA2-DNA anchor [19]. Our analysis of EBNA2 ChIP-Seq datasets from GEO database (accession number: GSM2039170) revealed that EBNA2 peaks at the miR-34a promoter.…”

Section: Discussionmentioning

confidence: 78%

“…It does not bind directly to DNA but activates transcription of many target genes by binding to the transcription factor, RBP-Jk [17]. EBNA2 colocalizes with another B-cell-specific DNA binding transcription factor, EBF1 [16], which is essential for the commitment and maintenance of B-cell transcription program [18, 19].…”

Section: Introductionmentioning

confidence: 99%

Epstein−Barr virus-encoded EBNA2 alters immune checkpoint PD-L1 expression by downregulating miR-34a in B-cell lymphomas

et al. 2018

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Cancer cells subvert host immune surveillance by altering immune checkpoint (IC) proteins. Some Epstein−Barr virus (EBV)-associated tumors have higher Programmed Cell Death Ligand, PD-L1 expression. However, it is not known how EBV alters ICs in the context of its preferred host, the B lymphocyte and in derived lymphomas. Here, we found that latency III-expressing Burkitt lymphoma (BL), diffuse large B-cell lymphomas (DLBCL) or their EBNA2-transfected derivatives express high PD-L1. In a DLBCL model, EBNA2 but not LMP1 is sufficient to induce PD-L1. Latency III-expressing DLBCL biopsies showed high levels of PD-L1. The PD-L1 targeting oncosuppressor microRNA miR-34a was downregulated in EBNA2-transfected lymphoma cells. We identified early B-cell factor 1 (EBF1) as a repressor of miR34a transcription. Short hairpin RNA (shRNA)-mediated knockdown of EBF1 was sufficient to induce miR-34a transcription, which in turn reduced PD-L1. MiR-34a reconstitution in EBNA2-transfected DLBCL reduced PD-L1 expression and increased its immunogenicity in mixed lymphocyte reactions (MLR) and in three-dimensional biomimetic microfluidic chips. Given the importance of PD-L1 inhibition in immunotherapy and miR-34a dysregulation in cancers, our findings may have important implications for combinatorial immunotherapy, which include IC inhibiting antibodies and miR-34a, for EBV-associated cancers.

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“…EBNA3A ChIP-seq has demonstrated that EBNA3A binding sites are less enriched for EBF1 than EBNA3C or EBNA3B binding sites ( 13 ). The cellular factor EBF1 has been shown to interact with the EBV transcription factor EBNA2 and recruits the viral protein to a specific genomic location ( 41 , 42 ). However, EBNA2 does not seem to be involved in the STK39 mRNA regulation ( 43 , 44 ), and no EBNA2 binding site has been found at STK39 in EBNA2 ChIP-seq studies ( 33 ).…”

Section: Discussionmentioning

confidence: 99%

Epstein-Barr Virus (EBV) Latent Protein EBNA3A Directly Targets and Silences the STK39 Gene in B Cells Infected by EBV

Bazot

Paschos

Allday

2018

J Virol

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Epstein-Barr virus (EBV) establishes latent infection in human B cells and is associated with a wide range of cancers. The EBV nuclear antigen 3 (EBNA3) family proteins are critical for B cell transformation and function as transcriptional regulators. It is well established that EBNA3A and EBNA3C cooperate in the regulation of cellular genes. Here, we demonstrate that the gene STK39 is repressed only by EBNA3A. This is the first example of a gene regulated only by EBNA3A in EBV-transformed lymphoblastoid cell lines (LCLs) without the help of EBNA3C. This was demonstrated using a variety of LCLs carrying either knockout, revertant, or conditional EBNA3 recombinants. Investigating the kinetics of EBNA3A-mediated changes in STK39 expression showed that STK39 becomes derepressed quickly after EBNA3A inactivation. This derepression is reversible as EBNA3A reactivation represses STK39 in the same cells expressing a conditional EBNA3A. STK39 is silenced shortly after primary B cell infection by EBV, and no STK39-encoded protein (SPAK) is detected 3 weeks postinfection. Chromatin immunoprecipitation (ChIP) analysis indicates that EBNA3A directly binds to a regulatory region downstream of the STK39 transcription start site. For the first time, we demonstrated that the polycomb repressive complex 2 with the deposition of the repressive mark H3K27me3 is not only important for the maintenance of an EBNA3A target gene (STK39) but is also essential for the initial establishment of its silencing. Finally, we showed that DNA methyltransferases are involved in the EBNA3A-mediated repression of STK39.IMPORTANCE EBV is well known for its ability to transform B lymphocytes to continuously proliferating lymphoblastoid cell lines. This is achieved in part by the reprogramming of cellular gene transcription by EBV transcription factors, including the EBNA3 proteins that play a crucial role in this process. In the present study, we found that EBNA3A epigenetically silences STK39. This is the first gene where EBNA3A has been found to exert its repressive role by itself, without needing its coregulators EBNA3B and EBNA3C. Furthermore, we demonstrated that the polycomb repressor complex is essential for EBNA3A-mediated repression of STK39. Findings in this study provide new insights into the regulation of cellular genes by the transcription factor EBNA3A.

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EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells

Cited by 29 publications

References 80 publications

Enhancer Control of MicroRNA miR-155 Expression in Epstein-Barr Virus-Infected B Cells

Enhancer Control of MicroRNA miR-155 Expression in Epstein-Barr Virus-Infected B Cells

Epstein−Barr virus-encoded EBNA2 alters immune checkpoint PD-L1 expression by downregulating miR-34a in B-cell lymphomas

Epstein-Barr Virus (EBV) Latent Protein EBNA3A Directly Targets and Silences the STK39 Gene in B Cells Infected by EBV

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