RUNXsuper-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth

Abstract

In B cells infected by the cancer-associated Epstein-Barr virus (EBV), RUNX3 and RUNX1 transcription is manipulated to control cell growth. The EBV-encoded EBNA2 transcription factor (TF) activates RUNX3 transcription leading to RUNX3-mediated repression of the RUNX1 promoter and the relief of RUNX1-directed growth repression. We show that EBNA2 activates RUNX3 through a specific element within a −97 kb super-enhancer in a manner dependent on the expression of the Notch DNA-binding partner RBP-J. We also reveal that the EBV TFs EBNA3B and EBNA3C contribute to RUNX3 activation in EBV-infected cells by targeting the same element. Uncovering a counter-regulatory feed-forward step, we demonstrate EBNA2 activation of a RUNX1 super-enhancer (−139 to −250 kb) that results in low-level RUNX1 expression in cells refractory to RUNX1-mediated growth inhibition. EBNA2 activation of the RUNX1 super-enhancer is also dependent on RBP-J. Consistent with the context-dependent roles of EBNA3B and EBNA3C as activators or repressors, we find that these proteins negatively regulate the RUNX1 super-enhancer, curbing EBNA2 activation. Taken together our results reveal cell-type-specific exploitation of RUNX gene super-enhancers by multiple EBV TFs via the Notch pathway to fine tune RUNX3 and RUNX1 expression and manipulate B-cell growth.

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

“…Despite the ubiquitous expression of its anchor protein CBF1, EBNA2 is preferentially recruited to B cell specific enhancers and super enhancers [10, 11, 20, 34, 35]. The underlying mechanism that recruits EBNA2 specifically to these sites in B cells is still not understood and hard to study in the constitutive presence of CBF1.…”

Super-Enhancer-Driven Transcriptional Dependencies in Cancer

“…Broadly speaking, inappropriate SE formation and function may stem from (i) alterations in cis -regulatory elements (cis-REs) [38, 53, 54], (ii) focal and large-scale chromosomal rearrangements [20, 30, 55–59], and (iii) rewiring of the cellular TF network by viral oncogenes [60–62]. …”

“…For example, during infection of human B cells by Epstein-Barr virus (EBV), the TFs encoded (EBNA2, 3A, 3C and EBNALP) or activated (RelA, RelB) by EBV induce the formation of SEs at key pro-survival and anti-apoptotic genes — MYC, MIR155, IKZF3 and BCL2 — resulting in massively upregulated transcription [60, 61]. This dependency on oncogenic transcription is highlighted by the observation that inhibiting viral oncoproteins and BRD4 result in the collapse of SE domains and the inhibition of cell growth [61].…”

Current Progress in EBV-Associated B-Cell Lymphomas

“…EBV super-enhancers (ESEs) with higher H3K27c signals involve the oncogenes MYC and Bcl2 to promote LCL growth and survival, which provides new insights on EBV-induced lymphoproliferation [60]. EBNA2, EBNA3A, and EBNA3C can enhance RUNX3 expression via RBPJκ to regulate the upstream RUNX3 super-enhancer and meanwhile control the downstream RUNX1 expression [61]. Additionally, abundant enhancers (eRNAs) are also transcribed from ESEs and are regulated by the activity of ESEs [62].…”