A distinct isoform of lymphoid enhancer binding factor 1 (LEF1) epigenetically restricts EBV reactivation to maintain viral latency

As a human tumor virus, EBV is present as a latent infection in its
associated malignancies where genetic and epigenetic changes have been
shown to impede cellular differentiation and viral reactivation. We
reported previously that levels of the Wnt signaling effector, lymphoid
enhancer binding factor 1 (LEF1) increased following EBV epithelial
infection and an epigenetic reprogramming event was maintained even after
loss of the viral genome. Elevated LEF1 levels are also observed in
nasopharyngeal carcinoma and Burkitt lymphoma. To determine the role
played by LEF1 in the EBV life cycle, we used in silico analysis of EBV
type 1 and 2 genomes to identify over 20 Wnt-response elements, which
suggests that LEF1 may bind directly to the EBV genome and regulate the
viral life cycle. Using CUT&RUN-seq, LEF1 was shown to bind the
latent EBV genome at various sites encoding viral lytic products that
included the immediate early transactivator BZLF1 and viral primase BSLF1
genes. The LEF1 gene encodes various long and short protein isoforms.
siRNA depletion of specific LEF1 isoforms revealed that the
alternative-promoter derived isoform with an N-terminal truncation (∆N
LEF1) transcriptionally repressed lytic genes associated with LEF1
binding. In addition, forced expression of the ∆N LEF1 isoform antagonized
EBV reactivation. As LEF1 repression requires histone deacetylase activity
through either recruitment of or direct intrinsic histone deacetylase
activity, siRNA depletion of LEF1 resulted in increased histone 3 lysine 9
and lysine 27 acetylation at LEF1 binding sites and across the EBV genome.
Taken together, these results indicate a novel role for LEF1 in
maintaining EBV latency and restriction viral reactivation via repressive
chromatin remodeling of critical lytic cycle factors.