004-22 – ZNF91 and KAP1 Binding Localise to SVA Retrotransposons at Neurodegenerative Disease Relevant Loci

SINE-VNTR-Alu (SVA) Retrotransposons are a hominid specific class of transposable
elements that are capable of mobilisation throughout the human genome. SVA
insertions have contributed to genome evolution through the generation of novel
transcription factor binding sites and epigenetic modification. SVAs are implicated in the
pathology of multiple diseases and are present at loci associated with neurodegenerative
disorders. The evolution of KRAB zinc-finger protein 91 (ZNF91) was driven by the
emergence of SVAs, and has been hypothesised to bind and repress these elements via
recruitment of KAP1, which acts as a scaffold for histone modifiers, inducing local
heterochromatin. SVAs encode a CCCTCTn repeat element, containing consensus
sequence for other zinc finger proteins such as CTCF. We therefore investigated the
potential binding of ZNF91 and KAP1 to the 5’ of SVAs (CT elements) to explore the
potential KAP1-mediated repression of SVAs at neurodegenerative disease relevant loci.
To this end, we performed chromatin immunoprecipitation for ZNF91 and KAP1 in
ZNF91-GFP transfected HEK293 cells, followed by endpoint PCR for the 5’ of SVAs. Our
data shows an enrichment of ZNF91-GFP and KAP1 binding to the 5’ of 3 independent
SVAs. Densitometry analysis of the ZNF91-GFP ChIP-PCR products reveals that
enrichment positively correlates with CT element repeat number, indicating that
additional repeats would allow the binding of more ZNF91 proteins. Overall, these
results provide a basis to direct functional work to characterise the effect of ZNF91-KAP1
mediated repression of these elements, its effect on proximal genes and 3D chromatin
architecture.