Z-Flipon Variants reveal the many roles of Z-DNA and Z-RNA in health and disease

Abstract

Identifying roles for Z-flipons remains challenging given their dynamic nature. Here we perform genome-wide interrogation with the DNABERT transformer algorithm trained on experimentally identified Z-DNA sequences. We show Z-flipons are enriched in promoters and telomeres and overlap quantitative trait loci for RNA expression, RNA editing, splicing and disease associated variants. Surprisingly, many effects are mediated through Z-RNA formation. We describe Z-RNA motifs present in SCARF2, SMAD1 and CACNA1 transcripts and others in non-coding RNAs. We also provide evidence for another Z-RNA motif that likely enables an adaptive anti-viral intracellular defense through alternative splicing of KRAB domain zinc finger proteins. An analysis of OMIM and gnomAD predicted loss-of-function datasets reveals an overlap of predicted and experimentally validated Z-flipons with disease causing variants in 8.6% and 2.9% of mendelian disease genes respectively, with frameshift variants present in 22% of cases. The work greatly extends the number of phenotypes mapped to Z-flipon variants.

Z-DNA formation in promoters conserved between human and mouse are associated with increased transcription initiation rates

“…In line with our previous studies 23,26,27 we observed enrichment of Z-flipons in promoters. The result for Z-forming sequences in CpG-promoters is unsurprising as alternating d(CG) d(C1-3G1-3) where the cytosines are in the anti-conformation (as in B-DNA), are prone to Z-DNA formation.…”

“…As it was shown by us and others based on sequence analysis alone ( 18,19,24,27,35,(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54) ), Zflipons are enriched in promoters. Here we find Z-flipon enrichment in conserved humanmouse sequences is even higher and we found common pattern of omics features colocalized with conserved Z-flipons at bidirectional promoters.…”

Z-Flipons conserved between human and mouse are associated with increased transcription initiation rates

“…Figure 2A presents the list of TFs with high percent of overlap with Z-flipons shared between human and mouse genomes. In line with our previous studies 23,26,27 we observed enrichment of Z-flipons in promoters. Since GC-repeats are prone to Z-formation we observe significant enrichment of Z-forming sequences in CpG-promoters.…”

“…Example of Wnt Family Member 5A (WNT5A) human and mouse genes with Z-flipons from the presynapse assembly pathway is given in Supplementary Figure 3. This gene harbors many Zflipons detected by three methods -DeepZ, experimental KEx permanganate/S1 nuclease detection method, 21 , and also with Z-DNABERT model 27 . Z-flipons in WNT5A gene are located in 5'UTR, near splice-sites, in exons, at alternative promoters.…”

Analysis of live cell data with G-DNABERT supports a role for G-quadruplexes in chromatin looping

“…Large language models are the next generation predictive models that outperformed CNNs in many areas due to their ability to learn context. We previously applied DNABERT to reveal Z-DNA forming potential in human and mouse genomes 22 , and here we apply DNABERT to predict G4s. As the training set, we use Kouzine et al data set generated with permanganate/S1 Nuclease Footprinting methods 11 .…”