Fig. 4: Neomers alter the activity of gene regulatory elements.
From: Leveraging sequences missing from the human genome to diagnose cancer
a Schematic describing the luciferase reporter assay. Created in Biorender. Ahituv, N. (2025) https://biorender.com/08yc3gj. Integrative Genomics Viewer track snapshot showing the location of a prostate cancer-associated neomer in the promoters of RPS2-SNHG9 (b) and TMEM127-CIAO1 (c). The top track shows the gene location (GENCODE V36), beneath it the ENCODE layered H3K27ac marks in this region, below that the promoter location (red line) according to ENCODE cCRE annotations and the most lower track shows the neomer sequence. d Relative luciferase units from a luciferase promoter assay (n = 4 per condition) containing either the wild-type (WT) or nullomer variant. Transfection efficiency was normalized using Renilla luciferase and significance is calculated using a two-way ANOVA with multiple testing and Šidák correction. e Schematic showing the lentiMPRA workflow testing 4906 wild type (WT) and neomer (NEO) sequences. f The regulatory impact of 4609 neomer creating mutations, presented as log2 fold change of neomers containing sequence over wild type sequence (x-axis) and ordered from highest to lowest (y-axis). g A neomer in the CTNNA1 locus had the highest activating score and is postulated to lead to a gain of a TCF7 motif, as predicted by FIMO71.
