Fig. 2: Germline complex variant (MNLP) regulates IRX4 expression. | Nature Communications

Fig. 2: Germline complex variant (MNLP) regulates IRX4 expression.

From: A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus

Fig. 2: Germline complex variant (MNLP) regulates IRX4 expression.The alternative text for this image may have been generated using AI.

a Categorical scatter plot showing correlation between SNP genotype, complex variant genotype and IRX4 expression levels in TCGA PRAD samples (n = 121). All non-recombinant samples (n = 103) marked by transparent gray dots. The following recombinant (n = 18) cases were identified and color coded: heterozygous MNLP (L/S=orange) with homozygous SNP (T/T (n = 6) or C/C (n = 4)) and homozygous MNLP (L/L=green) (n = 6) or (S/S=light blue) (n = 2) with heterozygous SNP. Note, some dots may overlap, see recombinant categories on Supplementary Fig. S2b. Deeper explanation of the dots color codes are shown on panel b. b Homozygous and heterozygous parental haplotypes (without recombination), indicated by gray dots (upper panel). Bottom panel shows the possible recombinant genotypes (recombination between MNLP and rs12653946 index SNP), labeled by orange, blue, and green dots. Blue lines are illustrating one or the other haplotypes and the existing recombination events between MNLP and rs12653946 index SNP. c Aggregated H3K27ac signal plot from human prostate tumor samples (n = 27) at the MNLP position across 3 genotypes. The MNLP region indicated by vertical light blue highlight, genotypes are color coded; L/L = green (n = 6), L/S = orange (n = 18), and S/S=light blue (n = 3). Human tissue data shows genotype-dependent chromatin activity at the MNLP region, the presence of L allele associates with higher H3K27ac signal. d IRX4 expression levels in the function of MNLP genotypes using the GSE130408 data set. e H3K27ac ChIP-seq signal intensitieat chr5:1888500-1890500 (hg19) in the function of MNLP genotypes using the GSE130408 data set. f AR ChIP-seq signal intensities at chr5:1888500-1890500 (hg19) in the function of MNLP genotypes using the GSE130408 data set. For boxplots (panel d-f), lower and upper hinges indicate 25th and 75th percentiles; whiskers extend to 1.5 x the inter-quartile ranges (IQR). P values are for Pearson correlation between fpkm and genotype. Data source for panel c and d–f is listed in Supplementary Data 5.

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