Four Core Genotypes mice harbour a 3.2MB X-Y translocation that perturbs Tlr7 dosage

Abstract

The Four Core Genotypes (FCG) is a mouse model system used to disentangle the function of sex chromosomes and hormones. We report that a copy of a 3.2 MB region of the X chromosome has translocated to the Y^Sry- chromosome and thus increased the expression of X-linked genes including the single-stranded RNA sensor and autoimmune disease mediator Tlr7. This previously-unreported X-Y translocation complicates the interpretation of studies reliant on C57BL/6J FCG mice.

Fig. 1. Transcriptional dosage of genes within a PAR-adjacent 3.2 MB region of the X chromosome is doubled in C57BL/6 J FCG XY mice.

a Schematic representation of the FCG model. b A 3.2 MB region is flanking the PAR of the X chromosome, containing nine genes. c, f Differential expression analysis of X chromosome genes on pseudo-bulked single-cell RNA sequencing from all spleen cells between (c) XYT and XXT mice and between (f) XYO and XXO mice. d–h Differential expression analysis of X chromosome genes on pseudo-bulked single-nucleus RNA sequencing of liver (d–g) Kupffer cells and (e–h) hepatocytes isolated from XYT and XXT mice. The x-axis indicates the expression level as total read counts. Highlighted in orange are all genes in the PAR-adjacent region that have a positive fold change and an adjusted p-value < 0.1 (DESeq2 Wald test). The chromosome, spleen and liver icons were created using BioRender.com. Icons in the figure panels (1a, 1c–h) were created with BioRender.com and are released under a CC-BY-NC-ND license.

Fig. 2. Whole genome sequencing and DNA FISH reveal an X-Y translocation in C57BL/6J FCG XY mice.

a Overview of the X-chromosome, where orange indicates the location of the amplified region, and purple indicates the PAR. b Coverage of sequencing reads normalised to the median autosomal coverage in 1 kb windows of a C57BL/6 J wild-type male (top) and the FCG XYT founder mouse (bottom). c Schematic of the F1 cross between the XYT-B6 male mice and the XXO-CAST female mice. The sex chromosomes in F1 mice are shown, the Y^Sry- chromosome holds the duplication. d Ratio of haplotype-resolved coverages in an F1 FCG XYT hybrid. The presence of B6-specific reads in the amplified region reveals a paternally inherited 3.2 MB region duplicated in the B6 FCG model. e DNA FISH of the whole Y chromosome (magenta) and a 200 kb domain of the X amplification (green) in C57BL/6 J wild-type male (top row) and B6 FCG XYT (bottom row) primary splenocytes. Images represent maximum intensity projections. Scale bars represent 5 µm. f, g DNA FISH of the whole Y chromosome (magenta) and a ~200 kb domain, centred on Msl3 and located in the middle of the X chromosome amplification (green). Quantification of X domain number (f) and Euclidean distance between the Y domain and its nearest X domain (g). n = 100 cells across five fields of view per genotype. Vertical lines represent the median. Error bars represent standard deviation (g). Source data are provided as a Source Data file. The mouse icons were created with BioRender.com. Icons in the figure panel (2c) was created with BioRender.com and is released under a CC-BY-NC-ND license.