Sex-specific differences in the function and differentiation of ABCs contribute to the female bias in lupus pathogenesis

We report the application of RNA-seq, ATAC-seq, and CUT and RUN technology for high-throughput profiling of H3K27me3 epigenetic marks in mice SWAP-70 and DEF6 double knockout (DKO) B-lymphocytes (ABCs and FoBs) flow sorted from spleen. We show that ABCs from female and male DKO mice have unique transcriptional profiles, chromatin accessibility, and that there is a selective loss of repressive chromatin marks like H3K27me3 in ABCs of DKO females can contribute to the increased expression of X-chromosome linked genes like Tlr7 and several other loci among which Tbx21, the classical ABC marker, showed strongest loss in F-ABCs as compared to F-FoBs. RNAseq: 16 RNAseq samples with 2-4 replicas separated between two experiment ATACseq: 3 ATACseq samples with 2 replicas each Cut and Run: 8 samples with 3 replicas each