Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues.

ABSTRACT: Several X-linked genes escape from X chromosome inactivation (XCI), while differences in escape across cell types and tissues are still poorly characterized. Here, we developed scLinaX for directly quantifying relative gene expression from the inactivated X chromosome with droplet-based single-cell RNA sequencing (scRNA-seq) data. The scLinaX and differentially expressed gene analyses with large-scale blood scRNA-seq datasets consistently identified the stronger escape in lymphocytes than in myeloid cells. An extension of scLinaX to a 10x multiome dataset (scLinaX-multi) suggested a stronger escape in lymphocytes than in myeloid cells at the chromatin-accessibility level. The scLinaX analysis of human multiple-organ scRNA-seq datasets also identified the relatively strong degree of escape

SUBMITTER: Tomofuji Y 

PROVIDER: S-EPMC11406184 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature