Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues.
Cell Genom
; 4(8): 100625, 2024 Aug 14.
Article
in En
| MEDLINE
| ID: mdl-39084228
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 from XCI in lymphoid tissues and lymphocytes. Finally, effect size comparisons of genome-wide association studies between sexes suggested the underlying impact of escape on the genotype-phenotype association. Overall, scLinaX and the quantified escape catalog identified the heterogeneity of escape across cell types and tissues.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
X Chromosome Inactivation
/
Single-Cell Analysis
Limits:
Animals
/
Female
/
Humans
/
Male
Language:
En
Journal:
Cell Genom
Year:
2024
Document type:
Article
Country of publication:
United States