Single cell expression data as a direct measure for identifying human genes that escape X-inactivation

Sex chromosomes pose an inherent genetic imbalance between genders. In mammals, one of the female’s X-chromosomes undergoes inactivation (Xi). Indirect measurements estimate 15- 25% of Xi genes to completely or partially escape inactivation. The identity of these escaper genes, and their propensity for escape remain unsolved. We applied a direct method to identify escapees based on RNA-Seq from 25 single-cell lymphoblasts and a pooled version. We quantified the differential allelic expression by assigning reads from expressed genes to SNPs with distinct maternal or paternal identities. We confirmed that X-inactivation occurs and is maintained in single cells. Using strict and relaxed protocols, we confidently identified 27 and 35 escaper genes, respectively. Using 30 published datasets, we compiled a genes’ catalogue characterized as escapees or inhibited along with a confidence value. The nature of most reported genes (454 in total) as escapees and inhibited is mixed across many biological contexts. We report a strong statistical overlap between escapees identified from single cells and those reported in the literature-based catalogue. We confirmed the usefulness of single cells’ expression data for studying allelic bias phenomena. We conclude that escaping X-inactivation is less deterministic than previously reported with only few genes acting as exclusive escapees