Kubasova, NadiyaAlves-Pereira, Clara F.Gupta, SaumyaVinogradova, SvetlanaGimelbrant, AlexanderBarreto, Vasco M.2022-09-052022-09-052022-08-082296-634XPURE: 46368643PURE UUID: bed16c90-e308-44d4-8e7d-ce4f2c89ac19Scopus: 85136528059PubMed: 36003148http://hdl.handle.net/10362/143511Funding Information: This work has received funding from the FCT (Fundação para a Ciência e a Tecnologia) under grants PTDC/BEX-BCM/5900/2014 and IF/ 1823 01721/2014/CP1252/CT0005, and European Union’s Horizon 2020 research and innovation programme under grant agreement No. 752806. NK received a fellowship (PD/BD/114164/2016) from FCT. Publisher Copyright: Copyright © 2022 Kubasova, Alves-Pereira, Gupta, Vinogradova, Gimelbrant and Barreto.Evaluating the epigenetic landscape in the stem cell compartment at the single-cell level is essential to assess the cells’ heterogeneity and predict their fate. Here, using a genome-wide transcriptomics approach in vivo, we evaluated the allelic expression imbalance in the progeny of single hematopoietic cells (HSCs) as a read-out of epigenetic marking. After 4 months of extensive proliferation and differentiation, we found that X-chromosome inactivation (XCI) is tightly maintained in all single-HSC derived hematopoietic cells. In contrast, the vast majority of the autosomal genes did not show clonal patterns of random monoallelic expression (RME). However, a persistent allele-specific autosomal transcription in HSCs and their progeny was found in a rare number of cases, none of which has been previously reported. These data show that: 1) XCI and RME in the autosomal chromosomes are driven by different mechanisms; 2) the previously reported high frequency of genes under RME in clones expanded in vitro (up to 15%) is not found in clones undergoing multiple differentiation steps in vivo; 3) prior to differentiation, HSCs have stable patterns of autosomal RME. We propose that most RME patterns in autosomal chromosomes are erased and established de novo during cell lineage differentiation.4678981engallele-specific expressionallelic imbalance (AI)clonal analysisepigeneticshematopoietic stem cell (HSC)random monoallelic expression (RME)RNA-seqX-chromosome inactivation (XCI)Developmental BiologyCell Biologyjournal article10.3389/fcell.2022.827774https://www.scopus.com/pages/publications/85136528059