High prevalence of clonal monoallelic expression/Reply

• Published in: Nature genetics Vol. 50; no. 9; pp. 1198 - 1200
• Main Authors: Vigneau, Sébastien, Vinogradova, Svetlana, Savova, Virginia, Gimelbrant, Alexander, Reinius, Björn, Sandberg, Rickard
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group 01.09.2018
• Subjects: Bias; Cloning; Fibroblasts; Gene expression; Genomes; Sweden
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/s41588-018-0189-6

[...]most genes known to escape XCI in mouse fibroblasts were correctly identified as biallelic in a significant fraction of cells2. [...]to Gimelbrant's statements1, our thresholds have been extensively validated and are well suited for analyses of monoallelic gene expression. Another emerging issue is that clonal aRME genes tend to be expressed at very low levels in the cells in which they were identified, typically at approximately two mRNA transcripts per cell2,11,12. Because transcription is stochastic and occurs on single alleles, it is more likely for weakly expressed genes to have allelic imbalance or aRME at any given time point of inquiry. [...]Gimelbrant and colleagues suggest that single-cell RNA-seq may not be suitable (or may be underpowered) for allelic gene expression analyses. When XCI is used as an internal control in the cells, it is apparent that single-cell RNA-seq has sufficient power to identify essentially all genes on the X chromosome as having clonal monoallelic gene expression. [...]the single-cell RNA-seq in our study identified the same imprinted genes as bulk RNA-seq performed on the same primary cells2, thus again confirming power and accuracy.