title: Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
abstract: Expression from both alleles is generally observed in analyses of diploid cell populations, but studies addressing allelic expression patterns genome-wide in single cells are lacking. Here, we present global analyses of allelic expression across individual cells of mouse preimplantation embryos of mixed background (CAST/EiJ × C57BL/6J). We discovered abundant (12 to 24%) monoallelic expression of autosomal genes and that expression of the two alleles occurs independently. The monoallelic expression appeared random and dynamic because there was considerable variation among closely related embryonic cells. Similar patterns of monoallelic expression were observed in mature cells. Our allelic expression analysis also demonstrates the de novo inactivation of the paternal X chromosome. We conclude that independent and stochastic allelic transcription generates abundant random monoallelic expression in the mammalian cell.
authors.affiliation: Ludwig Institute for Cancer Research, Box 240, 171 77 Stockholm, Sweden.
authors.forename: Qiaolin
authors.initials: Q
authors.lastname: Deng
authors.forename: Daniel
authors.initials: D
authors.lastname: Ramsköld
authors.forename: Björn
authors.initials: B
authors.lastname: Reinius
authors.forename: Rickard
authors.initials: R
authors.lastname: Sandberg
mesh_terms: D000483:Alleles; D000818:Animals; D047108:Embryonic Development / Q000235:genetics; D005260:Female; D018507:Gene Expression Regulation, Developmental; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D023121:RNA, Messenger, Stored / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D059010:Single-Cell Analysis / Q000379:methods; D014960:X Chromosome / Q000235:genetics; D049951:X Chromosome Inactivation / Q000235:genetics*
chemical_list: D023121:RNA, Messenger, Stored