Deterministic and stochastic allele specific gene expression in single mouse blastomeres

Stochastic and deterministic allele specific gene expression (ASE) might influence single cell phenotype, but the extent and nature of the phenomenon at the onset of early mouse development is unknown. Here we performed single cell RNA-Seq analysis of single blastomeres of mouse embryos, which revea...

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Bibliographic Details
Published in:PloS one 2011-06, Vol.6 (6), p.e21208-e21208
Main Authors: Tang, Fuchou, Barbacioru, Catalin, Nordman, Ellen, Bao, Siqin, Lee, Caroline, Wang, Xiaohui, Tuch, Brian B, Heard, Edith, Lao, Kaiqin, Surani, M Azim
Format: Article
Language:English
Subjects:
3' Untranslated Regions - genetics
Accuracy
Alleles
Allelic Imbalance - genetics
Alternative Splicing - genetics
Analysis
Animals
Biology
Blastocyst - cytology
Blastocyst - metabolism
Blastomeres
Blastomeres - cytology
Blastomeres - metabolism
Cancer
Cell cycle
Developmental biology
Embryonic development
Embryonic Development - genetics
Embryos
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Developmental
Genes
Genetic polymorphisms
Genomics
House mouse
Isoforms
Laboratories
Mammals
Medical research
Mice
MicroRNAs
MicroRNAs - genetics
MicroRNAs - metabolism
miRNA
Polymorphism, Single Nucleotide - genetics
Principal Component Analysis
Principal components analysis
Protein Isoforms - genetics
Protein Isoforms - metabolism
Proteomics
Ribonucleic acid
RNA
RNA sequencing
RNA, Untranslated - genetics
RNA, Untranslated - metabolism
Stem cells
Stochastic Processes
Stochasticity
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Summary:Stochastic and deterministic allele specific gene expression (ASE) might influence single cell phenotype, but the extent and nature of the phenomenon at the onset of early mouse development is unknown. Here we performed single cell RNA-Seq analysis of single blastomeres of mouse embryos, which revealed significant changes in the transcriptome. Importantly, over half of the transcripts with detectable genetic polymorphisms exhibit ASE, most notably, individual blastomeres from the same two-cell embryo show similar pattern of ASE. However, about 6% of them exhibit stochastic expression, indicated by altered expression ratio between the two alleles. Thus, we demonstrate that ASE is both deterministic and stochastic in early blastomeres. Furthermore, we also found that 1,718 genes express two isoforms with different lengths of 3'UTRs, with the shorter one on average 5-6 times more abundant in early blastomeres compared to the transcripts in epiblast cells, suggesting that microRNA mediated regulation of gene expression acquires increasing importance as development progresses.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0021208