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Constraint and divergence of global gene expression in the mammalian embryo

ABSTRACT: We profiled genome-wide gene expression of 170 individual mid-gestation (embryonic day 11.5) whole mouse embryos derived from a 2-generation interspecies mouse cross and asked to what extent genetic variation drives four important parameters of regulatory architecture: allele-specific expression (ASE), imprinting, trans-regulatory effects, and maternal effect. The inbred strain C57BL/6J and wild-derived inbred strain CAST/EiJ were used in reciprocal crosses to generate F1 embryos. F1 progeny were backcrossed to C57BL/6J in reciprocal crosses to generate 154 N2 embryos. We employed a backcross design, in which N2 offspring have genotypically distinct parents, to enable comparison of gene expression for offspring from each side of the reciprocal cross. Our findings demonstrate that genetic variation contributes to widespread gene expression differences during mammalian embryogenesis. Transcriptome analysis of E11.5 mouse embryos: 16 F1 embryos from reciprocally crossed C57BL/6J and CastEi/J parents; and 154 N2 embryos from reciprocal backcross of F1s to the C57BL/6J parent.

ORGANISM(S): Mus musculus  

SUBMITTER: Arend Sidow   Julie C Baker  Noah Spies  Cheryl L Smith  Serafim Batzoglou  Jesse M Rodriguez 

PROVIDER: E-GEOD-62967 | ArrayExpress | 2015-04-14



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Constraint and divergence of global gene expression in the mammalian embryo.

Spies Noah N   Smith Cheryl L CL   Rodriguez Jesse M JM   Baker Julie C JC   Batzoglou Serafim S   Sidow Arend A  

eLife 20150414

The effects of genetic variation on gene regulation in the developing mammalian embryo remain largely unexplored. To globally quantify these effects, we crossed two divergent mouse strains and asked how genotype of the mother or of the embryo drives gene expression phenotype genomewide. Embryonic expression of 331 genes depends on the genotype of the mother. Embryonic genotype controls allele-specific expression of 1594 genes and a highly overlapping set of cis-expression quantitative trait loci  ...[more]

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