Transcriptomics

Dataset Information

298

The relationship between gene network structure and expression variation among individuals and species


ABSTRACT: Variation among individuals is a prerequisite of evolution by natural selection. As such, identifying the origins of variation is a fundamental goal of biology. We investigated the link between gene interactions and variation in gene expression among individuals and species, using the mammalian limb as a model system. We first built interaction networks for key genes regulating early (outgrowth; E9.5-11) and late (expansion and elongation; E11-13) limb development in mouse. This resulted in an Early (ESN) and Late (LSN) Stage Network. Computational perturbations of these networks suggest that the ESN is more robust. We then quantified levels of the same key genes among mouse individuals, and found that they vary less at earlier limb stages and that variation in gene expression is heritable. Finally, we quantified variation in gene expression levels among four mammals with divergent limbs (bat, opossum, mouse and pig), and found that levels vary less among species at earlier limb stages. We also found that variation in gene expression levels among individuals and species are correlated for earlier and later limb development. In conclusion, results are consistent with the robustness of the ESN buffering among-individual variation in gene expression levels early in mammalian limb development, and constraining the evolution of early limb development among mammalian species. Bat, mouse, opossum, and pig mRNA profiles at early and late developmental stages on each species fore and hind-limbs . Various replicates of each library were generated by single-end sequencing using Illumina HiSeq 2500. Please note that the De novo transcriptome assembly for bat (Trinity.fasta) was generated from pooled RNA-seq data of fore and hind-limbs at various embryonic developmental stages; Beginning stage (Wanek stage 2: 3 FL and 3 HL samples), early-stage (Wanek stage 3/4: 2 FL and 2 HL samples), and late_stage (Wanke stage 6: 2 FL and 2 HL samples).

SUBMITTER: Karen E Sears   Kari Kosog  Marcelo Rivas-Astroza  Zoi Rapti  Richard R Behringer  Chris J Cretekos  Rachel Poe  Jennifer A Maier  Sheng Zhong  Jonathan D Marcot  Marcelo Rivas  John J Rasweiler IV 

PROVIDER: E-GEOD-71390 | ArrayExpress | 2015-08-24

SECONDARY ACCESSION(S): GSE71390SRP061644PRJNA291081

REPOSITORIES: GEO, ArrayExpress, ENA

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