The transcriptional legacy of developmental stochasticity

• Published in: Nature communications Vol. 14; no. 1; p. 7226
• Main Authors: Ballouz, Sara, Kawaguchi, Risa Karakida, Pena, Maria T., Fischer, Stephan, Crow, Megan, French, Leon, Knight, Frank M., Adams, Linda B., Gillis, Jesse
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09.11.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/91; 45; 45/91; 631/136; 631/208/176; 631/208/199; Alleles; Animals; Armadillos - physiology; DNA methylation; Environmental factors; Epigenetics; Gene expression; Genetic diversity; Genetics; Genomics; Humanities and Social Sciences; Humans; Inactivation; multidisciplinary; Penetrance; Perturbation; Phenotype; Phenotypes; Science; Science (multidisciplinary); Stochasticity; Transcriptomes; Variability; X chromosomes
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-43024-5

Genetic and environmental variation are key contributors during organism development, but the influence of minor perturbations or noise is difficult to assess. This study focuses on the stochastic variation in allele-specific expression that persists through cell divisions in the nine-banded armadillo ( Dasypus novemcinctus ). We investigated the blood transcriptome of five wild monozygotic quadruplets over time to explore the influence of developmental stochasticity on gene expression. We identify an enduring signal of autosomal allelic variability that distinguishes individuals within a quadruplet despite their genetic similarity. This stochastic allelic variation, akin to X-inactivation but broader, provides insight into non-genetic influences on phenotype. The presence of stochastically canalized allelic signatures represents a novel axis for characterizing organismal variability, complementing traditional approaches based on genetic and environmental factors. We also developed a model to explain the inconsistent penetrance associated with these stochastically canalized allelic expressions. By elucidating mechanisms underlying the persistence of allele-specific expression, we enhance understanding of development’s role in shaping organismal diversity. Minor perturbations or noise can significantly impact development but are difficult to assess. Here, the authors detail allelic expression imbalance across the development of nine-banded armadillos that indicate stochastic developmental canalization.