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泛转录组揭示了酵母中大量辅助基因组对基因表达变异的贡献。

Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast.

作者信息

Caudal Élodie, Loegler Victor, Dutreux Fabien, Vakirlis Nikolaos, Teyssonnière Élie, Caradec Claudia, Friedrich Anne, Hou Jing, Schacherer Joseph

机构信息

Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France.

Institut Universitaire de France (IUF), Paris, France.

出版信息

Nat Genet. 2024 Jun;56(6):1278-1287. doi: 10.1038/s41588-024-01769-9. Epub 2024 May 22.

DOI:10.1038/s41588-024-01769-9
PMID:38778243
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11176082/
Abstract

Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at the species level. Here we generated and analyzed the pan-transcriptome of ~1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of transcriptome divergence. Global gene expression patterns combined with population structure showed that variation in heritable expression mainly lies within subpopulation-specific signatures, for which accessory genes are overrepresented. Genome-wide association analyses consistently highlighted that accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.

摘要

基因表达是将基因型转化为表型的关键步骤。然而，在物种水平上，对于转录组结构和潜在的遗传效应知之甚少。在此，我们生成并分析了约1000个酵母自然分离株的泛转录组，涵盖4977个核心基因和1468个辅助基因。我们发现辅助基因组是转录组差异中一个未被充分认识的驱动因素。全球基因表达模式与群体结构相结合表明，可遗传表达的变异主要存在于亚群体特异性特征中，而辅助基因在这些特征中占比过高。全基因组关联分析一致强调，辅助基因与比例上更多的具有较大效应大小的变异相关联，这说明了辅助基因组在群体内部和群体之间的转录景观上的关键作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/6258a4bbe753/41588_2024_1769_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/e05afc5d3457/41588_2024_1769_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/9911bf5703ea/41588_2024_1769_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/46d9b8c328ed/41588_2024_1769_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/4b5feb569cfc/41588_2024_1769_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/6258a4bbe753/41588_2024_1769_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/e05afc5d3457/41588_2024_1769_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/4cf266725bb2/41588_2024_1769_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/f84612347ced/41588_2024_1769_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/9911bf5703ea/41588_2024_1769_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/46d9b8c328ed/41588_2024_1769_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/4b5feb569cfc/41588_2024_1769_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d22/11176082/6258a4bbe753/41588_2024_1769_Fig7_HTML.jpg

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