The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees.

Bibliographic Collection: 
Publication Type: Journal Article
Authors: Barr, Kenneth A; Rhodes, Katherine L; Gilad, Yoav
Year of Publication: 2023
Journal: Genome Biol
Volume: 24
Issue: 1
Pagination: 207
Date Published: 2023 Sep 11
Publication Language: eng
ISSN: 1474-760X
Keywords: Animals, Cell Line, Embryoid Bodies, Gene Expression Profiling, Humans, Pan troglodytes, Transcriptome

BACKGROUND: Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees.

RESULTS: We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation likely evolves under directional selection in one or a handful of cell types. Using embryoid bodies from a human-chimpanzee fused cell line, we also infer the proportion of inter-species regulatory differences due to changes in cis and trans elements between the species. Using the cis/trans inference and an analysis of transcription factor binding sites, we identify dozens of transcription factors whose inter-species differences in expression are affecting expression differences between humans and chimpanzees in hundreds of target genes.

CONCLUSIONS: Here, we present the most comprehensive dataset of comparative gene expression from humans and chimpanzees to date, including a catalog of regulatory mechanisms associated with inter-species differences.

DOI: 10.1186/s13059-023-03019-3
Alternate Journal: Genome Biol