Cargando…

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

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 chimpanz...

Descripción completa

Detalles Bibliográficos
Autores principales: Barr, Kenneth A., Rhodes, Katherine L., Gilad, Yoav
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10496171/
https://www.ncbi.nlm.nih.gov/pubmed/37697401
http://dx.doi.org/10.1186/s13059-023-03019-3
_version_ 1785105051350466560
author Barr, Kenneth A.
Rhodes, Katherine L.
Gilad, Yoav
author_facet Barr, Kenneth A.
Rhodes, Katherine L.
Gilad, Yoav
author_sort Barr, Kenneth A.
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03019-3.
format Online
Article
Text
id pubmed-10496171
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-104961712023-09-13 The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees Barr, Kenneth A. Rhodes, Katherine L. Gilad, Yoav Genome Biol Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03019-3. BioMed Central 2023-09-11 /pmc/articles/PMC10496171/ /pubmed/37697401 http://dx.doi.org/10.1186/s13059-023-03019-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Barr, Kenneth A.
Rhodes, Katherine L.
Gilad, Yoav
The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees
title The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees
title_full The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees
title_fullStr The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees
title_full_unstemmed The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees
title_short The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees
title_sort relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10496171/
https://www.ncbi.nlm.nih.gov/pubmed/37697401
http://dx.doi.org/10.1186/s13059-023-03019-3
work_keys_str_mv AT barrkennetha therelationshipbetweenregulatorychangesincisandtransandtheevolutionofgeneexpressioninhumansandchimpanzees
AT rhodeskatherinel therelationshipbetweenregulatorychangesincisandtransandtheevolutionofgeneexpressioninhumansandchimpanzees
AT giladyoav therelationshipbetweenregulatorychangesincisandtransandtheevolutionofgeneexpressioninhumansandchimpanzees
AT barrkennetha relationshipbetweenregulatorychangesincisandtransandtheevolutionofgeneexpressioninhumansandchimpanzees
AT rhodeskatherinel relationshipbetweenregulatorychangesincisandtransandtheevolutionofgeneexpressioninhumansandchimpanzees
AT giladyoav relationshipbetweenregulatorychangesincisandtransandtheevolutionofgeneexpressioninhumansandchimpanzees