Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures

García-Pérez, Raquel; Esteller-Cucala, Paula; Mas, Glòria; Lobón, Irene; Riera, Meritxell; Kuhlwilm, Martin; Navarro, Arcadi; Blancher, Antoine; Croce, Luciano Di; Gómez-Skármeta, José Luis; Juan, David

doi:10.1038/s41467-021-23397-1

Cited by 26 publications

(25 citation statements)

References 110 publications

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“…All 40 studies we considered included at least one unadmixed individual of Western ancestry. In contrast, only two studies sampled a Nigeria-Cameroon chimpanzee (as we later discovered, this was the same individual); and only S35 ( García-Pérez et al 2021 ) sampled a purely Central chimpanzee. None of the studies considered subspecies when sampling.…”

Section: Discussionmentioning

confidence: 78%

Genetic Diversity in Chimpanzee Transcriptomics Does Not Represent Wild Populations

Shukla

Shaban

Romero

2021

Genome Biology and Evolution

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Chimpanzees (Pan troglodytes) are a genetically diverse species, consisting of four highly distinct subspecies. As humans’ closest living relative, they have been a key model organism in the study of human evolution, and comparisons of human and chimpanzee transcriptomes have been widely used to characterize differences in gene expression levels that could underlie the phenotypic differences between the two species. However, the subspecies from which these transcriptomic data sets have been derived is not recorded in metadata available in the public NCBI Sequence Read Archive (SRA). Furthermore, labeling of RNA sequencing (RNA-seq) samples is for the most part inconsistent across studies, and the true number of individuals from whom transcriptomic data are available is difficult to ascertain. Thus, we have evaluated genetic diversity at the subspecies and individual level in 486 public RNA-seq samples available in the SRA, spanning the vast majority of public chimpanzee transcriptomic data. Using multiple population genetics approaches, we find that nearly all samples (96.6%) have some degree of Western chimpanzee ancestry. At the individual donor level, we identify multiple samples that have been repeatedly analyzed across different studies and identify a total of 135 genetically distinct individuals within our data, a number that falls to 89 when we exclude likely first- and second-degree relatives. Altogether, our results show that current transcriptomic data from chimpanzees are capturing low levels of genetic diversity relative to what exists in wild chimpanzee populations. These findings provide important context to current comparative transcriptomics research involving chimpanzees.

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Section: Discussionmentioning

confidence: 78%

Genetic Diversity in Chimpanzee Transcriptomics Does Not Represent Wild Populations

Shukla

Shaban

Romero

2021

Genome Biology and Evolution

View full text Add to dashboard Cite

show abstract

“…All 40 studies we considered included at least one unadmixed individual of Western ancestry. In contrast, only two studies sampled a Nigeria-Cameroon chimpanzee (as we later discovered, this was the same individual); and only S35 [30] sampled a purely Central chimpanzee. None of the studies considered subspecies when sampling.…”

Section: Discussionmentioning

confidence: 97%

Genetic diversity in chimpanzee transcriptomics does not represent wild populations

Shukla

Shaban

Romero

2021

Preprint

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Chimpanzees (Pan troglodytes) are a genetically diverse species, consisting of 4 highly distinct subspecies. As humans' closest living relative they have been a key model organism in the study of human evolution, and comparisons of human and chimpanzee transcriptomes have been widely used to characterise differences in gene expression levels that could underlie the phenotypic differences between the two species. However, the subspecies from which these transcriptomic datasets have been derived is not recorded in metadata available in the public NCBI Sequence Read Archive (SRA). Furthermore, labelling of RNA-seq samples is for the most part inconsistent across studies, and the true number of individuals from whom transcriptomic data is available is difficult to ascertain. Thus we have evaluated genetic diversity at the subspecies and individual level in 486 public RNA-seq samples available in the SRA, spanning the vast majority of public chimpanzee transcriptomic data. Using multiple population genetics approaches we find that nearly all samples (96.6%) have some degree of Western chimpanzee ancestry. At the individual donor level, we identify multiple samples that have been repeatedly analysed across different studies, and identify a total of 135 genetically distinct individuals within our data, a number that falls to 89 when we exclude likely first and second-degree relatives. Altogether, our results show that current transcriptomic data from chimpanzees is capturing low levels of genetic diversity relative to what exists in wild chimpanzee populations. These findings provide important context to current comparative transcriptomics research involving chimpanzees.

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“…GM19238 (human) and EB185(JC) (orangutan) were purchased from Coriell Institute and Sigma-Aldrich, respectively. The remaining cell lines used in this article are described in García-Pérez et al (2021). Detailed information for the panel of LCLs is provided in Supplemental Table S1.…”

Section: Lymphoblastoid Cell Lines Origin and Culturementioning

confidence: 99%

“…GG05, CRL-1850, GM19238, CH507, CH170, CH322, EB185 and R94011, while the RNA-seq for the remaining LCLs (except for GM12878) was generated in (García-Pérez et al 2021). RNA-seq data from GM12878 was retrieved from NCBI (accession SRR998197 and SRR998198).…”

Section: Rna-seq Data Production and Processingmentioning

confidence: 99%

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

et al. 2022

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Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.

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Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures

Cited by 26 publications

References 110 publications

Genetic Diversity in Chimpanzee Transcriptomics Does Not Represent Wild Populations

Genetic Diversity in Chimpanzee Transcriptomics Does Not Represent Wild Populations

Genetic diversity in chimpanzee transcriptomics does not represent wild populations

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

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