Publication Date
5-14-2025
Journal
Cell Genomics
DOI
10.1016/j.xgen.2025.100823
PMID
40187355
PMCID
PMC12143330
PubMedCentral® Posted Date
4-4-2025
PubMedCentral® Full Text Version
Post-print
Abstract
Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected from 12 age-matched healthy olive baboons (Papio anubis) for genome-wide ASE analysis. By sequencing their genomes at a minimum depth of 30×, we identified over 16 million single-nucleotide variants (SNVs). We also generated long-read sequencing data, enabling the phasing of all variants present within the coding regions of 96.5% of assayable protein-coding genes as a single haplotype block. Given the extensive heterozygosity of baboons relative to humans, we could quantify ASE across 72% of the total annotated protein-coding gene set. We identified genes that exhibit ASE and affect specific tissues and genotypes. We discovered ASE SNVs that also exist in human populations with identical alleles and that are designated as pathogenic by both the PrimateAI-3D and AlphaMissense models.
Keywords
Animals, Alleles, Polymorphism, Single Nucleotide, Male, Humans, Papio, Haplotypes, Papio anubis, Genome, Organ Specificity, Mammals, Genome-Wide Association Study, allele-specific-expression, baboon, primates, sequencing, haplotype phasing, heterozygosity, allele switching, haplotype switching, imprinting, pathogenic SNVs
Published Open-Access
yes
Recommended Citation
Ramasamy, Ramesh; Raveendran, Muthuswamy; Harris, R Alan; et al., "Genome-Wide Allele-Specific Expression in Multi-Tissue Samples From Healthy Male Baboons Reveals the Transcriptional Complexity of Mammals" (2025). Faculty and Staff Publications. 5091.
https://digitalcommons.library.tmc.edu/baylor_docs/5091
Graphical Abstract
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