Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression

Pierre, Celine L. St.; Macias-Velasco, Juan F; Wayhart, Jessica P; Li, Yin; Semenkovich, Clay F.; Lawson, Heather A.

doi:10.1101/gr.276193.121

Cited by 12 publications

(12 citation statements)

References 86 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Allele-specific expression has been shown to be modulated by genetic, epigenetic and environmental mechanisms (Handunnetthi et al, 2010;St. Pierre et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Expression diversity of cichlid MHC alleles

Bracamonte,

Hablützel,

Lozano-Martín

et al. 2024

Preprint

View full text Add to dashboard Cite

Diversification by natural selection is a major source of biodiversity. The selective pressures imposed by parasites on their hosts have the potential to increase diversity at immunologically relevant genes and maintain high polymorphism within and among populations. The immune genes of the major histocompatibility complex (MHC) are a hallmark of parasite-mediated selection. These genes frequently show local adaptation to the prevailing parasites. Although associations between parasites and alleles have been identified, they are often imperfect, indicating that parasite-mediated selection goes beyond sequence identity. Here, we explored allele-specific expression of MHC class IIB in cichlid fish and its relationship with sequence diversity. This revealed a few highly abundant alleles with consistently low expression, and many relatively rare alleles with high expression levels that were variable among individuals. Alleles that formed functional supertypes also had similar expression. This suggests that rare alleles may be those responding to parasites and that similar functionality may be provided by different alleles in different individuals. Our results further suggest that there could be an optimal number of MHC alleles per individual and that deviations from this optimum are compensated by adjusting expression levels. The common and lowly expressed alleles may have attained different functions, a patterns that appears to be consistent in Neotropical and African cichlids. Our study shows that MHC expression is highly variable among alleles potentially interacting with parasites, providing an additional substrate for selection. Furthermore, our study exemplifies how combining genetic diversity with detailed expression information can help identifying functionally relevant diversity.

show abstract

“…Allele-specific expression has been shown to be modulated by genetic, epigenetic and environmental mechanisms (Handunnetthi et al, 2010;St. Pierre et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

“…Also for the African MHC class II, we observed large expression differences among putative loci with variation both within and among species. Allele-specific expression has been shown to be modulated by genetic, epigenetic and environmental mechanisms (Handunnetthi et al, 2010; St. Pierre et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Expression diversity of cichlid MHC alleles

Bracamonte,

Hablützel,

Lozano-Martín

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…For example, plasticity in expression owing to cis -acting changes tend to accumulate in Arabidopsis to magnify pre-existing plasticity of expression [ 83 ]. Emerging studies that employ allele-specific expression to detect biased expression among a wide array of tissues and other contexts offer a potentially powerful means to address questions about different mechanisms of plastic gene regulation with respect to expression contexts [ 84 , 85 ]. In addition, it remains unresolved how often it is the case that observed context-dependent expression is, in fact, adaptive.…”

Section: Mechanisms Of Gene Regulatory Plasticity Over Developmental ...mentioning

confidence: 99%

Sexual conflict, heterochrony and tissue specificity as evolutionary problems of adaptive plasticity in development

Cutter

2023

Proc. R. Soc. B.

View full text Add to dashboard Cite

Differential gene expression represents a fundamental cause and manifestation of phenotypic plasticity. Adaptive phenotypic plasticity in gene expression as a trait evolves when alleles that mediate gene regulation serve to increase organismal fitness by improving the alignment of variation in gene expression with variation in circumstances. Among the diverse circumstances that a gene encounters are distinct cell types, developmental stages and sexes, as well as an organism's extrinsic ecological environments. Consequently, adaptive phenotypic plasticity provides a common framework to consider diverse evolutionary problems by considering the shared implications of alleles that produce context-dependent gene expression. From this perspective, adaptive plasticity represents an evolutionary resolution to conflicts of interest that arise from any negatively pleiotropic effects of expression of a gene across ontogeny, among tissues, between the sexes, or across extrinsic environments. This view highlights shared properties within the general relation of fitness, trait expression and context that may nonetheless differ substantively in the grain of selection within and among generations to influence the likelihood of adaptive plasticity as an evolutionary response. Research programmes that historically have focused on these separate issues may use the insights from one another by recognizing their shared dependence on context-dependent gene regulatory evolution.

show abstract

“…Mammalian genomes are diploid and consist of 2 parental copies for each gene locus [ 1 ]. Allele-specific expression (ASE) occurs in diploid genomes when one allele is preferentially expressed over the other [ 2 , 3 ]. Genetic and epigenetic differences between alleles are frequently associated with ASEs occurring at different developmental stages and leading to functional consequences for a variety of biological processes [ 2 , 3 ].…”

Section: Introductionmentioning

confidence: 99%

Allele-specific regulatory effects on the pig transcriptome

Lin,

Li,

Chen

et al. 2022

GigaScience

View full text Add to dashboard Cite

Background Allele-specific expression (ASE) refers to the preferential expression of one allele over the other and contributes to adaptive phenotypic plasticity. Here, we used a reciprocal cross-model between phenotypically divergent European Berkshire and Asian Tibetan pigs to characterize 2 ASE classes: imprinting (i.e., the unequal expression between parental alleles) and sequence dependent (i.e., unequal expression between breed-specific alleles). We examined 3 transcript types, including protein-coding genes (PCGs), long noncoding RNAs, and transcripts of unknown coding potential, across 7 representative somatic tissues from hybrid pigs generated by reciprocal crosses. Results We identified a total of 92 putative imprinted transcripts, 69 (75.00%) of which are described here for the first time. By combining the transcriptome from purebred Berkshire and Tibetan pigs, we found ∼6.59% of PCGs are differentially expressed between breeds that are regulated by trans-elements (e.g., transcriptional factors), while only ∼1.35% are attributable to cis (e.g., promoters). The higher prevalence of trans-PCGs indicates the dominated effects of trans-regulation in driving expression differences and shaping adaptive phenotypic plasticity between breeds, which were supported by functional enrichment analysis. We also found strong evidence that expression changes mediated by cis-effects were associated with accumulated variants in promoters. Conclusions Our study provides a comprehensive map of expression regulation that constitutes a valuable resource for the agricultural improvement of pig breeds.

show abstract

Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression

Cited by 12 publications

References 86 publications

Expression diversity of cichlid MHC alleles

Expression diversity of cichlid MHC alleles

Sexual conflict, heterochrony and tissue specificity as evolutionary problems of adaptive plasticity in development

Allele-specific regulatory effects on the pig transcriptome

Contact Info

Product

Resources

About