ArticleMolecular ecology2010
Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing.
Article in Molecular ecology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 80 citations in OpenAlex.
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- Analysis of subcellular RNA fractions demonstrates significant genetic regulation of gene expression in human brain post-transcriptionally.Scientific reports · 2023Article
- Power calculator for detecting allelic imbalance using hierarchical Bayesian model.BMC research notes · 2021Article
- Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas.G3 (Bethesda, Md.) · 2021Article
- Comparative Transcriptomic Analysis of Gene Expression Inheritance Patterns Associated with Cabbage Head Heterosis.Plants (Basel, Switzerland) · 2021Article
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- Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets.Scientific reports · 2019Article
- Tissue-Specific cis-Regulatory Divergence Implicates eloF in Inhibiting Interspecies Mating in Drosophila.Current biology : CB · 2018Article
- The genomic basis of environmental adaptation in house mice.PLoS genetics · 2018Article
- Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations.Genome biology and evolution · 2017Article
- No Excess of Cis-Regulatory Variation Associated with Intraspecific Selection in Wild Pearl Millet (Cenchrus americanus).Genome biology and evolution · 2017Article
- RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data.Nucleic acids research · 2016Article
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- A flexible Bayesian method for detecting allelic imbalance in RNA-seq data.BMC genomics · 2014Article
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Authors and funding
7 authors at 5 institutions in 3 countries.
Funding
Abstract
Differences in gene expression are thought to be an important source of phenotypic diversity, so dissecting the genetic components of natural variation in gene expression is important for understanding the evolutionary mechanisms that lead to adaptation. Gene expression is a complex trait that, in diploid organisms, results from transcription of both maternal and paternal alleles. Directly measuring allelic expression rather than total gene expression offers greater insight into regulatory variation. The recent emergence of high-throughput sequencing offers an unprecedented opportunity to study allelic transcription at a genomic scale for virtually any species. By sequencing transcript pools derived from heterozygous individuals, estimates of allelic expression can be directly obtained. The statistical power of this approach is influenced by the number of transcripts sequenced and the ability to unambiguously assign individual sequence fragments to specific alleles on the basis of transcribed nucleotide polymorphisms. Here, using mathematical modelling and computer simulations, we determine the minimum sequencing depth required to accurately measure relative allelic expression and detect allelic imbalance via high-throughput sequencing under a variety of conditions. We conclude that, within a species, a minimum of 500-1000 sequencing reads per gene are needed to test for allelic imbalance, and consequently, at least five to 10 millions reads are required for studying a genome expressing 10 000 genes. Finally, using 454 sequencing, we illustrate an application of allelic expression by testing for cis-regulatory divergence between closely related Drosophila species.
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