ArticleGenetics2009
Global analysis of allele-specific expression in Arabidopsis thaliana.
Article in Genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
89 citing papers in PubMed, 155 citations in OpenAlex.
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- Integrating Multi-omics Analysis to Decipher the Genetic Basis of Heterosis in Xieyou9308.Rice (New York, N.Y.) · 2025Article
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.PLoS computational biology · 2025Article
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.bioRxiv : the preprint server for biology · 2025Article
- The regulatory architecture of gene expression variation in Caenorhabditis elegans revealed by multi-strain allele-specific analysis.Genetics · 2025Article
- The regulatory architecture of gene expression variation inbioRxiv : the preprint server for biology · 2025Article
- Impact of Allele-Specific Expression on Ripening and Quality Characteristics of ABB Banana Fruit.International journal of molecular sciences · 2025Article
- Intraspecific gene regulation in cis- and trans.Evolution; international journal of organic evolution · 2025Review
- High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.Plant physiology · 2024Article
- Impact of the acquired subgenome on the transcriptional landscape in Brettanomyces bruxellensis allopolyploids.G3 (Bethesda, Md.) · 2023Article
- Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel.International journal of molecular sciences · 2023Article
- Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits.Genome biology · 2023Article
- Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage.BMC plant biology · 2022Article
- Transposon insertions regulate genome-wide allele-specific expression and underpin flower colour variations in apple (Malus spp.).Plant biotechnology journal · 2022Article
- Can double PPO mutations exist in the same allele and are such mutants functional?Pest management science · 2022Article
- RNA-Seq Analysis Reveals Expression Regulatory Divergence of W-Linked Genes between Two Contrasting Chicken Breeds.Animals : an open access journal from MDPI · 2022Article
- Limited allele-specific gene expression in highly polyploid sugarcane.Genome research · 2022Article
- Inheritance of gene expression throughout fruit development in chili pepper.Scientific reports · 2021Article
- Molecular and evolutionary processes generating variation in gene expression.Nature reviews. Genetics · 2021Review
- Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression is a complex trait determined by various genetic and nongenetic factors. Among the genetic factors, allelic difference may play a critical role in gene regulation. In this study we globally dissected cis (allelic) and trans sources of genetic variation in F(1) hybrids between two Arabidopsis thaliana wild accessions, Columbia (Col) and Vancouver (Van), using a new high-density SNP-tiling array. This array tiles the whole genome with 35-bp resolution and interrogates 250,000 SNPs identified from resequencing of 20 diverse A. thaliana strains. Quantitative assessment of 12,311 genes identified 3811 genes differentially expressed between parents, 1665 genes with allele-specific expression, and 1688 genes controlled by composite trans-regulatory variation. Loci with cis- or trans-regulatory variation were mapped onto sequence polymorphisms, epigenetic modifications, and transcriptional specificity. Genes regulated in cis tend to be located in polymorphic chromosomal regions, are preferentially associated with repressive epigenetic marks, and exhibit high tissue expression specificity. Genes that vary due to trans regulation reside in relatively conserved chromosome regions, show activating epigenetic marks and generally constitutive gene expression. Our findings demonstrate a method of global functional characterization of allele-specific expression and highlight that chromatin structure is intertwined with evolution of cis- and trans-regulatory variation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.