ArticlePloS one2014
Hybrid mice reveal parent-of-origin and Cis- and trans-regulatory effects in the retina.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
- Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation.bioRxiv : the preprint server for biology · 2026Article
- Overexpression of placenta-specific noncanonical imprinted genes causes placental enlargement in intersubspecific hybrid mice†.Biology of reproduction · 2026Article
- Evolution of gene expression across brain regions in behaviourally divergent deer mice.Molecular ecology · 2025Article
- Intraspecific gene regulation in cis- and trans.Evolution; international journal of organic evolution · 2025Review
- The dynamic genetic determinants of increased transcriptional divergence in spermatids.Nature communications · 2024Article
- Non-additive genetic components contribute significantly to population-wide gene expression variation.Cell genomics · 2024Article
- Environmentally robustProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Regulatory Divergence as a Mechanism for X-Autosome Incompatibilities in Caenorhabditis Nematodes.Genome biology and evolution · 2023Article
- Allele-specific regulatory effects on the pig transcriptome.GigaScience · 2022Article
- Characterization of sequence determinants of enhancer function using natural genetic variation.eLife · 2022Article
- Mapping theProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Convergent evolution of gene expression in two high-toothed stickleback populations.PLoS genetics · 2018Article
- The role of retinol dehydrogenase 10 in the cone visual cycle.Scientific reports · 2017Article
- Article
- Gene regulation and speciation in house mice.Genome research · 2016Article
- Circadian and light-driven regulation of rod dark adaptation.Scientific reports · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
A fundamental challenge in genomics is to map DNA sequence variants onto changes in gene expression. Gene expression is regulated by cis-regulatory elements (CREs, i.e., enhancers, promoters, and silencers) and the trans factors (e.g., transcription factors) that act upon them. A powerful approach to dissecting cis and trans effects is to compare F1 hybrids with F0 homozygotes. Using this approach and taking advantage of the high frequency of polymorphisms in wild-derived inbred Cast/EiJ mice relative to the reference strain C57BL/6J, we conducted allele-specific mRNA-seq analysis in the adult mouse retina, a disease-relevant neural tissue. We found that cis effects account for the bulk of gene regulatory divergence in the retina. Many CREs contained functional (i.e., activating or silencing) cis-regulatory variants mapping onto altered expression of genes, including genes associated with retinal disease. By comparing our retinal data with previously published liver data, we found that most of the cis effects identified were tissue-specific. Lastly, by comparing reciprocal F1 hybrids, we identified evidence of imprinting in the retina for the first time. Our study provides a framework and resource for mapping cis-regulatory variants onto changes in gene expression, and underscores the importance of studying cis-regulatory variants in the context of retinal disease.
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What OpenQuestion holds
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.