ArticleBMC genomics2013
Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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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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
21 citing papers in PubMed, 39 citations in OpenAlex.
- Sex-biased transcriptome in in vitro produced bovine early embryos.Cell & bioscience · 2025Article
- Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus.Nature communications · 2024Article
- Review
- TAF4b transcription networks regulating early oocyte differentiation.Development (Cambridge, England) · 2022Article
- Epigenetics drive the evolution of sex chromosomes in animals and plants.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Review
- Dosage Compensation of the X Chromosomes in Bovine Germline, Early Embryos, and Somatic Tissues.Genome biology and evolution · 2019Article
- GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis.Translational neurodegeneration · 2018Article
- RNA-Seq Analyses Identify Frequent Allele Specific Expression and No Evidence of Genomic Imprinting in Specific Embryonic Tissues of Chicken.Scientific reports · 2017Article
- Evolution of Sex Chromosome Dosage Compensation in Animals: A Beautiful Theory, Undermined by Facts and Bedeviled by Details.Genome biology and evolution · 2017Review
- Dosage compensation of the sex chromosomes and autosomes.Seminars in cell & developmental biology · 2016Review
- Article
- Dosage Compensation in the African Malaria Mosquito Anopheles gambiae.Genome biology and evolution · 2016Article
- Evolution of vertebrate sex chromosomes and dosage compensation.Nature reviews. Genetics · 2016Review
- Using mixtures of biological samples as process controls for RNA-sequencing experiments.BMC genomics · 2015Article
- Sex Chromosome Dosage Compensation in Heliconius Butterflies: Global yet Still Incomplete?Genome biology and evolution · 2015Article
- Complete Dosage Compensation in Anopheles stephensi and the Evolution of Sex-Biased Genes in Mosquitoes.Genome biology and evolution · 2015Article
- Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance.Nature genetics · 2015Article
- Facts and artifacts in studies of gene expression in aneuploids and sex chromosomes.Chromosoma · 2014Review
- The evolution of X chromosome inactivation in mammals: the demise of Ohno's hypothesis?Cellular and molecular life sciences : CMLS · 2014Review
- Complete dosage compensation and sex-biased gene expression in the moth Manduca sexta.Genome biology and evolution · 2014Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
backgroundAn enduring question surrounding sex chromosome evolution is whether effective hemizygosity in the heterogametic sex leads inevitably to dosage compensation of sex-linked genes, and whether this compensation has been observed in a variety of organisms. Incongruence in the conclusions reached in some recent reports has been attributed to different high-throughput approaches to transcriptome analysis. However, recent reports each utilizing RNA-seq to gauge X-linked gene expression relative to autosomal gene expression also arrived at diametrically opposed conclusions regarding X chromosome dosage compensation in mammals.
resultsHere we analyze RNA-seq data from X-monosomic female human and mouse tissues, which are uncomplicated by genes that escape X-inactivation, as well as published RNA-seq data to describe relative X expression (RXE). We find that the determination of RXE is highly dependent upon a variety of computational, statistical and biological assumptions underlying RNA-seq analysis. Parameters implemented in short-read mapping programs, choice of reference genome annotation, expression data distribution, tissue source for RNA and RNA-seq library construction method have profound effects on comparing expression levels across chromosomes.
conclusionsOur analysis shows that the high number of paralogous gene families on the mammalian X chromosome relative to autosomes contributes to the ambiguity in RXE calculations, RNA-seq analysis that takes into account that single- and multi-copy genes are compensated differently supports the conclusion that, in many somatic tissues, the mammalian X is up-regulated compared to the autosomes.
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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.