Journal
BMC GENOMICS
Volume 14, Issue -, Pages -Publisher
BMC
DOI: 10.1186/1471-2164-14-150
Keywords
RNA-seq; X chromosome; Dosage compensation
Funding
- NINDS [1R01NS057607]
- NSF [IOS- 0920088, MRI-R2, DBI-0959365]
- Division Of Integrative Organismal Systems
- Direct For Biological Sciences [0920088] Funding Source: National Science Foundation
- Div Of Biological Infrastructure
- Direct For Biological Sciences [0959365] Funding Source: National Science Foundation
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Background: An 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. Results: Here 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. Conclusions: Our 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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