Determination of dosage compensation of the mammalian X chromosome by RNA-Seq is dependent on analytical approach

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.

Here, researchers at the University of Connecticut 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). They 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.

Their 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.

  •  Jue NK, Murphy MB, Kasowitz SD, Qureshi SM, Obergfell CJ, Elsisi S, Foley RJ, O’Neill RJ, O’Neill MJ. (2013) Determination of dosage compensation of the mammalian X chromosome by RNA-Seq is dependent on analytical approach. BMC Genomics [Epub ahead of print]. [abstract]