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

Nathaniel K. Jue, Michael B. Murphy, Seth D. Kasowitz, Sohaib M. Qureshi, Craig J. Obergfell, Sahar Elsisi, Robert J. Foley, Rachel J. O’Neill, Michael J. O’Neill

Research output: Contribution to journalArticlepeer-review


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.
Original languageAmerican English
JournalBMC Genomics
StatePublished - 2013
Externally publishedYes


  • Dosage compensation
  • RNA-seq
  • X chromosome


  • Life Sciences
  • Molecular Biology

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