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X-chromosome upregulation is driven by increased burst frequency

Abstract

Ohno's hypothesis postulates that upregulation of X-linked genes rectifies their dosage imbalance relative to autosomal genes, which are present in two active copies per cell. Here we have dissected X-chromosome upregulation into the kinetics of transcription, inferred from allele-specific single-cell RNA sequencing data from somatic and embryonic mouse cells. We confirmed increased X-chromosome expression levels in female and male cells and found that the X chromosome achieved upregulation by elevated burst frequencies. By monitoring transcriptional kinetics in differentiating female mouse embryonic stem cells, we found that increased burst frequency was established on the active X chromosome when X inactivation took place on the other allele. Thus, our study provides mechanistic insights into X-chromosome upregulation.

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Fig. 1: Investigating X-chromosome upregulation by transcriptional kinetics.
Fig. 2: Classification of cells based on X inactivation status.
Fig. 3: Elevated expression levels of X-linked genes.
Fig. 4: Transcriptional kinetics of X-chromosome upregulation.
Fig. 5: X-chromosome burst frequencies during differentiation of ESCs.

Data availability

The sequencing data are available at the European Nucleotide Archive (E-MTAB-7098), ArrayExpress (E-MTAB-6385) and GEO (GSE74155).

Code availability

The computational code used for calculations and plotting of data is available at https://sourceforge.net/projects/kinetics-of-x-upregulation.

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Acknowledgements

This study was made possible by grants to B.R. from the Ragnar Söderberg Foundation, the Swedish Research Council (2017-01723) and Åke Wiberg’s Foundation; and grants to R.S. from the European Research Council (648842) and the Swedish Research Council (2017-01062). The authors thank D. Camsund for providing insightful comments to the manuscript.

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B.R. conceived and supervised the study. A.J.M.L. and B.R. analyzed the data and wrote the manuscript. A.J.M.L., C.C., R.S. and B.R. participated in interpreting the data and editing the manuscript.

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Correspondence to Björn Reinius.

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The authors declare no competing interests.

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Peer review information Anke Sparmann was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Supplementary Figs. 1–9 and Supplementary Tables 1 and 2.

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Larsson, A.J.M., Coucoravas, C., Sandberg, R. et al. X-chromosome upregulation is driven by increased burst frequency. Nat Struct Mol Biol 26, 963–969 (2019). https://doi.org/10.1038/s41594-019-0306-y

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