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X-chromosome upregulation operates on a gene-by-gene basis at RNA and protein levels

By: Ryan N. Allsop, Jeffrey Boeren, Beatrice F. Tan, Sarra Merzouk, Suresh Poovanthingal, Wilfred F. J. van IJcken, Jeroen A. A. Demmers, Hegias Mira Bontenbal, Cristina Gontan, Joost Gribnau & Vincent Pasque

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Researchers at KU Leuven and Erasmus MC uncovered how mammalian cells maintain balance when one copy of a gene is missing. The study demonstrates that the genome can increase the activity of the remaining functional copy, a process known as gene-specific upregulation. This mechanism is most strongly developed on the X chromosome, but evidence shows that autosomes also possess some capacity to compensate for gene loss. These findings reshape the scientific understanding of sex chromosomes and dosage compensation.


This fundamental genetic mechanism — the ability to sense and respond to deletions — provides insight into how cells preserve stability. A clearer understanding of how compensation works could support the development of improved strategies for diseases in which patients retain one healthy allele.

Image 1. Diagram illustrating gene-specific X-chromosome upregulation. The left panel shows two active X chromosomes. The right panel shows a targeted deletion on one active X chromosome and increased expression from the corresponding region of the intact X chromosome.
Image 1. Diagram illustrating gene-specific X-chromosome upregulation. The left panel shows two active X chromosomes. The right panel shows a targeted deletion on one active X chromosome and increased expression from the corresponding region of the intact X chromosome.

The research team processed and analyzed more than one billion sequencing reads to uncover these genome-wide dynamics.


Image 2. 3D rendering of human X chromosomes highlighting the region affected by deletion and compensatory upregulation, consistent with the study’s findings.
Image 2. 3D rendering of human X chromosomes highlighting the region affected by deletion and compensatory upregulation, consistent with the study’s findings.

Quote from Ryan Allsop

“The VSC enabled us to quickly and efficiently process over one billion of sequencing reads in order to analyze our dataset.”

Further readings


Read the full publication in Nature Communications here

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