X-chromosome-inactivation

X chromosome inactivation

Many animal species employ sex chromosomes to determine sex and start gender specific gene expression programs. In mammals female cells have two X chromosomes, whereas male cells carry an X and Y chromosome. The Y is a small chromosome with not more than 70 coding genes, in contrast to the X chromosome harbours more than 1000 genes. As a consequence, expression of X linked genes will potentially be two-fold higher in female compared to male cells. Therefore, intricate mechanisms are established to equalize the dosage of X-linked genes between male and female cells. In mammals this involves upregulation of dosage sensitive X-linked genes, and inactivation of one X chromosome in every female somatic cell. X chromosome inactivation (XCI) is regulated by the X-linked X inactivation centre (Xic). This Xic covers a region of ~800kb, and harbors a plethora of long non-coding RNA (lncRNA) genes involved in XCI. Located within the Xic, Xist plays a crucial role in XCI. Xist lncRNA accumulates in cis, thereby recruiting silencing complexes that render the X inactive.  

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One key intriguing question in XCI is how a cell determines the number of X chromosomes and initiates XCI. Our work involving studies of tetraploid, triploid and diploid mouse ES cells revealed that initiation of XCI is a stochastic process, and indicated the presence of X-linked activators of XCI. The activity of these XCI-activators is counterbalanced by autosomally encoded XCI-inhibitors, many of which are pluripotency factors involved in repression of Xist, providing a powerful link between loss of pluripotency and XCI initiation. We identified X-encoded RNF12 as an activator of XCI. Rnf12 is located just 500 kb telomeric of Xist and encodes an E3 ubiquitin ligase, which catalyzes dose-dependent breakdown of the pluripotency factor REX1 by targeting REX1 for proteasomal degradation. When present at an effective concentration, REX1 inhibits Xist transcription, thereby blocking initiation of XCI. Breakdown of REX1 is more prominent in differentiating female cells, which still have two active copies of Rnf12, resulting in female specific initiation of XCI. The REX1-RNF12 axis provides a strong link between female specific initiation of XCI and loss of pluripotency, but our studies and studies of others also indicate the presence of more XCI-activators. Our present research is aimed at identifying novel XCI-activators, elucidate the mechanisms by which they direct female exclusive XCI, and translate these findings to human.  

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Relevant publications:

Loda A, Brandsma JH, Vassilev I, Servant N, Loos F, Amirnasr A, Splinter E, Barillot E, Poot RA, Heard E, Gribnau J. 2017. Genetic and epigenetic features direct differential efficiency of Xist-mediated silencing at X-chromosomal and autosomal locations. Nat Commun. 81:690-712.

Loos F, Maduro C, Loda A, Lehmann J, Kremers GJ, Ten Berge D, Grootegoed JA, Gribnau J. (2016) Xist and Tsix Transcription Dynamics Is Regulated by the X-to-Autosome Ratio and Semistable Transcriptional States. Mol Cell Biol. 36:2656-2667.

Barakat TS, Loos F, van Staveren S, Myronova E, Ghazvini M, Grootegoed JA, Gribnau J. 2014. The trans-activator RNF12 and cis-acting elements effectuate X chromosome inactivation independent of X-pairing. Mol Cell 53: 965-978.

Gontan C, Achame EM, Demmers J, Barakat TS, Rentmeester E, van IW, Grootegoed JA, Gribnau J. 2012. RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation. Nature 485: 386-390.

Barakat TS, Gunhanlar N, Pardo CG, Achame EM, Ghazvini M, Boers R, Kenter A, Rentmeester E, Grootegoed JA, Gribnau J. 2011. RNF12 activates Xist and is essential for X chromosome inactivation. PLoS Genet 7: e1002001.

Jonkers I, Barakat TS, Achame EM, Monkhorst K, Kenter A, Rentmeester E, Grosveld F, Grootegoed JA, Gribnau J. 2009. RNF12 is an X-Encoded dose-dependent activator of X chromosome inactivation. Cell 139: 999-1011.

Monkhorst K, Jonkers I, Rentmeester E, Grosveld F, Gribnau J. 2008. X inactivation counting and choice is a stochastic process: evidence for involvement of an X-linked activator. Cell 132: 410-421. 

Groupleader: Joost Gribnau

Group members: Cristina Gontan, Hegias Mira, Sarra Merzouk, Teresa Robert, Eveline Rentmeester, Joana Carvalho, Jeffrey Boeren