PT  - JOURNAL ARTICLE
AU  - Rutger A.F. Gjaltema
AU  - Till Schwämmle
AU  - Pauline Kautz
AU  - Michael Robson
AU  - Robert Schöpflin
AU  - Liat Ravid Lustig
AU  - Lennart Brandenburg
AU  - Ilona Dunkel
AU  - Carolina Vechiatto
AU  - Evgenia Ntini
AU  - Verena Mutzel
AU  - Vera Schmiedel
AU  - Annalisa Marsico
AU  - Stefan Mundlos
AU  - Edda G. Schulz
TI  - Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at the <em>Xist</em> locus
AID  - 10.1101/2021.03.29.437476
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.03.29.437476
4099  - http://biorxiv.org/content/early/2021/03/29/2021.03.29.437476.short
4100  - http://biorxiv.org/content/early/2021/03/29/2021.03.29.437476.full
AB  - Developmental genes such as Xist, the master regulator of X-chromosome inactivation (XCI), are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatio-temporal expression patterns. Xist integrates information on X-chromosomal dosage and developmental stage to trigger XCI at the primed pluripotent state in females only. Through a pooled CRISPR interference screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist during the onset of random XCI. By quantifying how enhancer activity is modulated by X-dosage and differentiation, we find that X-dosage controls the promoter-proximal region in a binary switch-like manner. By contrast, differentiation cues activate a series of distal elements and bring them into closer spatial proximity of the Xist promoter. The strongest distal element is part of an enhancer cluster ∼200 kb upstream of the Xist gene which is associated with a previously unannotated Xist-enhancing regulatory transcript, we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. Our study is the first step to disentangle how multiple, functionally distinct regulatory regions interact to generate complex expression patterns in mammals.Competing Interest StatementThe authors have declared no competing interest.