Derivation of a minimal functional XIST by combining human and mouse interaction domains

Abstract

XIST is a 17-19 kb long non-coding RNA critical for X-chromosome inactivation. Tandem repeats within the RNA serve as functional domains involved in the cis-limited recruitment of heterochromatic changes and silencing. To explore the sufficiency of these domains while generating a functional miniXIST for targeted silencing approaches, we tested inducible constructs integrated into 8p in a male cell line. Previous results suggested silencing could be accomplished with a transgene comprised of the repeat A which is highly conserved and critical for silencing; the repeat F which overlaps regulatory elements and the repeat E region which contributes to XIST localization by binding proteins such as CIZ1. As PRC1 is recruited through HNRNPK binding of repeats B - C - D we included a second miniXIST comprising AFE with the mouse PID, a 600-nucleotide region of repeat B and C. Silencing of nearby genes was possible with and without PID, however, silencing more distally required the addition of PID. The recruitment of heterochromatic marks, evaluated by IF combined with RNA FISH, revealed that the AFE domains were sufficient only for the recruitment of CIZ1. However, miniXIST transgene recruited all marks, albeit not to full XIST levels. The ability of the PID domain to facilitate silencing and heterochromatic marks recruitment was unexpected, and inhibition of PRC1 suggested that many of these are PRC1-independent. These results suggest that the addition of this small region allowed the partial recruitment of all the changes induced by a full XIST, demonstrating the feasibility of finding a minimal functional XIST.