XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [RNA-seq]

XIST long non-coding RNA is responsible for X chromosome inactivation (XCI) in placental mammals, yet it accumulates on both X chromosomes in human female pre-implantation embryos without triggering X chromosome silencing. The long non-coding RNA XACT co-accumulates with XIST on active Xs and may antagonize XIST function. Here we used human ES cells in a naïve state of pluripotency to assess the function of XIST and XACT in shaping the X chromosome chromatin and transcriptional landscapes during pre-implantation development. We show that XIST triggers the deposition of polycomb-mediated repressive histone modifications and attenuates transcription of most X-linked genes in a SPEN-dependent manner, while XACT deficiency does not significantly affect XIST activity or X-linked gene expression. Our study demonstrates that XIST is functional prior to XCI, confirms the existence of a transient process of X chromosome dosage compensation, and reveals that X chromosome inactivation and dampening rely on the same set of factors. Overall design: RNA-seq on 3 independent clones of XIST CRISPRi naïve hESCs treated with doxycyclin. Untreated clones were used as controls. Also RNA-seq on 3 replicates of 1 XIST KO clone and WT. RNA-seq on 3 independent clones of XACT KO (naïve) and WT (primed). RNA-seq after siRNA knockdown of SPEN protein using two different mixes of siRNAs.