XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells

Abstract

X-chromosome inactivation (XCI), the dosage compensation process that equalizes X-linked gene expression between sexes, has mostly been studied in the mouse, where the central role for the non-coding RNA Xist in the initiation and spreading of the process was demonstrated. Although Xist is conserved in humans [1], very little is known concerning its regulation and function in this species. Several lines of evidence moreover suggest that different strategies have been adopted in the human to control XCI as compared to the mouse. In particular, in human pre-implantation development, XIST RNA coats the X chromosome(s) in both male and female embryos without inducing X-chromosome silencing [2]. This indicates that XIST expression and X-inactivation can be uncoupled during human embryogenesis and that other elements likely participate to the control of X chromosome activity in humans.XCI is established early during embryonic development, and embryonic stem cells can be used to decipher the kinetics and the molecular actors of the process. Human female embryonic stem cells (hESC) can be found in different configurations regarding XIST expression: most female hESC have already undergone XCI but tend to spontaneously lose XIST expression [3]. In the course of an RNA-seq analysis of female hESC, we identified an extended and un-annotated transcribed region producing a long unspliced, likely non-coding nuclear RNA. RNA-FISH analysis reveals that this transcript is expressed from, and coats the active X chromosome. We called this transcript XACT, for X-active coating transcript. In female hESC in which XIST is repressed, XACT is expressed from and coats both Xs, and this correlates with significant reactivation of the inactive X chromosome. Expression of XACT appears to be specific for pluripotent cells as its expression decreases during differentiation. Finally, we provide evidence that XACT is not conserved in the mouse.In conclusion, we have identified XACT as the first long ncRNA that coats the active X chromosome in human. Given its expression profile and lack of conservation, it is tempting to speculate that XACT is involved in the peculiar control of XCI initiation in human.

Ribosome-omics of the human ribosome

“…Comparing the data across the tissues represented in the Body Map (Supplemental Table S6), the expression of RPS4X is consistently greater in female than in male tissues. Surprisingly, a data set from Xist negative cells (Vallot et al 2013) showed no increase in the expression either of RPS4X, or of RPL36A and RPL39, both of which are on the X chromosome.…”

Species-specific differences in X chromosome inactivation in mammals

“…Recently, another X-linked lncRNA, termed XACT, has been identified in humans, which appears to be transcribed from a more than 250 kb genomic region as a polyadenylated transcript (Vallot et al 2013). Unlike Xist/XIST and Rsx, XACT RNA is unique in that it is expressed only from an active X chromosome and coats it in cis in both XX and XY human ES cells.…”

The pluripotent state in mouse and human

“…The process of X-inactivation varies between human and mouse (Okamoto et al, 2011;van den Berg et al, 2009). X-inactivation is not coupled to the expression of the X inactive specific transcript (XIST) in the human, as it is in the mouse, and much more of the TFCP2L1 TBX3 TDGF1 IFITM1 IFITM2 KRT19 TCF7L DNMT3B KLF114 ZFP42 GDF3 POU5F1 SOX2 ANOG Late_blastocyst_2_cell_1 Late_blastocyst_2_cell_3 Late_blastocyst_3_cell_1 Late_blastocyst_3_cell_4 Late_blastocyst_3_cell_5 Late_blastocyst_2_cell_2 hESC_P0_cell_1 hESC_P0_cell_7 hESC_P0_cell_5 hESC_P0_cell_4 hESC_P0_cell_2 hESC_P10_cell_4 hESC_P10_cell_15 hESC_P10_cell_6 hESC_P10_cell_18 hESC_P10_cell_21 hESC_P0_cell_8 hESC_P0_cell_3 hESC_P0_cell_6 hESC_P10_cell_11 hESC_P10_cell_26 hESC_P10_cell_24 hESC_P10_cell_9 hESC_P10_cell_5 hESC_P10_cell_22 hESC_P10_cell_7 hESC_P10_cell_20 hESC_P10_cell_23 hESC_P10_cell_3 hESC_P10_cell_2 hESC_P10_cell_25 hESC_P10_cell_10 hESC_P10_cell_14 hESC_P10_cell_17 hESC_P10_cell_8 hESC_P10_cell_1 hESC_P10_cell_12 hESC_P10_cell_13 hESC_P10_cell_16 …”