Allele-specific distribution of RNA polymerase II on female X chromosomes

Abstract

While the distribution of RNA polymerase II (PolII) in a variety of complex genomes is correlated with gene expression, the presence of PolII at a gene does not necessarily indicate active expression. Various patterns of PolII binding have been described genome wide; however, whether or not PolII binds at transcriptionally inactive sites remains uncertain. The two X chromosomes in female cells in mammals present an opportunity to examine each of the two alleles of a given locus in both active and inactive states, depending on which X chromosome is silenced by X chromosome inactivation. Here, we investigated PolII occupancy and expression of the associated genes across the active (Xa) and inactive (Xi) X chromosomes in human female cells to elucidate the relationship of gene expression and PolII binding. We find that, while PolII in the pseudoautosomal region occupies both chromosomes at similar levels, it is significantly biased toward the Xa throughout the rest of the chromosome. The general paucity of PolII on the Xi notwithstanding, detectable (albeit significantly reduced) binding can be observed, especially on the evolutionarily younger short arm of the X. PolII levels at genes that escape inactivation correlate with the levels of their expression; however, additional PolII sites can be found at apparently silenced regions, suggesting the possibility of a subset of genes on the Xi that are poised for expression. Consistent with this hypothesis, we show that a high proportion of genes associated with PolII-accessible sites, while silenced in GM12878, are expressed in other female cell lines.

The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer

“…4B). A gene-based analysis detected several previously described X-linked escapees (including DHRSX, TRAPPC2, CD99, or KDM6A) (Carrel and Willard 2005;Kucera et al 2011;Cotton et al 2013), confirming the efficiency of this approach. We used known escapees and genes subject to XCI (Carrel and Willard 2005;Cotton et al 2013) to define a threshold to consider that a given X-linked gene is expressed from inactive and active alleles.…”

“…Based on microscopy, XIST RNA coating was often found to be highly dispersed, with variable H3K27me3 enrichment, and a marked absence of an RNA Pol II-depleted nuclear compartment. Based on ChIP-seq, abnormal presence of both RNA Pol II and H3K4me3 was observed at "cancer-specific" escapees, reminiscent of the chromatin organization of the normally escapees from XCI in noncancer cells (Kucera et al 2011;Cotton et al 2013). Importantly, however, virtually all informative "cancer-specific" escapees displayed simultaneously repressive (H3K27me3) and active (H3K4me3, RNA Pol II recruitment) chromatin marks (see Supplemental Fig.…”

“…In somatic cells, the majority of X-linked genes are stably repressed on the Xi, with spontaneous reactivation of single genes being observed at a frequency of <10 −8 , presumably due to synergistic epigenetic mechanisms (Csankovszki et al 2001). However, a subset of genes can escape XCI in somatic cells (Carrel and Willard 2005;Kucera et al 2011;Cotton et al 2013). In cancer, aberrant escape from XCI has previously been speculated to occur (Pageau et al 2007;Agrelo and Wutz 2010;Carone and Lawrence 2013;Yildirim et al 2013).…”

Random replication of the inactive X chromosome

“…S1). These cell lines show severe XCI skewing, in which the same copy of the X chromosome is inactive in >90% of the cells in a culture (McDaniell et al 2010;Kucera et al 2011). For both daughter cell lines, the paternally derived X chromosome was the clonally inactive copy (McDaniell et al 2010;Kucera et al 2011).…”

Fifty years of X-inactivation research

“…He reported new work from his group concerning the allele-specific distribution of RNA polymerase II (Pol II) across the Xi and the Xa in a human ENCODE cell line showing skewed XCI (Kucera et al, 2011). They found that Pol II binding is significantly reduced over the Xi, with the exception of the pseudo-autosomal region and escape genes, which led them to define several gene classes; in particular, monoallelically expressed genes with or without Pol II at their promoters, suggesting that some silenced genes might be poised for expression in specific tissues or in other individuals.…”