Extended Data Fig. 10: Xist O-MAP-Seq enriches nascent transcripts of XCI-escape genes.

a, Enrichment of the Xist gene itself. Note different scales for input RNA and O-MAP-Seq tracks. The lack of intronic reads suggests that O-MAP-Seq has predominantly targeted and captured the mature Xist transcript. The absence of reads mapping to the antisense noncoding RNA TsiX, a lncRNA that is monoallelically expressed from the Xa (gray), confirms that O-MAP-Seq is precisely labeling the Xi. b, Enriched XCI-escape genes appear to be nascent transcripts. In all cases, read densities for both Input RNA (gray) and O-MAP-Seq (red) are shown, using matched scales. Note prominent intronic read density for all XCI-escape genes (Shroom4, Pbdc1, Magee1, Mid1, Erdr1). Transcript structures denoting the most prominent isoforms are displayed; other nearby genes not known to escape XCI are denoted in gray. c, Xist O-MAP-Seq does not appear to preferentially capture nascent transcripts of non-XCI-escape genes. Two examples (Tspan6 and Rps4x) are shown, neither of which was enriched by Xist O-MAP-Seq. Note the absence of prominent intronic read density, suggesting that the intronic signatures observed in (b) are not general artifacts of the O-MAP-Seq pipeline.