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. 2020 Dec 2;11:6163. doi: 10.1038/s41467-020-20040-3

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a m⁶A on the human mature XIST RNA. K562 RBM15 eCLIP was normalized against input in 100-nt windows³⁶ and plotted in two scales to highlight the differences in binding the 5’ end and other regions. HEK293 cell m⁶A iCLIP track was from ref. ⁴⁷. m⁶A motif density was calculated in 300-nt windows and 50-nt steps. b Gene structure for the alleles. WT and ΔSX (~900 bp deletion in Xist 5’ end) alleles were under the control of tetracycline-inducible promoter. A-repeat relocation alleles KI5, KI14, and KI17 were derived from ΔSX by A-repeat insertion in the indicated locations. c MeRIP-seq analysis pipeline. Global analysis of m⁶A changes was performed on data mapped to the mm10 genome, while targeted analysis was performed on the mature mouse Xist transcript. d m⁶A sites are changed after relocating the A-repeat domain. The mouse Xist RNA PARIS model is the same as in Fig. 3a. m⁶A domains are labeled under the genome browser tracks. Y-axis is the same in each track. All data including the A-repeat relocation alleles were mapped to the same wild-type Xist mature RNA. e–j Zoom-in view of all m⁶A domains. Location of the original A-repeat is indicated in e. The A-repeat knockin locations are indicated in f, i, j. Y-axis scales are the same for all tracks. k Quantification of m⁶A changes relative to wild type in log scale in pre-defined m⁶A domains shown in d. One replicate was available for each sequencing library. l A mechanistic model of RNA structures in guiding m⁶A modifications. The A-repeat domain recruits the m⁶A methylase complex to modify sequences physically close to the domain. The residual modification on Xist after A-repeat deletion was due to its intrinsic ability to recruit m⁶A methylase complex. Relocation of the A-repeat to the inside of the large domains (KI5 and KI14) induces local modifications (m6AKI5 and m6AKI14). Relocation of the A-repeat to the end of the transcript (KI17) induces modification in physical proximity (m6AD1, m6AD2, m6AD3, and m6AD4). Source data are provided as a Source data file.