title: High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation.
abstract: The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes. During XCI, Xist coats the future inactive X chromosome (Xi) and recruits Polycomb repressive complex 2 (PRC2) to the X-inactivation centre (Xic). How Xist spreads silencing on a 150-megabases scale is unclear. Here we generate high-resolution maps of Xist binding on the X chromosome across a developmental time course using CHART-seq. In female cells undergoing XCI de novo, Xist follows a two-step mechanism, initially targeting gene-rich islands before spreading to intervening gene-poor domains. Xist is depleted from genes that escape XCI but may concentrate near escapee boundaries. Xist binding is linearly proportional to PRC2 density and H3 lysine 27 trimethylation (H3K27me3), indicating co-migration of Xist and PRC2. Interestingly, when Xist is acutely stripped off from the Xi in post-XCI cells, Xist recovers quickly within both gene-rich and gene-poor domains on a timescale of hours instead of days, indicating a previously primed Xi chromatin state. We conclude that Xist spreading takes distinct stage-specific forms. During initial establishment, Xist follows a two-step mechanism, but during maintenance, Xist spreads rapidly to both gene-rich and gene-poor regions.
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114.|Dept. of Molecular Biophysics and Biochemistry, and Chemical Biology Institute, Yale University, West Haven, CT, 06516.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Simon
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114.|Howard Hughes Medical Institute.
authors.forename: Stefan F
authors.initials: SF
authors.lastname: Pinter
authors.affiliation: Dept. of Molecular Biophysics and Biochemistry, and Chemical Biology Institute, Yale University, West Haven, CT, 06516.
authors.forename: Rui
authors.initials: R
authors.lastname: Fang
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114.|Howard Hughes Medical Institute.
authors.forename: Kavitha
authors.initials: K
authors.lastname: Sarma
authors.affiliation: Dept. of Molecular Biophysics and Biochemistry, and Chemical Biology Institute, Yale University, West Haven, CT, 06516.
authors.forename: Michael
authors.initials: M
authors.lastname: Rutenberg-Schoenberg
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114.
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Bowman
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114.|Howard Hughes Medical Institute.
authors.forename: Barry A
authors.initials: BA
authors.lastname: Kesner
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114.|Howard Hughes Medical Institute.
authors.forename: Verena K
authors.initials: VK
authors.lastname: Maier
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Kingston
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114.|Howard Hughes Medical Institute.
authors.forename: Jeannie T
authors.initials: JT
authors.lastname: Lee
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000378:metabolism; D005260:Female; D005347:Fibroblasts / Q000378:metabolism; D020868:Gene Silencing; D005796:Genes; D011495:Histone-Lysine N-Methyltransferase / Q000378:metabolism; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D008239:Lysine / Q000378:metabolism; D008745:Methylation; D051379:Mice; D008957:Models, Genetic; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism*; D014960:X Chromosome / Q000235:genetics / Q000378:metabolism*; D049951:X Chromosome Inactivation / Q000235:genetics
chemical_list: D002843:Chromatin; D006657:Histones; D062085:RNA, Long Noncoding; C077885:XIST non-coding RNA; D011495:Histone-Lysine N-Methyltransferase; D008239:Lysine