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During mammalian X-chromosome inactivation, the Xist long noncoding RNA coats the future inactive X chromosome and recruits polycomb repressive complex 2 to a nucleation site, but how Xist spreads silencing across the entire X chromosome is unclear; here high-resolution maps of Xist binding sites across the X chromosome are generated and show that Xist does not spread across the inactive X chromosome uniformly but in two steps, initially targeting gene-rich islands before later spreading to intervening gene-poor domains. Mapping Xist long noncoding RNA During mammalian X-chromosome inactivation (XCI), the Xist long noncoding RNA coats the future inactive X (Xi) and recruits polycomb repressive complex 2 (PRC2) to a nucleation site, but how Xist spreads silencing across the entire X chromosome is unclear. Here, Jeannie Lee and colleagues generate high-resolution maps of Xist binding sites across the X chromosome using a technique termed CHART-seq. By following four early developmental stages in female mouse cells undergoing XCI, they show that Xist does not spread across the Xi uniformly but in two steps -- initially targeting gene-rich islands and later spreading to intervening gene-poor domains. 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.sup.1,2,3. During XCI, Xist coats the future inactive X chromosome (Xi).sup.4 and recruits Polycomb repressive complex 2 (PRC2) to the X-inactivation centre (Xic).sup.5. 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., Author(s): Matthew D. Simon [sup.1] [sup.2] , Stefan F. Pinter [sup.1] [sup.3] , Rui Fang [sup.2] , Kavitha Sarma [sup.1] [sup.3] , Michael Rutenberg-Schoenberg [sup.2] , Sarah K. Bowman [sup.1] [...]

Research has been conducted on histone methylation. The patterns of this methylation studied during human cell cycle progression are discussed and the results indicate that histone H4 methyltransferase activity is cell cycle-regulated.

A novel histone H3 methyltransferase, Set 9, that facilitates transcription by precluding histone tail modifications necessary for heterochromatin formation is discussed. Set 9 was isolated from human cells. Study results suggest that the methylation of histone tails can have distinct effects on transcription, depending on its chromosomal location, combination of postranslational modificatoin, and the enzyme or protein complex involved.

The crystal structure of a ternary complex of the enzyme Pr-Set7 that methylates Lys 20 of histone H4 [H4-K20] is presented. The results demonstrate that the enzyme is exclusively a mono-methylase and is therefore responsible for a signaling role quite distinct from that established by other enzymes that target this histone residue.

H3-K9 and H4-K20 trimehtylation is enriched at pericentric heterochromatin in mammals. The research data indicates a function for H4-K20 trimethylation in gene silencing and further suggest H3-K9 and H4-K20 trimethylation as important components of a repressive pathway that can index pericentric heterochromatin.

The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes1-3. During XCI, Xist coats the future inactive X (Xi)4 and recruits Polycomb Repressive Complex 2 (PRC2) to the X-inactivation center (Xic)5. How Xist spreads silencing on a 150 Mb 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), suggesting co-migration of Xist and PRC2. Interestingly, when the Xi is acutely stripped off Xist in post-XCI cells, Xist recovers quickly within both gene-rich and -poor domains on a time-scale of hours instead of days, suggesting 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 -poor regions.

Cellular responses to environmental stimuli are typically thought to be governed by genetically encoded programs. We demonstrate that melanoma cells can form and maintain cellular memories during the acquisition of therapy resistance that exhibit characteristics of cellular learning and are dependent on the transcription factor AP-1. We show that cells exposed to a low dose of therapy adapt to become resistant to a high dose, demonstrating that resistance was not purely selective. The application of therapy itself results in the encoding of transient gene expression into cellular memory and that this encoding occurs for both transiently induced and probabilistically arising expression. Chromatin accessibility showed concomitant persistence. A two-color AP-1 reporter system showed that these memories are encoded in cis , constituting an example of activating cis epigenetics. Our findings establish the formation and maintenance of cellular memories as a critical aspect of gene regulation during the development of therapy resistance., Competing Interests: Declaration of interests A.R. receives royalties related to Stellaris RNA FISH probes. A.R. serves on the scientific advisory board of Spatial Genomics. All other authors declare no competing interests.