Project description:X chromosome inactivation (XCI) is a dosage compensation mechanism that silences the majority of genes on one X chromosome in each female cell. In order to characterize epigenetic changes that accompany this process, we measured DNA methylation levels in both 45,X Turner syndrome patients, who carry a single active X chromosome (Xa) and normal 46,XX females, who carry one Xa and one inactive X (Xi). Methylated DNA was immunoprecipitated and hybridized to tiling oligonucleotide arrays, generating epigenetic profiles of active and inactive X chromosomes. We observed that XCI is accompanied by changes in DNA methylation specifically at CpG islands. While the majority of CpG islands show increased methylation levels on the Xi, XCI results in reduced methylation at ~20% of CpG islands. Both intra- and inter-genic CpG islands are epigenetically modified, with the biggest increase in methylation occuring at the promoters of genes silenced by XCI. In contrast, genes escaping XCI have low levels of promoter methylation, while genes that undergo polymorphic silencing show intermediate increases in methylation proportionate to their frequency of inactivation. Thus promoter methylation and susceptibility to XCI are correlated. We observed a global correlation between CpG island methylation and the evolutionary age of different X chromosome strata, and that genes escaping XCI show increased methylation within gene bodies. We utilized our epigenetic map to predict both novel genes escaping XCI, and to identify sequence features that may contribute to the XCI process. Finally, as our study included Turner syndrome patients with single X chromosomes of both maternal and paternal origin we searched for parent-of-origin specific methylation differences, but found no evidence to support imprinting on the human X chromosome. Our study provides the first epigenetic profile of active and inactive X chromosomes, giving novel insights into the phenomenon of dosage compensation. Methylated DNA was enriched by immunoprecipitation using antibodies against 5-methylcytosine. meDIP and input DNA was labeled with cy5 and cy3 respectively and hybridized to Nimblegen arrays comprising 2.1 million 50-85mers covering human chromosomes 20, 21, 22, X and Y at a mean density of ~1 probe per 100bp. Resulting log2 fluorescence ratios correspond to methylation levels. Seven patients with Turner syndrome (45,X karyotype), and three normal females (46,XX karyotype) were analyzed. Of the Turner syndrome cases, four had a maternally-derived X, and three had a paternally-derived X chromosome.

Project description:X chromosome inactivation (XCI) is a dosage compensation mechanism that silences the majority of genes on one X chromosome in each female cell. In order to characterize epigenetic changes that accompany this process, we measured DNA methylation levels in both 45,X Turner syndrome patients, who carry a single active X chromosome (Xa) and normal 46,XX females, who carry one Xa and one inactive X (Xi). Methylated DNA was immunoprecipitated and hybridized to tiling oligonucleotide arrays, generating epigenetic profiles of active and inactive X chromosomes. We observed that XCI is accompanied by changes in DNA methylation specifically at CpG islands. While the majority of CpG islands show increased methylation levels on the Xi, XCI results in reduced methylation at ~20% of CpG islands. Both intra- and inter-genic CpG islands are epigenetically modified, with the biggest increase in methylation occuring at the promoters of genes silenced by XCI. In contrast, genes escaping XCI have low levels of promoter methylation, while genes that undergo polymorphic silencing show intermediate increases in methylation proportionate to their frequency of inactivation. Thus promoter methylation and susceptibility to XCI are correlated. We observed a global correlation between CpG island methylation and the evolutionary age of different X chromosome strata, and that genes escaping XCI show increased methylation within gene bodies. We utilized our epigenetic map to predict both novel genes escaping XCI, and to identify sequence features that may contribute to the XCI process. Finally, as our study included Turner syndrome patients with single X chromosomes of both maternal and paternal origin we searched for parent-of-origin specific methylation differences, but found no evidence to support imprinting on the human X chromosome. Our study provides the first epigenetic profile of active and inactive X chromosomes, giving novel insights into the phenomenon of dosage compensation.

Project description:BackgroundPromoting active (i.e., conscious, autonomous, informed, and value-congruent) choices may improve the effectiveness of physical activity interventions. This web-based four-arm experimental study investigated the effect of promoting an active versus passive choice regarding physical activity on behavioural and psychological outcomes (e.g., physical activity intentions and behaviours, autonomy, commitment) among physically inactive adults.MethodsDutch inactive adults were randomized into four groups: physical activity guideline only (control group G), guideline & information (GI), guideline & active choice (GA), or guideline & active choice & action planning (GA +). GA and GA + participants were stimulated to make an active choice by weighing advantages and disadvantages of physical activity, considering personal values, and identifying barriers. GA + participants additionally completed action/coping planning exercises. Passive choice groups G and GI did not receive exercises. Self-reported behavioural outcomes were assessed by a questionnaire pre-intervention (T0, n = 564) and at 2-4 weeks follow-up (T2, n = 493). Psychological outcomes were assessed post-intervention (T1, n = 564) and at follow-up. Regression analyses compared the outcomes of groups GI, GA and GA + with group G. We also conducted sensitivity analyses and a process evaluation.ResultsAlthough promoting an active choice process (i.e., interventions GA and GA +) did not improve intention (T1) or physical activity (T2 versus T0), GA + participants reported higher commitment at T1 (β = 0.44;95%CI:0.04;0.84) and more frequently perceived an increase in physical activity between T0 and T2 (β = 2.61;95%CI:1.44;7.72). GA participants also made a more active choice at T1 (β = 0.16;95%CI:0.04;0.27). The GA and GA + intervention did not significantly increase the remaining outcomes. GI participants reported higher intention strength (β = 0.64;95%CI:0.15;1.12), autonomy (β = 0.50;95%CI:0.05;0.95), and commitment (β = 0.39;95%CI:0.04;0.74), and made a more active choice at T1 (β = 0.13;95%CI:0.02;0.24). Interestingly, gender and health condition modified the effect on several outcomes. The GA + intervention was somewhat more effective in women. The process evaluation showed that participants varied in how they perceived the intervention.ConclusionsThere is no convincing evidence of a beneficial effect of an active versus passive choice intervention on physical activity intentions and behaviours among inactive adults. Further research should determine whether and how active choice interventions that are gender-sensitized and consider health conditions can effectively increase physical activity.Trial registrationClinicalTrials.gov: NCT04973813 . Retrospectively registered.

Dataset Information

RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes.

Publications

RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes.

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