X chromosomes alternate between two states prior to random X-inactivation.
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ABSTRACT:
SUBMITTER: Mlynarczyk-Evans S
PROVIDER: S-EPMC1457015 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundCondensation differences along the lengths of homologous, mitotic metaphase chromosomes are well known. This study reports molecular cytogenetic data showing quantifiable localized differences in condensation between homologs that are related to differences in accessibility (DA) of associated DNA probe targets. Reproducible DA was observed for ~10% of locus-specific, short (1.5-5 kb) single copy DNA probes used in fluorescence in situ hybridization.ResultsFourteen probes (from chromosomes 1, 5, 9, 11, 15, 17, 22) targeting genic and intergenic regions were developed and hybridized to cells from 10 individuals with cytogenetically-distinguishable homologs. Differences in hybridization between homologs were non-random for 8 genomic regions (RGS7, CACNA1B, GABRA5, SNRPN, HERC2, PMP22:IVS3, ADORA2B:IVS1, ACR) and were not unique to known imprinted domains or specific chromosomes. DNA probes within CCNB1, C9orf66, ADORA2B:Promoter-Ex1, PMP22:IVS4-Ex 5, and intergenic region 1p36.3 showed no DA (equivalent accessibility), while OPCML showed unbiased DA. To pinpoint probe locations, we performed 3D-structured illumination microscopy (3D-SIM). This showed that genomic regions with DA had 3.3-fold greater volumetric, integrated probe intensities and broad distributions of probe depths along axial and lateral axes of the 2 homologs, compared to a low copy probe target (NOMO1) with equivalent accessibility. Genomic regions with equivalent accessibility were also enriched for epigenetic marks of open interphase chromatin (DNase I HS, H3K27Ac, H3K4me1) to a greater extent than regions with DA.ConclusionsThis study provides evidence that DA is non-random and reproducible; it is locus specific, but not unique to known imprinted regions or specific chromosomes. Non-random DA was also shown to be heritable within a 2 generation family. DNA probe volume and depth measurements of hybridized metaphase chromosomes further show locus-specific chromatin accessibility differences by super-resolution 3D-SIM. Based on these data and the analysis of interphase epigenetic marks of genomic intervals with DA, we conclude that there are localized differences in compaction of homologs during mitotic metaphase and that these differences may arise during or preceding metaphase chromosome compaction. Our results suggest new directions for locus-specific structural analysis of metaphase chromosomes, motivated by the potential relationship of these findings to underlying epigenetic changes established during interphase.
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Project description:Imprinted X-inactivation silences genes exclusively on the paternally-inherited X-chromosome and is a paradigm of transgenerational epigenetic inheritance in mammals. Here, we test the role of maternal vs. zygotic Polycomb repressive complex 2 (PRC2) protein EED in orchestrating imprinted X-inactivation in mouse embryos. In maternal-null (Eedm-/-) but not zygotic-null (Eed-/-) early embryos, the maternal X-chromosome ectopically induced Xist and underwent inactivation. Eedm-/- females subsequently stochastically silenced Xist from one of the two X-chromosomes and displayed random X-inactivation. This effect was exacerbated in embryos lacking both maternal and zygotic EED (Eedmz-/-), suggesting that zygotic EED can also contribute to the onset of imprinted X-inactivation. Xist expression dynamics in Eedm-/- embryos resemble that of early human embryos, which lack oocyte-derived maternal PRC2 and only undergo random X-inactivation. Thus, expression of PRC2 in the oocyte and transmission of the gene products to the embryo may dictate the occurrence of imprinted X-inactivation in mammals.
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Project description:BACKGROUND:Pairwise and network meta-analyses using fixed effect and random effects models are commonly applied to synthesize evidence from randomized controlled trials. The models differ in their assumptions and the interpretation of the results. The model choice depends on the objective of the analysis and knowledge of the included studies. Fixed effect models are often used because there are too few studies with which to estimate the between-study SD from the data alone. OBJECTIVES:The aim of this study was to propose a framework for eliciting an informative prior distribution for the between-study SD in a Bayesian random effects meta-analysis model to genuinely represent heterogeneity when data are sparse. METHODS:We developed an elicitation method using external information, such as empirical evidence and expert beliefs, on the "range" of treatment effects to infer the prior distribution for the between-study SD. We also developed the method to be implemented in R. RESULTS:The 3-stage elicitation approach allows uncertainty to be represented by a genuine prior distribution to avoid making misleading inferences. It is flexible to what judgments an expert can provide and is applicable to all types of outcome measures for which a treatment effect can be constructed on an additive scale. CONCLUSIONS:The choice between using a fixed effect or random effects meta-analysis model depends on the inferences required and not on the number of available studies. Our elicitation framework captures external evidence about heterogeneity and overcomes the assumption that studies are estimating the same treatment effect, thereby improving the quality of inferences in decision making.
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Project description:Genome rearrangement often produces chromosomes with two centromeres (dicentrics) that are inherently unstable because of bridge formation and breakage during cell division. However, mammalian dicentrics, and particularly those in humans, can be quite stable, usually because one centromere is functionally silenced. Molecular mechanisms of centromere inactivation are poorly understood since there are few systems to experimentally create dicentric human chromosomes. Here, we describe a human cell culture model that enriches for de novo dicentrics. We demonstrate that transient disruption of human telomere structure non-randomly produces dicentric fusions involving acrocentric chromosomes. The induced dicentrics vary in structure near fusion breakpoints and like naturally-occurring dicentrics, exhibit various inter-centromeric distances. Many functional dicentrics persist for months after formation. Even those with distantly spaced centromeres remain functionally dicentric for 20 cell generations. Other dicentrics within the population reflect centromere inactivation. In some cases, centromere inactivation occurs by an apparently epigenetic mechanism. In other dicentrics, the size of the alpha-satellite DNA array associated with CENP-A is reduced compared to the same array before dicentric formation. Extra-chromosomal fragments that contained CENP-A often appear in the same cells as dicentrics. Some of these fragments are derived from the same alpha-satellite DNA array as inactivated centromeres. Our results indicate that dicentric human chromosomes undergo alternative fates after formation. Many retain two active centromeres and are stable through multiple cell divisions. Others undergo centromere inactivation. This event occurs within a broad temporal window and can involve deletion of chromatin that marks the locus as a site for CENP-A maintenance/replenishment.
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Project description:Recent studies have demonstrated the benefits of water-dielectric interfaces in electrostatic energy harvesting. Most efforts have been focused on extracting the kinetic energy from the motions of water drops on hydrophobic surfaces, and thus, the resulting schemes inherently prefer cases where the water drops move at a high speed, or vibrate at a high frequency. Here we report a method for directly harvesting ambient mechanical energy as electric potential energy through water droplets by making alternate contacts with CYTOP and PTFE thin films. Because CYTOP and PTFE acquire significantly different surface charge densities during contact with water, such a difference can be utilized to effectively generate electricity. We demonstrate this concept using prototype devices fabricated on silicon substrates with a simple procedure. In the experiments conducted, a water drop of 400??L alone could generate a peak open-circuit voltage of 42?V under a 0.25?Hz vibration. Under a 2.5?Hz vibration, the peak open-circuit voltage reached 115?V under an external bias of 8?V. The demonstrated efficiency is orders of magnitude higher than those of existing devices of similar dimensions.
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Project description:BACKGROUND:X chromosome inactivation (XCI) is an indispensable process in the development of human female embryos. Reportedly, XCI occurs when a blastocyst contains 10-12 embryonic progenitor cells. To date, it remains unclear whether XCI ratios are normally preserved in Klinefelter syndrome (KS) patients with 47,XXY karyotype. METHODS:We examined XCI ratios in 18 KS patients through DNA methylation analysis for the polymorphic trinucleotide locus in the AR gene. The results of the KS patients were compared to previous data from healthy young women. RESULTS:XCI ratios in KS patients followed a normal distribution. Skewed XCI was observed in two patients, one of whom exhibited extremely skewed XCI. The frequencies of skewed and extremely skewed XCI in the KS cohort were comparable to those in healthy women. CONCLUSION:This study confirmed the rarity of skewed XCI in KS patients. These results indicate that the presence of a supernumerary X chromosome during the cleavage and early blastocyst stages does not affect the developmental tempo of embryos. Our data deserve further validation.
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