Cis-acting modifiers of trinucleotide repeat instability

The dynamic expansion of CAG.CTG repeats in otherwise unrelated genes is responsible for a growing number of late-onset progressive disorders, including Huntington disease, myotonic dystrophy type 1 (DM1) and the spinocerebellar ataxias. As toxicity increases with repeat length, the intergenerational expansion of unstable CAG.CTG repeats leads to anticipation, an earlier age-at-onset in successive generations in these disorders. Crucially, disease associated alleles are also somatically unstable and continue to expand throughout the lifetime of the individual. In addition, evidence suggests that c/s-acting elements may be major modifiers of instability. Here it was found that the toxicity of expanded polyQ-encoding CAG.CTG tracts correlates with both the expandability of the underlying CAG.CTG repeat and the GC content of the genomic DNA flanking sequences. PolyQ toxicity does not correlate with properties of mRNA or protein sequences, or with polyQ location within the gene or protein. These data thus strongly suggest that the observed inter-locus differences in polyQ. toxicity are not mediated by protein context effects, but that the rate at which somatic expansion of the DNA delivers proteins to their cytotoxic state is a critical factor in expanded polyQ-disease age-at-onset. Using human and mouse cell lines transgenic for an expanded human DM1 locus, it was found that an expanded CTGhz repeat alone is not sufficient for instability. Moreover, by generating mouse cell lines stably transfected with both a stable and unstable expanded CTG[142] repeat, it was possible to assay the effect of cis-elements on these two loci in the same cell line over time. The sequences flanking the unstable repeat were hypermethylated, whereas the sequences flanking the stable transgenic repeat were unmethylated, suggesting an association between CpG methylation and repeat instability. However, methylation of the stable transgenic repeat failed to induce instability. In addition, it was revealed that transcription of an expanded repeat was not sufficient to induce instability. Analysis of genome-wide CAG.CTG microsatellite instability revealed a significant correlation between flanking sequence GC content and microsatellite mutability. This association was most significant for short (< 7 repeats) microsatellites and for those microsatellites located within exons. However, comparison of microsatellite lengths in the human and chimpanzee genomes revealed a complex association between flanking GC content and misalignment mutations at microsatellite loci, suggesting that the modifying effect of flanking GC content on expanded repeat instability may be specific to the expanded repeat disease loci In conclusion, this work suggests that the rate of somatic repeat expansion is a major modifier of disease progression, and that cis-acting elements in turn, modify repeat instability

DNA methylation in infants with low and high body fatness

The authors gratefully thank the parents and children that participated in the PATHOS study.Background: Birth weight is determined by the interplay between infant genetics and the intrauterine environment and is associated with several health outcomes in later life. Many studies have reported an association between birth weight and DNA methylation in infants and suggest that altered epigenetics may underlie birthweight-associated health outcomes. However, birth weight is a relatively nonspecific measure of fetal growth and consists of fat mass and fat-free mass which may have different effects on health outcomes which motivates studies of infant body composition and DNA methylation. Here, we combined genome-wide DNA methylation profiling of buccal cells from 47 full-term one-week old infants with accurate measurements of infant fat mass and fat-free mass using air-displacement plethysmography. Results: No significant association was found between DNA methylation in infant buccal cells and infant body composition. Moreover, no association between infant DNA methylation and parental body composition or indicators of maternal glucose metabolism were found. Conclusions: Despite accurate measures of body composition, we did not identify any associations between infant body fatness and DNA methylation. These results are consistent with recent studies that generally have identified only weak associations between DNA methylation and birthweight. Although our results should be confirmed by additional larger studies, our findings may suggest that differences in DNA methylation between individuals with low and high body fatness may be established later in childhood.Swedish Research Council FormasSwedish Research Council 2015-03495Swedish Cancer Society CAN 2017/625Spanish Ministry of Economy, Industry and Competitiveness (MINE CO)European Union (EU) RYC-2016-21199 ENDORE SAF2017-87526Linkoping University LibraryBo and Vera Ax:son Johnsons Foundatio

Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques

The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cost-effective methods for the enrichment of 5hmC marked DNA for downstream analysis. We tested three commonly used affinity-based enrichment techniques; (i) antibody, (ii) chemical capture and (iii) protein affinity enrichment and assessed their ability to accurately and reproducibly report 5hmC profiles in mouse tissues containing high (brain) and lower (liver) levels of 5hmC. The protein-affinity technique is a poor reporter of 5hmC profiles, delivering 5hmC patterns that are incompatible with other methods. Both antibody and chemical capture-based techniques generate highly similar genome-wide patterns for 5hmC, which are independently validated by standard quantitative PCR (qPCR) and glucosyl-sensitive restriction enzyme digestion (gRES-qPCR). Both antibody and chemical capture generated profiles reproducibly link to unique chromatin modification profiles associated with 5hmC. However, there appears to be a slight bias of the antibody to bind to regions of DNA rich in simple repeats. Ultimately, the increased specificity observed with chemical capture-based approaches makes this an attractive method for the analysis of locus-specific or genome-wide patterns of 5hm

Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns

ABSTRACT: BACKGROUND: Aberrant CpG island promoter DNA hypermethylation is frequently observed in cancer and is believed to contribute to tumor progression by silencing the expression of tumor suppressor genes. Previously, we observed that promoter hypermethylation in breast cancer reflects cell lineage rather than tumor progression and occurs at genes that are already repressed in a lineage-specific manner. To investigate the generality of our observation we analyzed the methylation profiles of 1,154 cancers from 7 different tissue types. RESULTS: We find that 1,009 genes are prone to hypermethylation in these 7 types of cancer. Nearly half of these genes varied in their susceptibility to hypermethylation between different cancer types. We show that the expression status of hypermethylation prone genes in the originator tissue determines their propensity to become hypermethylated in cancer; specifically, genes that are normally repressed in a tissue are prone to hypermethylation in cancers derived from that tissue. We also show that the promoter regions of hypermethylation-prone genes are depleted of repetitive elements and that DNA sequence around the same promoters is evolutionarily conserved. We propose that these two characteristics reflect tissue-specific gene promoter architecture regulating the expression of these hypermethylation prone genes in normal tissues. CONCLUSIONS: As aberrantly hypermethylated genes are already repressed in pre-cancerous tissue, we suggest that their hypermethylation does not directly contribute to cancer development via silencing. Instead aberrant hypermethylation reflects developmental history and the perturbation of epigenetic mechanisms maintaining these repressed promoters in a hypomethylated state in normal cells.Publisher PDFPeer reviewe

Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome.

BACKGROUND: Induction and promotion of liver cancer by exposure to non-genotoxic carcinogens coincides with epigenetic perturbations, including specific changes in DNA methylation. Here we investigate the genome-wide dynamics of 5-hydroxymethylcytosine (5hmC) as a likely intermediate of 5-methylcytosine (5mC) demethylation in a DNA methylation reprogramming pathway. We use a rodent model of non-genotoxic carcinogen exposure using the drug phenobarbital. RESULTS: Exposure to phenobarbital results in dynamic and reciprocal changes to the 5mC/5hmC patterns over the promoter regions of a cohort of genes that are transcriptionally upregulated. This reprogramming of 5mC/5hmC coincides with characteristic changes in the histone marks H3K4me2, H3K27me3 and H3K36me3. Quantitative analysis of phenobarbital-induced genes that are involved in xenobiotic metabolism reveals that both DNA modifications are lost at the transcription start site, while there is a reciprocal relationship between increasing levels of 5hmC and loss of 5mC at regions immediately adjacent to core promoters. CONCLUSIONS: Collectively, these experiments support the hypothesis that 5hmC is a potential intermediate in a demethylation pathway and reveal precise perturbations of the mouse liver DNA methylome and hydroxymethylome upon exposure to a rodent hepatocarcinogen.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment

Background: Translational research typically aims to identify and functionally validate individual, disease-specific genes. However, reaching this aim is complicated by the involvement of thousands of genes in common diseases, and that many of those genes are pleiotropic, that is, shared by several diseases. Methods: We integrated genomic meta-analyses with prospective clinical studies to systematically investigate the pathogenic, diagnostic and therapeutic roles of pleiotropic genes. In a novel approach, we first used pathway analysis of all published genome-wide association studies (GWAS) to find a cell type common to many diseases. Results: The analysis showed over-representation of the T helper cell differentiation pathway, which is expressed in T cells. This led us to focus on expression profiling of CD4(+) T cells from highly diverse inflammatory and malignant diseases. We found that pleiotropic genes were highly interconnected and formed a pleiotropic module, which was enriched for inflammatory, metabolic and proliferative pathways. The general relevance of this module was supported by highly significant enrichment of genetic variants identified by all GWAS and cancer studies, as well as known diagnostic and therapeutic targets. Prospective clinical studies of multiple sclerosis and allergy showed the importance of both pleiotropic and disease specific modules for clinical stratification. Conclusions: In summary, this translational genomics study identified a pleiotropic module, which has key pathogenic, diagnostic and therapeutic roles

Молекуларно-дијагностички методи, ризици и превенција на фамилијарната хиперхолестеролемија

методи, ризици и превенција на фамилијарната хиперхолестеролемија Апстракт Фамилијарната хиперхолестеролемија (FH – Familiar Hypercholesterolemia) претставува генетичко заболување на организмот предизвикана најчесто од мутација во генот за рецепторот за липопротеини со мала густина (LDLR) и аполипопротеин Б генот (apoB). Претставува наследно заболување и како такво се карактеризира со покачени количества на вкупен холестерол и LDL – холестерол, како резултат на присуство на дисфункционални рецептори за LDL – холестерол или недостаток од рецептори за LDL- холестерол во црниот дроб со кои организмот, поточно црниот дроб, би го чистел LDL – холестеролот од циркулацијата во организмот. Пациентите со оваа болест се со голем ризик на многу млада возраст да развијат кардиоваскуларна, цереброваскуларна или периферна васкуларна болест како резултат на атероматозни промени во крвните садови, а со тоа и голем ризик од фатален исход доколку состојбата не се открие и третира соодветно. Во овој истражувачки труд се користени резултатите од лабораториски испитувања од амбулантскиот дневник на ПЗУ ДЛ „Павлина” – Виница, во временски период од две години 2010-2011 година. Трудот има за цел да ја прикаже преваленцата и ризикот од појава на можна хиперхолестеролемија, дефинирана по пол и возраст. Според анализираните резултати, заклучивме дека кај машката популација најмногу пациенти со високи концентрации на холестерол има во возрасната група од 40 до 60 години, додека кај женскиот пол во возрасната групата на жени над 60 години има најмногу пациенти со покачени концентрации на холестерол. Утврдено е и генерациска врска, т.е. покачени концентрации на холестерол во две генерации во една фамилија. Фамилијарната хиперхолестеролемија е болест која е проценето дека е присутна кај најмалку 250 милиони луѓе во светот и е од особена важност нејзината брза и рана детекција. Тоа се прави со помош на клиничко лабораториски методи и критериуми и молекуларно-дијагностички методи за откривање на генетската причина за појава на оваа болест

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes

BACKGROUND: DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their genomic targeting. However, whether this role of DNA methylation is important in the context of transcriptional regulation is unclear. RESULTS: By genome-wide mapping of the Polycomb Repressive Complex 2-signature histone mark, H3K27me3, in severely DNA hypomethylated mouse somatic cells, we show that hypomethylation leads to widespread H3K27me3 redistribution, in a manner that reflects the local DNA methylation status in wild-type cells. Unexpectedly, we observe striking loss of H3K27me3 and Polycomb Repressive Complex 2 from Polycomb target gene promoters in DNA hypomethylated cells, including Hox gene clusters. Importantly, we show that many of these genes become ectopically expressed in DNA hypomethylated cells, consistent with loss of Polycomb-mediated repression. CONCLUSIONS: An intact DNA methylome is required for appropriate Polycomb-mediated gene repression by constraining Polycomb Repressive Complex 2 targeting. These observations identify a previously unappreciated role for DNA methylation in gene regulation and therefore influence our understanding of how this epigenetic mechanism contributes to normal development and disease