Epigenetic regulation of heterochromatic DNA stability

In this review we summarize recent studies that demonstrate the importance of epigenetic mechanisms for maintaining genome integrity, specifically with respect to repeated DNAs within heterochromatin. Potential problems that arise during replication, recombination, and repair of repeated sequences are counteracted by post-translational histone modifications and associated proteins, including the cohesins. These factors appear to ensure repeat stability by multiple mechanisms: suppressing homologous recombination, controlling the three-dimensional organization of damaged repeats to reduce the probability of aberrant recombination, and promoting the use of less problematic repair pathways. The presence of such systems may facilitate repeat and chromosome evolution, and their failure can lead to genome instability, chromosome rearrangements, and the onset of pathogenesis.     

A heterochromatic satellite DNA is highly amplified in a single chromosome of Muscari (Hyacinthaceae)

We examined the composition and evolution of a large heterochromatic region present in the genomes of certain species of the genus Muscari (Hyacinthaceae). We found that in Muscari comosum this heterochromatic region is composed mainly of a satellite DNA family, which we named MCSAT. Molecular analyses and in situ hybridization revealed that, through the evolution of Muscari species, the MCSAT sequences have been progressively amplified in several species of the genus, such as M. matritensis and M. dionysicum, attaining enormous amplification in the genome of M. comosum. We discuss the characteristics of this satellite DNA family, which, being exclusively amplified in one chromosome pair of M. comosum, constitute the major exception to the equilocal model of satellite DNA and heterochromatin distribution. Also, we discuss the possibility that the amplification of these sequences in a single chromosome could have contributed to a progressive increase in the asymmetry of the karyotypes in Muscari species.     

Distribution of satellite DNA fractions within major heterochromatic regions of human chromosomes as revealed by PleI and TfiI digestion.

Banding patterns induced by selective DNA extraction with the restriction endonucleases PleI and TfiI reveal the distribution of human satellite DNAs within the major heterochromatic blocks on human metaphase chromosomes. PleI and TfiI are able to discriminate HinfI target sites, depending on the nature of the central base. PleI digestion specifically reveals regions, within major C-bands, that include the major sites of satellite II DNA and permits more precise localization of satellite II domains than does radioactive in situ hybridization. The close correspondence between the cytogenetic results presented here and previously reported molecular data seems to support the idea that the frequency of enzyme target sequences is the main factor in determining the action produced by restriction endonucleases on fixed human chromosomes and that chromatin conformation is not an important factor in limiting enzyme accessibility.     

The ins and outs of heterochromatic DNA repair

Repetitive DNA is often packaged into heterochromatin structures that prevent illicit recombination events that cause genomic instability. A recent study by Chiolo et?al. (2011) published in Cell finds that DNA double-strand breaks formed within heterochromatin are shuttled to adjacent sites that are "safe" to complete repair by recombination.     

DNA profiling

Although some concerns still remain in standard DNA profiling technology over the assumptions from population genetics used to calculate expected match frequencies, forensic scientists are preparing for the introduction of the next generation of DNA profiling techniques based on the polymerase chain reaction. These new techniques offer the prospect of dramatically increasing the speed and sensitivity of DNA profiling and have already been applied in some casework studies.     

DNA double-strand break repair within heterochromatic regions

DNA DSBs (double-strand breaks) represent a critical lesion for a cell, with misrepair being potentially as harmful as lack of repair. In mammalian cells, DSBs are predominantly repaired by non-homologous end-joining or homologous recombination. The kinetics of repair of DSBs can differ widely, and recent studies have shown that the higher-order chromatin structure can dramatically affect the pathway utilized, the rate of repair and the genetic factors required for repair. Studies of the repair of DSBs arising within heterochromatic DNA regions have provided insight into the constraints that higher-order chromatin structure poses on repair and the processing that is uniquely required for the repair of such DSBs. In the present paper, we provide an overview of our current understanding of the process of heterochromatic DSB repair in mammalian cells and consider the evolutionary conservation of the processes.     

Methylation of satellite DNA

The lower amount of 5 methylcytosine in DNA from bull sperm relative to DNA of other bovine tissues is a result of the absence of this minor base from several of the satellite DNAs in sperm. This applies particularly to the 1.715, 1.711b and 1.709 satellites and less so to the 1.706 and 1.711a satellites. Mouse sperm DNA is also partially undermethylated.     

DNA损伤修复过程表观遗传学改变

多种化学、物理及生物因素可诱发细胞DNA损伤,损伤后DNA损伤位点被相关损伤感受器识别,激活相应的修复通路进行DNA修复。越来越多的证据表明DNA甲基化状态、蛋白翻译后修饰、染色质重塑、miRNA等修饰方式参与了DNA的损伤修复。文章通过不同损伤修复通路中这些修饰的特点,阐述表观遗传学改变在DNA损伤修复发展过程中的作用机制。     

表观遗传DNA甲基化与糖尿病研究进展

糖尿病是受遗传和环境共同调控的一种代谢性疾病,发病率高且难以治愈。表观遗传DNA甲基化与糖尿病进程密切相关,是联通环境因素与基因因素的桥梁,DNA甲基化通过其对基因表达的调节作用影响疾病的发生与发展。肠道微生物菌群是糖尿病研究的新兴热点方向,能够提供甲基供体等有利于甲基化的便利条件。与肠道微生物菌群及其他相关代谢通路有关的DNA甲基化与糖尿病存在着密切的关系,其为解释糖尿病的致病机理及寻找有效干预糖尿病的手段提供了新的研究线索和思路。     

Epigenetic profiling of the antitumor natural product psammaplin A and its analogues

A collection of analogues of the dimeric natural product psammaplin A that differ in the substitution on the (halo)tyrosine aryl ring, the oxime and the diamine connection has been synthesized. The effects on cell cycle, induction of differentiation and apoptosis of the natural-product inspired series were measured on the human leukaemia U937 cell line. Epigenetic profiling included induction of p21(WAF1), effects on global H3 histone and tubulin acetylation levels as well as in vitro enzymatic assays using HDAC1, DNMT1, DNMT3A, SIRT1 and a peptide domain with p300/CBP HAT activity. Whereas the derivatives of psammaplin A with modifications in the length of the connecting chain, the oxime bond and the disulfide unit showed lower potency, the analogues with changes on the bromotyrosine ring exhibited activities comparable to those of the parent compound in the inhibition of HDAC1 and in the induction of apoptosis. The lack of HDAC1 activity of analogues modified on the disulfide bond suggests that its cleavage must occur in cells to produce the monomeric Zn(2+)-chelating thiol. This assumption is consistent with the molecular modelling of the complex of psammaplin A thiol with h-HDAC8. Only a weak inhibition of DNMT1, DNMT3A and residual activities with SIRT1 and a p300/CBP HAT peptide were measured for these compounds.     

Epigenetic drug discovery: targeting DNA methyltransferases

Epigenetic modification of DNA leads to changes in gene expression. DNA methyltransferases (DNMTs) comprise a family of nuclear enzymes that catalyze the methylation of CpG dinucleotides, resulting in an epigenetic methylome distinguished between normal cells and those in disease states such as cancer. Disrupting gene expression patterns through promoter methylation has been implicated in many malignancies and supports DNMTs as attractive therapeutic targets. This review focuses on the rationale of targeting DNMTs in cancer, the historical approach to DNMT inhibition, and current marketed hypomethylating therapeutics azacytidine and decitabine. In addition, we address novel DNMT inhibitory agents emerging in development, including CP-4200 and SGI-110, analogs of azacytidine and decitabine, respectively; the oligonucleotides MG98 and miR29a; and a number of reversible inhibitors, some of which appear to be selective against particular DNMT isoforms. Finally, we discuss future opportunities and challenges for next-generation therapeutics.     

Differential DNA synthesis in heterochromatic and euchromatic chromosome sets of Planococcus citri

In males of the mealy bug Planococcus citri, Nur (1966) counted five heterochromatic (H) and about 5, 10, 20, 40, or 80 euchromatic (E) chromosomes in testis sheath nuclei which were undergoing endomitosis. He suggested that the H chromosomes were not replicating and that the nuclei were becoming polyploid as a result of successive cycles of replication of only the E chromosomes. This hypothesis was tested using autoradiography with H³-thymidine to detect DNA synthesis and microspectrophotometric measurements of the Feulgen reaction in nuclei to detect quantitative changes in DNA. — The integrated absorbance of the whole nucleus and of the isolated clump of heterochromatic chromosomes (H body) in polyploid testis sheath nuclei were measured using the mechanical scanner of the CYDAC system. The absorbance of the H body was similar in all testis sheath nuclei examined and was not significantly different from the absorbance of a haploid set of H chromosomes measured after meiosis. The absorbance of the euchromatic component varied in different sheath nuclei, the values closely corresponding to the terms of the series 2c, 4c, 8c. This series is expected if the DNA in the E chromosomes is exactly doubled at each cycle of replication. — Autoradiographs showed that most labeled sheath nuclei had silver grains localized exclusively over euchromatin. With one exception, the remainder of the labeled nuclei had silver grains over both euchromatin and the H body. The observation that euchromatin was much more heavily labeled than the H body and that labeled H bodies occurred at a low frequency and only in the presence of labeled euchromatin suggests that the H body did not incorporate the label and that the silver grains over the H body were the result of -particles which originated in proximal euchromatin.