Recognition of 5-Hydroxymethylcytosine by the Uhrf1 SRA Domain

Recent discovery of 5-hydroxymethylcytosine (5hmC) in genomic DNA raises the question how this sixth base is recognized by cellular proteins. In contrast to the methyl-CpG binding domain (MBD) of MeCP2, we found that the SRA domain of Uhrf1, an essential factor in DNA maintenance methylation, binds 5hmC and 5-methylcytosine containing substrates with similar affinity. Based on the co-crystal structure, we performed molecular dynamics simulations of the SRA:DNA complex with the flipped cytosine base carrying either of these epigenetic modifications. Our data indicate that the SRA binding pocket can accommodate 5hmC and stabilizes the flipped base by hydrogen bond formation with the hydroxyl group

Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development

Methylation of cytosine is a DNA modification associated with gene repression. Recently, a novel cytosine modification, 5-hydroxymethylcytosine (5-hmC) has been discovered. Here we examine 5-hmC distribution during mammalian development and in cellular systems, and show that the developmental dynamics of 5-hmC are different from those of 5-methylcytosine (5-mC); in particular 5-hmC is enriched in embryonic contexts compared to adult tissues. A detectable 5-hmC signal appears in pre-implantation development starting at the zygote stage, where the paternal genome is subjected to a genome-wide hydroxylation of 5-mC, which precisely coincides with the loss of the 5-mC signal in the paternal pronucleus. Levels of 5-hmC are high in cells of the inner cell mass in blastocysts, and the modification colocalises with nestin-expressing cell populations in mouse post-implantation embryos. Compared to other adult mammalian organs, 5-hmC is strongly enriched in bone marrow and brain, wherein high 5-hmC content is a feature of both neuronal progenitors and post-mitotic neurons. We show that high levels of 5-hmC are not only present in mouse and human embryonic stem cells (ESCs) and lost during differentiation, as has been reported previously, but also reappear during the generation of induced pluripotent stem cells; thus 5-hmC enrichment correlates with a pluripotent cell state. Our findings suggest that apart from the cells of neuronal lineages, high levels of genomic 5-hmC are an epigenetic feature of embryonic cell populations and cellular pluri- and multi-lineage potency. To our knowledge, 5-hmC represents the first epigenetic modification of DNA discovered whose enrichment is so cell-type specific

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

Enzymes catalysing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression and maintaining cellular identity. Recently, TET1 was found to hydroxylate the methyl group of mC, converting it to 5-hydroxymethyl cytosine (hmC). Here we show that TET1 binds throughout the genome of embryonic stem cells, with the majority of binding sites located at transcription start sites (TSSs) of CpG-rich promoters and within genes. The hmC modification is found in gene bodies and in contrast to mC is also enriched at CpG-rich TSSs. We provide evidence further that TET1 has a role in transcriptional repression. TET1 binds a significant proportion of Polycomb group target genes. Furthermore, TET1 associates and colocalizes with the SIN3A co-repressor complex. We propose that TET1 fine-tunes transcription, opposes aberrant DNA methylation at CpG-rich sequences and thereby contributes to the regulation of DNA methylation fidelity

TET family dioxygenases and DNA demethylation in stem cells and cancers

The methylation of cytosine and subsequent oxidation constitutes a fundamental epigenetic modification in mammalian genomes, and its abnormalities are intimately coupled to various pathogenic processes including cancer development. Enzymes of the Ten-eleven translocation (TET) family catalyze the stepwise oxidation of 5-methylcytosine in DNA to 5-hydroxymethylcytosine and further oxidation products. These oxidized 5-methylcytosine derivatives represent intermediates in the reversal of cytosine methylation, and also serve as stable epigenetic modifications that exert distinctive regulatory roles. It is becoming increasingly obvious that TET proteins and their catalytic products are key regulators of embryonic development, stem cell functions and lineage specification. Over the past several years, the function of TET proteins as a barrier between normal and malignant states has been extensively investigated. Dysregulation of TET protein expression or function is commonly observed in a wide range of cancers. Notably, TET loss-of-function is causally related to the onset and progression of hematologic malignancy in vivo. In this review, we focus on recent advances in the mechanistic understanding of DNA methylation-demethylation dynamics, and their potential regulatory functions in cellular differentiation and oncogenic transformation

Właściwości dielektryczne perowskitowych multiferroicznych grubych warstw Pb(Fe0.5Nb0.5)O3-Bi0.95Dy0.05FeO3

The paper reports the preparation and deposition of dielectric thick films exhibiting multiferroic properties. The developed layers are based on solid solutions of two multiferroic compounds with perovskite structure -- relaxor Pb(Fe0.5Nb0.5)O3 and Bi0.95Dy0.05FeO3. Complex impedance and dielectric permittivity of thick films were determined as a function of temperature (from - 55 to 450°C) and frequency (10 Hz - 2 MHz). DC resistivity was measured in the temperature range 20 - 400°C. Microstructure of the samples was studied using a scanning electron microscope. In complex plane impedance spectra there exists a single arc at a given temperature associated with grains which decreases and shifts to higher frequencies with increasing temperature. The maximum values of dielectric permittivity of the investigated layers were 2000 - 4000 in the temperature range from -55 to 150°C at 1 kHz. Two broad ε'maxima ascribed to relaxor ferroelectric transition and dielectric relaxation occur in the temperature range from -55 to 450°C. Low sintering temperature appropriate for the conventional thick film procedure, dense microstructure and high dielectric permittivity slightly changing over a wide frequency and temperature ranges are advantages of the developed compositions.W artykule opisano przygotowanie i nanoszenie dielektrycznych grubych warstw wykazujących multiferroiczne właściwości. Opracowane warstwy oparte są na dwóch multiferroicznych związkach o strukturze perowskitu - relaksorze Pb(Fe0.5Nb0.5)O3 i Bi0.95Dy0.05FeO3. Badano zespoloną impedancję i przenikalność elektryczną grubych warstw w funkcji temperatury (od -55 do 450°C) i częstotliwości (10 Hz - 2 MHz). Mierzono przewodnictwo dc w zakresie temperatur 20 - 400°C. Badano mikrostrukturę próbek przy użyciu mikroskopu skaningowego. Na wykresach zespolonej impedancji w danej temperaturze istnieje pojedynczy łuk, związany z ziarnami, który zmniejsza się i przesuwa w stronę wyższych częstotliwości ze wzrostem temperatury. Maksymalne wartości przenikalności elektrycznej badanych warstw wynoszą 2000 - 4000 w zakresie temperatur od -55 do 150°C dla 1 kHz. W zakresie temperatur od -55 do 450°C występują dwa szerokie maksima ε' przypisywane przemianie ferroelektrycznej i relaksacji dielektrycznej. Korzystnymi cechami opracowanych kompozycji są: niska temperatura spiekania odpowiednia dla konwencjonalnej procedury grubowarstwowej, zwarta mikrostruktura i wysoka przenikalność elektryczna słabo zmieniająca się w szerokim zakresie częstotliwości i temperatur