im5C-DSCGA: A Proposed Hybrid Framework Based on Improved DenseNet and Attention Mechanisms for Identifying 5-methylcytosine Sites in Human RNA

BACKGROUND

5-methylcytosine (m5C) is a key post-transcriptional modification that plays a critical role in RNA metabolism. Owing to the large increase in identified m5C modification sites in organisms, their epigenetic roles are becoming increasingly unknown. Therefore, it is crucial to precisely identify m5C modification sites to gain more insight into cellular processes and other mechanisms related to biological functions. Although researchers have proposed some traditional computational methods and machine learning algorithms, some limitations still remain. In this study, we propose a more powerful and reliable deep-learning model, im5C-DSCGA, to identify novel RNA m5C modification sites in humans.

METHODS

Our proposed im5C-DSCGA model uses three feature encoding methods initially-one-hot, nucleotide chemical property (NCP), and nucleotide density (ND)-to extract the original features in RNA sequences and ensure splicing; next, the original features are fed into the improved densely connected convolutional network (DenseNet) and Convolutional Block Attention Module (CBAM) mechanisms to extract the advanced local features; then, the bidirectional gated recurrent unit (BGRU) method is used to capture the long-term dependencies from advanced local features and extract global features using Self-Attention; Finally, ensemble learning is used and full connectivity is used to classify and predict the m5C site.

RESULTS

Unsurprisingly, the deep-learning-based im5C-DSCGA model performed well in terms of sensitivity (Sn), specificity (SP), accuracy (Acc), Matthew's correlation coefficient (MCC), and area under the curve (AUC), generating values of 81.0%, 90.8%, 85.9%, 72.1%, and 92.6%, respectively, in the independent test dataset following the use of three feature encoding methods.

CONCLUSIONS

We critically evaluated the performance of im5C-DSCGA using five-fold cross-validation and independent testing and compared it to existing methods. The MCC metric reached 72.1% when using the independent test, which is 3.0% higher than the current state-of-the-art prediction method Deepm5C model. The results show that the im5C-DSCGA model achieves more accurate and stable performances and is an effective tool for predicting m5C modification sites. To the authors' knowledge, this is the first time that the improved DenseNet, BGRU, CBAM Attention mechanism, and Self-Attention mechanism have been combined to predict novel m5C sites in human RNA.

Substrate DNA length regulates the activity of TET 5-methylcytosine dioxygenases

The ten-eleven translocation (TET) isoforms (TET1-3) play critical roles in epigenetic transcription regulation. In addition, mutations in the TET2 gene are frequently detected in patients with glioma and myeloid malignancies. TET isoforms can oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, by iterative oxidation. The in vivo DNA demethylation activity of TET isoforms may depend on many factors including enzyme's structural features, its interaction with DNA-binding proteins, chromatin context, DNA sequence, DNA length, and configuration. The rationale for this study is to identify the preferred DNA length and configuration in the substrates of TET isoforms. We have used a highly sensitive LC-MS/MS-based method to compare the substrate preference of TET isoforms. To this end, four DNA substrate sets (S1, S2, S3, S4) of different sequences were chosen. In addition, in each set, four different lengths of DNA substrates comprising 7-, 13-, 19-, and 25-mer nucleotides were synthesized. Each DNA substrate was further used in three different configurations, that is, double stranded symmetrically-methylated, double stranded hemi-methylated, and single stranded single-methylated to evaluate their effect on TET-mediated 5mC oxidation. We demonstrate that mouse TET1 (mTET1) and human TET2 (hTET2) have highest preference for 13-mer dsDNA substrates. Increasing or decreasing the length of dsDNA substrate reduces product formation. In contrast to their dsDNA counterparts, the length of ssDNA substrates did not have a predictable effect on 5mC oxidation. Finally, we show that substrate specificity of TET isoforms correlates with their DNA binding efficiency. Our results demonstrate that mTET1 and hTET2 prefer 13-mer dsDNA as a substrate over ssDNA. These results may help elucidate novel properties of TET-mediated 5mC oxidation and help develop novel diagnostic tools to detect TET2 function in patients.

Selective Functionalisation of 5-Methylcytosine by Organic Photoredox Catalysis

The epigenetic modification 5-methylcytosine plays a vital role in development, cell specific gene expression and disease states. The selective chemical modification of the 5-methylcytosine methyl group is challenging. Currently, no such chemistry exists. Direct functionalisation of 5-methylcytosine would improve the detection and study of this epigenetic feature. We report a xanthone-photosensitised process that introduces a 4-pyridine modification at a C(sp3 )-H bond in the methyl group of 5-methylcytosine. We propose a reaction mechanism for this type of reaction based on density functional calculations and apply transition state analysis to rationalise differences in observed reaction efficiencies between cyanopyridine derivatives. The reaction is initiated by single electron oxidation of 5-methylcytosine followed by deprotonation to generate the methyl group radical. Cross coupling of the methyl radical with 4-cyanopyridine installs a 4-pyridine label at 5-methylcytosine. We demonstrate use of the pyridination reaction to enrich 5-methylcytosine-containing ribonucleic acid.

DGA-5mC: A 5-methylcytosine site prediction model based on an improved DenseNet and bidirectional GRU method

The 5-methylcytosine (5mC) in the promoter region plays a significant role in biological processes and diseases. A few high-throughput sequencing technologies and traditional machine learning algorithms are often used by researchers to detect 5mC modification sites. However, high-throughput identification is laborious, time-consuming and expensive; moreover, the machine learning algorithms are not so advanced. Therefore, there is an urgent need to develop a more efficient computational approach to replace those traditional methods. Since deep learning algorithms are more popular and have powerful computational advantages, we constructed a novel prediction model, called DGA-5mC, to identify 5mC modification sites in promoter regions by using a deep learning algorithm based on an improved densely connected convolutional network (DenseNet) and the bidirectional GRU approach. Furthermore, we added a self-attention module to evaluate the importance of various 5mC features. The deep learning-based DGA-5mC model algorithm automatically handles large proportions of unbalanced data for both positive and negative samples, highlighting the model's reliability and superiority. So far as the authors are aware, this is the first time that the combination of an improved DenseNet and bidirectional GRU methods has been used to predict the 5mC modification sites in promoter regions. It can be seen that the DGA-5mC model, after using a combination of one-hot coding, nucleotide chemical property coding and nucleotide density coding, performed well in terms of sensitivity, specificity, accuracy, the Matthews correlation coefficient (MCC), area under the curve and Gmean in the independent test dataset: 90.19%, 92.74%, 92.54%, 64.64%, 96.43% and 91.46%, respectively. In addition, all datasets and source codes for the DGA-5mC model are freely accessible at https://github.com/lulukoss/DGA-5mC.

Integrated single-cell sequencing of 5-hydroxymethylcytosine and genomic DNA using scH&G-seq

The asymmetric distribution of 5-hydroxymethylcytosine (5hmC) between two DNA strands of a chromosome enables endogenous reconstruction of cellular lineages at an individual-cell-division resolution. Further, when integrated with data on genomic variants to infer clonal lineages, this combinatorial information accurately reconstructs larger lineage trees. Here, we provide a detailed protocol for single-cell 5-hydroxymethylcytosine and genomic DNA sequencing (scH&G-seq) to simultaneously quantify 5hmC and genomic DNA from the same cell to reconstruct lineage trees at a single-cell-division resolution.

For complete details on the use and execution of this protocol, please refer to Wangsanuwat et al., 2021.

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scH&G-seq enables quantification of 5hmC and genomic DNA (gDNA) from the same cell

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Strand-specific 5hmC enables reconstructing trees at a single-cell-division resolution

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Genomic variants allow identification of clonal subtrees within a lineage tree

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Integrated 5hmC and gDNA detection improves prediction accuracy of larger lineage trees

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function

We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties similar to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) generally lead to stiffer DNA than normal cytosine, with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). Conversely, our simulations suggest that methylated-DNA binding domains (MBDs), associated with repression activities, are sensitive to the substitution d(mCpG) ➔ d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) d(hmCpG) change. Overall, while gene activity changes due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding.

In Eukaryotic cells, DNA epigenetic modifications play an important role in gene expression and regulation, and protein recognition. In this work we investigate the physical implications of cytosine 5-hydroxymethylation on DNA, its structural and flexibility differences with methylated and unmodified cytosine using molecular dynamics, biophysical experiments and NMR spectroscopy.

In particular the effect of hydroxyl group on free energy of nucleosome and Methyl binding Protein (MBD) binding, comparing in silico and experimental data to shed light on the effect of the reduced flexibility and the direct protein-DNA recognition.

Biomimetic Iron Complex Achieves TET Enzyme Reactivity*

The epigenetic marker 5-methyl-2'-deoxycytidine (5mdC) is the most prevalent modification to DNA. It is removed inter alia via an active demethylation pathway: oxidation by Ten-Eleven Translocation 5-methyl cytosine dioxygenase (TET) and subsequent removal via base excision repair or direct demodification. Recently, we have shown that the synthetic iron(IV)-oxo complex [FeIV (O)(Py5 Me2 H)]2+ (1) can serve as a biomimetic model for TET by oxidizing the nucleobase 5-methyl cytosine (5mC) to its natural metabolites. In this work, we demonstrate that nucleosides and even short oligonucleotide strands can also serve as substrates, using a range of HPLC and MS techniques. We found that the 5-position of 5mC is oxidized preferably by 1, with side reactions occurring only at the strand ends of the used oligonucleotides. A detailed study of the reactivity of 1 towards nucleosides confirms our results; that oxidation of the anomeric center (1') is the most common side reaction.

Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays

The 5-carbon positions on cytosine nucleotides preceding guanines in genomic DNA (CpG) are common targets for DNA methylation (5mC). DNA methylation removal can occur through both active and passive mechanisms. Ten-eleven translocation enzymes (TETs) oxidize 5mC in a stepwise manner to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5mC can also be removed passively through sequential cell divisions in the absence of DNA methylation maintenance. In this chapter, we describe approaches that couple TET-assisted bisulfite (TAB) and oxidative bisulfite (OxBS) conversion to the Illumina MethylationEPIC BeadChIP (EPIC array) and show how these technologies can be used to distinguish active versus passive DNA demethylation. We also describe integrative bioinformatics pipelines to facilitate this analysis.

Genome-wide identification of 5-methylcytosine sites in bacterial genomes by high-throughput sequencing of MspJI restriction fragments

Single-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar identification of 5-methylcytosine sites is not as straightforward. In prokaryotic DNA, methylation typically occurs within specific sequence contexts, or motifs, that are a property of the methyltransferases that "write" these epigenetic marks. We present here a straightforward, cost-effective alternative to both SMRT and bisulfite sequencing for the determination of prokaryotic 5-methylcytosine methylation motifs. The method, called MFRE-Seq, relies on excision and isolation of fully methylated fragments of predictable size using MspJI-Family Restriction Enzymes (MFREs), which depend on the presence of 5-methylcytosine for cleavage. We demonstrate that MFRE-Seq is compatible with both Illumina and Ion Torrent sequencing platforms and requires only a digestion step and simple column purification of size-selected digest fragments prior to standard library preparation procedures. We applied MFRE-Seq to numerous bacterial and archaeal genomic DNA preparations and successfully confirmed known motifs and identified novel ones. This method should be a useful complement to existing methodologies for studying prokaryotic methylomes and characterizing the contributing methyltransferases.

Structural dynamics of double-stranded DNA with epigenome modification

Modification of cytosine plays an important role in epigenetic regulation of gene expression and genome stability. Cytosine is converted to 5-methylcytosine (5mC) by DNA methyltransferase; in turn, 5mC may be oxidized to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation enzyme. The structural flexibility of DNA is known to affect the binding of proteins to methylated DNA. Here, we have carried out a semi-quantitative analysis of the dynamics of double-stranded DNA (dsDNA) containing various epigenetic modifications by combining data from imino 1H exchange and imino 1H R1ρ relaxation dispersion NMR experiments in a complementary way. Using this approach, we characterized the base-opening (kopen) and base-closing (kclose) rates, facilitating a comparison of the base-opening and -closing process of dsDNA containing cytosine in different states of epigenetic modification. A particularly striking result is the increase in the kopen rate of hemi-methylated dsDNA 5mC/C relative to unmodified or fully methylated dsDNA, indicating that the Watson-Crick base pairs undergo selective destabilization in 5mC/C. Collectively, our findings imply that the epigenetic modulation of cytosine dynamics in dsDNA mediates destabilization of the GC Watson-Crick base pair to allow base-flipping in living cells.

Identifying Protein-(Hydroxy)Methylated DNA Interactions Using Quantitative Interaction Proteomics

In recent years, workflows coupling DNA affinity purifications from crude nuclear extracts with quantitative mass spectrometry-based proteomics have enabled comprehensive mapping of protein-DNA interactions in an unbiased manner. Here, we describe a detailed protocol for one such method in which affinity purifications with extracts from cells or tissues of interest are combined with a chemical stable isotope labeling method, dimethyl labeling, to identify specific interaction partners for (hydroxy)methylated and non-methylated DNA sequences of interest.

High-Fidelity CRISPR/Cas9-Based Gene-Specific Hydroxymethylation

Aberrant promoter hypermethylation leads to gene silencing and is associated with various pathologies including cancer and organ fibrosis. Active DNA demethylation is mediated by TET enzymes: TET1, TET2, and TET3, which convert 5-methylcytosine to 5-hydroxymethylcytosine. Induction of gene-specific hydroxymethylation via CRISPR/Cas9 gene technology provides an opportunity to reactivate a single target gene silenced in pathological conditions. We utilized a spCas9 variant fused with TET3 catalytic domain to mediate gene-specific hydroxymethylation with subsequent gene reactivation which holds promise for gene therapy. Here, we present guidelines for gene-specific hydroxymethylation targeting with a specific focus on designing sgRNA and functional assessments in vitro.

Bioinformatic Estimation of DNA Methylation and Hydroxymethylation Proportions

Simultaneous measurement of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level can be obtained by combining data from DNA processing methods including traditional bisulfite (BS), oxidative bisulfite (oxBS), or Tet-assisted (TAB) bisulfite conversion. Array-based technologies have been widely used in this task, due to their time and cost efficiency. For methylation studies using BS data, many protocols and related packages have been suggested in the literature to deal with limitations and confounders that arise from array data. In this chapter, we illustrate how the reader can make small adjustments to these protocols to obtain estimates of methylation and hydroxymethylation proportions.

Immunohistochemical Detection of 5-Hydroxymethylcytosine and 5-Carboxylcytosine in Sections of Zebrafish Embryos

5-methylcytosine (5mC) is an epigenetic modification to DNA which modulates transcription. 5mC can be sequentially oxidized to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Collectively, these marks are referred to as the oxidized derivatives of 5mC (i.e., oxi-mCs). Their formation is catalyzed by the ten-eleven translocation methylcytosine dioxygenases (TETs 1, 2 and 3). Various techniques have been developed for the detection of oxi-mCs. The following chapter describes an immunochemical protocol for the simultaneous detection of 5hmC and 5caC in embryonic zebrafish tissue sections. The embryos are fixed, permeabilized and embedded in paraffin blocks. The blocks are cut into sections that are mounted onto slides. Depurination of the DNA is performed to allow immunodetection of the oxi-mCs. The 5hmC is detected with the help of a mouse anti-5hmC monoclonal primary antibody and a goat anti-mouse Alexa Fluor 633-conjugated secondary antibody. The weak 5caC signal requires enzymatic amplification. Its detection involves a rabbit anti-5caC polyclonal primary antibody and a goat anti-rabbit secondary antibody that is conjugated to horseradish peroxidase (HRP). HRP amplifies the 5caC signal by catalyzing the deposition of large quantities of fluorescein-labeled tyramide. Sections immunostained for 5hmC and 5caC are analyzed by fluorescent light or confocal laser scanning microscopy. This immunochemical method allows for highly sensitive detection of 5hmC and 5caC in zebrafish tissues.

Purification of TET Proteins

The 5-methylcytosine (5mC) oxidation pathway mediated by TET proteins involves step-wise oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be removed from DNA by base excision repair and the completion of this pathway results in "demethylation" of 5mC by converting the modified base back into cytosine. In vitro studies with TET proteins aimed at analyzing their DNA substrate specificities and their activity within defined chromatin templates are relatively limited. Here we describe purification methods for mammalian TET proteins based on expression in insect cells or in 293T cells. We also briefly summarize a method that can be used to monitor 5-methylcytosine oxidase activity of the purified TET proteins in vitro.

Analyzing DNA-Immunoprecipitation Sequencing Data

Genome-wide profiling of DNA modifications has advanced our understanding of epigenetics in mammalian biology. Whereas several different methods for profiling DNA modifications have been developed over the last decade, DNA-immunoprecipitation coupled with high-throughput sequencing (DIP-seq) has proven a particularly adaptable and cost-effective approach. DIP-seq was especially valuable in initial studies of the more recently discovered DNA modifications, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine. As an enrichment-based profiling method, analysis of DIP-seq data poses several unique, and often unappreciated bioinformatics challenges, which if unmet, can profoundly affect the results and conclusions drawn from the data. Here, we outline key considerations in both the design of DIP-seq assays and analysis of DIP-seq data to ensure the accuracy and reproducibility of DIP-seq based studies.

TET-mediated 5-methylcytosine oxidation in tRNA promotes translation

Oxidation of 5-methylcytosine (5mC) in DNA by the ten-eleven translocation (TET) family of enzymes is indispensable for gene regulation in mammals. More recently, evidence has emerged to support a biological function for TET-mediated m5C oxidation in messenger RNA. Here, we describe a previously uncharacterized role of TET-mediated m5C oxidation in transfer RNA (tRNA). We found that the TET-mediated oxidation product 5-hydroxylmethylcytosine (hm5C) is specifically enriched in tRNA inside cells and that the oxidation activity of TET2 on m5C in tRNAs can be readily observed in vitro. We further observed that hm5C levels in tRNA were significantly decreased in Tet2 KO mouse embryonic stem cells (mESCs) in comparison with wild-type mESCs. Reciprocally, induced expression of the catalytic domain of TET2 led to an obvious increase in hm5C and a decrease in m5C in tRNAs relative to uninduced cells. Strikingly, we also show that TET2-mediated m5C oxidation in tRNA promotes translation in vitro. These results suggest TET2 may influence translation through impacting tRNA methylation and reveal an unexpected role for TET enzymes in regulating multiple nodes of the central dogma.

The Roles of Host 5-Methylcytosine RNA Methyltransferases during Viral Infections

Eukaryotic 5-methylcytosine RNA methyltransferases catalyze the transfer of a methyl group to the fifth carbon of a cytosine base in RNA sequences to produce 5-methylcytosine (m5C). m5C RNA methyltransferases play a crucial role in the maintenance of functionality and stability of RNA. Viruses have developed a number of strategies to suppress host innate immunity and ensure efficient transcription and translation for the replication of new virions. One such viral strategy is to use host m5C RNA methyltransferases to modify viral RNA and thus to affect antiviral host responses. Here, we summarize the latest findings concerning the roles of m5C RNA methyltransferases, namely, NOL1/NOP2/SUN domain (NSUN) proteins and DNA methyltransferase 2/tRNA methyltransferase 1 (DNMT2/TRDMT1) during viral infections. Moreover, the use of m5C RNA methyltransferase inhibitors as an antiviral therapy is discussed.

Demethylation Status of Somatic DNA Extracted From Pituitary Neuroendocrine Tumors Indicates Proliferative Behavior

BACKGROUND

Cytosine intermediaries 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), epigenetic hallmarks, have never been investigated in pituitary neuroendocrine tumors (PitNET).

OBJECTIVE

To examine methylation-demethylation status of global deoxyribonucleic acid (DNA) in PitNET tissues and to assess its correlation with clinical and biological parameters.

MATERIALS AND METHODS

Altogether, 57 PitNET and 25 corresponding plasma samples were collected. 5mC and 5hmC were investigated using liquid chromatography-tandem mass spectrometry. Expression of DNA methyltransferase 1 (DNMT1); tet methylcytosine dioxygenase 1 through 3 (TET1-3); and ubiquitin-like, containing PHD and RING finger domains 1 and 2 (UHRF1-2) were measured by reverse transcription-polymerase chain reaction. Levels of 5hmC and UHRF1-2 were explored by immunohistochemistry. Effect of demethylating agent decitabine was tested on pituitary cell lines.

RESULTS

5hmC/5mC ratio was higher in less differentiated PitNET samples. A negative correlation between Ki-67 proliferation index and 5hmC, 5hmC to 5mC ratio were revealed. Higher 5mC was observed in SF-1 + gonadotroph adenomas with a higher Ki-67 index. Expressions of TET2 and TET3 were significantly higher in adenomas with higher proliferation rate. UHRF1 showed gradually increased expression in higher proliferative adenoma samples, and a significant positive correlation was detected between UHRF2 expression and 5hmC level. Decitabine treatment significantly decreased 5mC and increased 5hmC levels in both cell lines, accompanied with decreased cell viability and proliferation.

CONCLUSION

The demethylation process negatively correlated with proliferation rate and the ratio of 5hmC to 5mC was higher in less differentiated adenomas. Therefore, epigenetic markers can be potential biomarkers for PitNET behavior. Altering the epigenome in adenoma cells by decitabine decreased proliferation, suggesting that this treatment might be a novel medical treatment for PitNET.

Structure-based screening of chemical libraries to identify small molecules that are likely to bind with the SET and RING-associated (SRA) domain of Ubiquitin-like, PHD and Ring Finger-containing 1 (UHRF1)

OBJECTIVES

UHRF1 is a multi-domain protein that recognizes both histone and DNA modification marks on chromatin. UHRF1 is involved in various cellular processes that lead to tumorigenesis and thus attracted considerable attention as a potential anti-cancer drug target. The SRA domain is a unique to the UHRF family. SRA domain recognizes 5-methylcytosine in hemimethylated DNA and necessary for maintenance DNA methylation mediated by DNMT1. Small molecules capable of interacting with the SRA domain may reduce aberrant methylation levels by preventing the interaction of 5-methylcytosine with the SRA domain and thereby blocking substrate access to the catalytic center of DNMT1. The data were collected to identify and predict an initial set of small molecules that are expected to bind to the SRA domain.

DATA DESCRIPTION

Nearly 2.4 million molecules from various chemical libraries were screened with the SRA domain of UHRF1 using Schrodinger's Small Molecule Drug Discovery Suite. The data is available in the form of a methodology presentation, MS Excel files listing the top hits, and Maestro pose viewer files that provide visualization of how the identified ligands interact with the SRA domain.

Multiple links between 5-methylcytosine content of mRNA and translation

BACKGROUND

5-Methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise.

RESULTS

We obtained ~ 1000 candidate m5C sites in the wider transcriptome, most of which were found in mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCaP and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m5C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in both mRNAs and noncoding RNAs. Candidate m5C sites in mRNAs are enriched in 5'UTRs and near start codons and are embedded in a local context reminiscent of the NSUN2-dependent m5C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that modification levels, at bulk and for many individual sites, were inversely correlated with ribosome association.

CONCLUSIONS

Our findings emphasise the major role of NSUN2 in placing the m5C mark transcriptome-wide. We further present evidence that substantiates a functional interdependence of cytosine methylation level with mRNA translation. Additionally, we identify several compelling candidate sites for future mechanistic analysis.

Precise genomic mapping of 5-hydroxymethylcytosine via covalent tether-directed sequencing

5-hydroxymethylcytosine (5hmC) is the most prevalent intermediate on the oxidative DNA demethylation pathway and is implicated in regulation of embryogenesis, neurological processes, and cancerogenesis. Profiling of this relatively scarce genomic modification in clinical samples requires cost-effective high-resolution techniques that avoid harsh chemical treatment. Here, we present a bisulfite-free approach for 5hmC profiling at single-nucleotide resolution, named hmTOP-seq (5hmC-specific tethered oligonucleotide–primed sequencing), which is based on direct sequence readout primed at covalently labeled 5hmC sites from an in situ tethered DNA oligonucleotide. Examination of distinct conjugation chemistries suggested a structural model for the tether-directed nonhomologous polymerase priming enabling theoretical evaluation of suitable tethers at the design stage. The hmTOP-seq procedure was optimized and validated on a small model genome and mouse embryonic stem cells, which allowed construction of single-nucleotide 5hmC maps reflecting subtle differences in strand-specific CG hydroxymethylation. Collectively, hmTOP-seq provides a new valuable tool for cost-effective and precise identification of 5hmC in characterizing its biological role and epigenetic changes associated with human disease.

This study describes hmTOP-seq, a bisulfite-free approach for profiling of the epigenetic mark 5-hydroxymethylcytosine (5hmC) at single-nucleotide resolution, based on direct sequence readout primed at an in situ tethered DNA oligonucleotide.

Oxidized Derivatives of 5-Methylcytosine Alter the Stability and Dehybridization Dynamics of Duplex DNA

The naturally occurring nucleobase 5-methylcytosine (mC) and its oxidized derivatives 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC) play important roles in epigenetic regulation and, along with cytosine (C), represent nucleobases currently implicated in the active cytosine demethylation pathway. Despite considerable interest in these modified bases, their impact on the thermodynamic stability of double-stranded DNA (dsDNA) remains ambiguous and their influence on hybridization kinetics and dynamics is even less well-understood. To address these unknowns, we employ steady-state and time-resolved infrared spectroscopy to measure the influence of cytosine modification on the thermodynamics and kinetics of hybridization by assessing the impact on local base pairing dynamics, shifts in the stability of the duplex state, and changes to the hybridization transition state. Modification with mC leads to more tightly bound base pairing below the melting transition and stabilizes the duplex relative to canonical DNA, but the free energy barrier to dehybridization at physiological temperature is nevertheless reduced slightly. Both hmC and fC lead to an increase in local base pair fluctuations, a reduction in the cooperativity of duplex melting, and a lowering of the dissociation barrier, but these effects are most pronounced when the 5-position is formylated. The caC nucleobase demonstrates little impact on dsDNA under neutral conditions, but we find that this modification can dynamically switch between C-like and fC-like behavior depending on the protonation state of the 5-position carboxyl group. Our results provide a consistent thermodynamic and kinetic framework with which to describe the modulation of the physical properties of double-stranded DNA containing these modified nucleobases.

YTHDF2 Binds to 5-Methylcytosine in RNA and Modulates the Maturation of Ribosomal RNA

5-Methylcytosine is found in both DNA and RNA; although its functions in DNA are well established, the exact role of 5-methylcytidine (m5C) in RNA remains poorly defined. Here we identified, by employing a quantitative proteomics method, multiple candidate recognition proteins of m5C in RNA, including several YTH domain-containing family (YTHDF) proteins. We showed that YTHDF2 could bind directly to m5C in RNA, albeit at a lower affinity than that toward N6-methyladenosine (m6A) in RNA, and this binding involves Trp432, a conserved residue located in the hydrophobic pocket of YTHDF2 that is also required for m6A recognition. RNA bisulfite sequencing results revealed that, after CRISPR-Cas9-mediated knockout of the YTHDF2 gene, the majority of m5C sites in rRNA (rRNA) exhibited substantially augmented levels of methylation. Moreover, we found that YTHDF2 is involved in pre-rRNA processing in cells. Together, our data expanded the functions of the YTHDF2 protein in post-transcriptional regulations of RNA and provided novel insights into the functions of m5C in RNA biology.

Epigenetic Modifications of mRNA and DNA in Plants

Advances in the detection and mapping of messenger RNA (mRNA) N⁶-methyladenosine (m⁶A) and 5-methylcytosine (m⁵C), and DNA N⁶-methyldeoxyadenosine (6mA) redefined our understanding of these modifications as additional tiers of epigenetic regulation. In plants, the most prevalent internal mRNA modifications, m⁶A and m⁵C, play crucial and dynamic roles in many processes, including embryo development, stem cell fate determination, trichome branching, leaf morphogenesis, floral transition, stress responses, fruit ripening, and root development. The newly identified and widespread epigenetic marker 6mA DNA methylation is associated with gene expression, plant development, and stress responses. Here, we review the latest research progress on mRNA and DNA epigenetic modifications, including the detection, dynamics, distribution, functions, regulatory proteins, and evolution, with a focus on m⁶A, m⁵C, and 6mA. We also provide some perspectives on future research of the newly identified and unknown epigenetic modifications of mRNA and DNA in plants.

Detection of DNA Methylation by MeDIP and MBDCap Assays: An Overview of Techniques

DNA methylation has been characterized as the representative example of epigenetic modifications and implicated in numerous biological processes, such as genomic imprinting and X chromosome inactivation. It primarily occurs at CpG dinucleotides in mammals and plays a critical role in transcriptional regulations. Examination of DNA methylation patterns in gene(s) or across a genome is vital to understand the role of epigenetic modulation in the progress of development and tumorigenesis. Currently, lots of approaches have been developed to investigate DNA methylation patterns for either limited regions or genome-scale studies, but some of them rely on using restriction enzymes. In this chapter, we describe two commonly used protocols to detect enrichment of methylated DNA regions, namely methylated immunoprecipitation (MeDIP) and capture of methylated DNA by methyl-CpG binding domain-based (MBD) proteins (MBDCap). They are the most economical and effective methods to study DNA methylation in either single locus or genome-wide scale.

Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells

G-quadruplexes (G4s) and i-motifs (iMs) are tetraplex DNA structures. Sequences capable of forming G4/iMs are abundant near the transcription start sites (TSS) of several genes. G4/iMs affect gene expression in vitro. Depending on the gene, the presence of G4/iMs can enhance or suppress expression, making it challenging to discern the underlying mechanism by which they operate. Factors affecting G4/iM structures can provide additional insight into their mechanism of regulation. One such factor is epigenetic modification. The 5-hydroxymethylated cytosines (5hmCs) are epigenetic modifications that occur abundantly in human embryonic stem cells (hESC). The 5hmCs, like G4/iMs, are known to participate in gene regulation and are also enriched near the TSS. We investigated genomic co-localization to assess the possibility that these two elements may play an interdependent role in regulating genes in hESC. Our results indicate that amongst 15,760 G4/iM-forming locations, only 15% have 5hmCs associated with them. A detailed analysis of G4/iM-forming locations enriched in 5hmC indicates that most of these locations are in genes that are associated with cell differentiation, proliferation, apoptosis and embryogenesis. The library generated from our analysis is an important resource for investigators exploring the interdependence of these DNA features in regulating expression of selected genes in hESC.

DeepMRMP: A new predictor for multiple types of RNA modification sites using deep learning

RNA modification plays an indispensable role in the regulation of organisms. RNA modification site prediction offers an insight into diverse cellular processing. Regarding different types of RNA modification site prediction, it is difficult to tell the most relevant feature combinations from a variant of RNA properties. Thereby, the performance of traditional machine learning based predictors relied on the skill of feature engineering. As a data-driven approach, deep learning can detect optimal feature patterns to represent input data. In this study, we developed a predictor for multiple types of RNA modifications method called DeepMRMP (Multiple Types RNA Modification Sites Predictor), which is based on the bidirectional Gated Recurrent Unit (BGRU) and transfer learning. DeepMRMP makes full use of multiple RNA site modification data and correlation among them to build predictor for different types of RNA modification sites. Through 10-fold cross-validation of the RNA sequences of H. sapiens, M. musculus and S. cerevisiae, DeepMRMP acted as a reliable computational tool for identifying N¹-methyladenosine (m¹A), pseudouridine (Ψ), 5-methylcytosine (m⁵C) modification sites.

Cytosine 5-hydroxymethylation regulated kit gene expression in acute myeloid leukemia

5-methyl cytosine (5mC) can be oxidized to 5-hydroxymethyl cytosine (5hmC) under the action of TET protein family, and 5hmC plays important roles in the pathogenesis of various tumors including acute myeloid leukemia (AML). In this study, we evaluated the role of 5mC and 5hmC levels in HL60 AML cells and bone marrow samples from AML patients for KIT gene expression to analyze 5hmC level in AML pathogenesis. Results showed that the expression and 5hmC level increased significantly of the KIT gene but the change of its 5mC level was not obvious after being treated by decitabine (DAC) in HL60 cells. IDH1 and IDH2 expression increased followed by increased KIT 5hmC level. In AML patients with IDH1 or IDH2 mutation, KIT expression and 5hmC were much lower than in those without mutation. The study indicated that the expression of KIT gene was regulated by 5hmC level in HL60 cells, and the 5hmC level was regulated by IDH1 and IDH2.

Electron Microscope Detection of 5-Methylcytosine on DNA and RNA

5-Methylcytosine is the major epigenetic modification occurring on DNA. It is known to be involved not only in gene expression regulation but also in the control of chromatin structure. However, this modification is also found on different types of RNA, including mRNA. Generally, biomolecular techniques are applied for studying the epigenetic profile of nucleic acids. Here, we describe the ultrastructural detection of 5-methylcytosine as an unusual approach to localize this modification on chromatin regions and/or RNA single molecules. This tool requires a careful sample preparation to preserve antigen epitopes that will be revealed immunocytochemically by a specific anti-5-methylcytosine antibody. The multiple staining procedures that can be adopted allow the identification of both DNA or RNA. A semiquantitative analysis can also be carried out.

Transcriptome-Wide Mapping 5-Methylcytosine by m5C RNA Immunoprecipitation Followed by Deep Sequencing in Plant

Transcriptome-wide mapping RNA modification is crucial to understand the distribution and function of RNA modifications. Here, we describe a protocol to transcriptome-wide mapping 5-methylcytosine (m⁵C) in plant, by a RNA immunoprecipitation followed by deep sequencing (m⁵C-RIP-seq) approach. The procedure includes RNA extraction, fragmentation, RNA immunoprecipitation, and library construction.

Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood

DNA methylation at cytosine-phosphate-guanine (CpG) dinucleotides changes as a function of age in humans and animal models, a process that may contribute to chronic disease development. Recent studies have investigated the role of an oxidized form of DNA methylation - 5-hydroxymethylcytosine (5hmC) - in the epigenome, but its contribution to age-related DNA methylation remains unclear. We tested the hypothesis that 5hmC changes with age, but in a direction opposite to 5-methylcytosine (5mC), potentially playing a distinct role in aging. To characterize epigenetic aging, genome-wide 5mC and 5hmC were measured in longitudinal blood samples (2, 4, and 10 months of age) from isogenic mice using two sequencing methods - enhanced reduced representation bisulfite sequencing and hydroxymethylated DNA immunoprecipitation sequencing. Examining the epigenome by age, we identified 28,196 unique differentially methylated CpGs (DMCs) and 8,613 differentially hydroxymethylated regions (DHMRs). Mouse blood showed a general pattern of epigenome-wide hypermethylation and hypo-hydroxymethylation with age. Comparing age-related DMCs and DHMRs, 1,854 annotated genes showed both differential 5mC and 5hmC, including one gene - Nfic - at five CpGs in the same 250 bp chromosomal region. At this region, 5mC and 5hmC levels both decreased with age. Reflecting these age-related epigenetic changes, Nfic RNA expression in blood decreased with age, suggesting that age-related regulation of this gene may be driven by 5hmC, not canonical DNA methylation. Combined, our genome-wide results show age-related differential 5mC and 5hmC, as well as some evidence that changes in 5hmC may drive age-related DNA methylation and gene expression.

Tet2 Regulates Osteoclast Differentiation by Interacting with Runx1 and Maintaining Genomic 5-Hydroxymethylcytosine (5hmC)

As a dioxygenase, Ten-Eleven Translocation 2 (TET2) catalyzes subsequent steps of 5-methylcytosine (5mC) oxidation. TET2 plays a critical role in the self-renewal, proliferation, and differentiation of hematopoietic stem cells, but its impact on mature hematopoietic cells is not well-characterized. Here we show that Tet2 plays an essential role in osteoclastogenesis. Deletion of Tet2 impairs the differentiation of osteoclast precursor cells (macrophages) and their maturation into bone-resorbing osteoclasts in vitro. Furthermore, Tet2-/- mice exhibit mild osteopetrosis, accompanied by decreased number of osteoclasts in vivo. Tet2 loss in macrophages results in the altered expression of a set of genes implicated in osteoclast differentiation, such as Cebpa, Mafb, and Nfkbiz. Tet2 deletion also leads to a genome-wide alteration in the level of 5-hydroxymethylcytosine (5hmC) and altered expression of a specific subset of macrophage genes associated with osteoclast differentiation. Furthermore, Tet2 interacts with Runx1 and negatively modulates its transcriptional activity. Our studies demonstrate a novel molecular mechanism controlling osteoclast differentiation and function by Tet2, that is, through interactions with Runx1 and the maintenance of genomic 5hmC. Targeting Tet2 and its pathway could be a potential therapeutic strategy for the prevention and treatment of abnormal bone mass caused by the deregulation of osteoclast activities.

Copper induces expression and methylation changes of early development genes in Crassostrea gigas embryos

Copper contamination is widespread along coastal areas and exerts adverse effects on marine organisms such as mollusks. In the Pacific oyster, copper induces severe developmental abnormalities during early life stages; however, the underlying molecular mechanisms are largely unknown. This study aims to better understand whether the embryotoxic effects of copper in Crassostrea gigas could be mediated by alterations in gene expression, and the putative role of DNA methylation, which is known to contribute to gene regulation in early embryo development. For that purpose, oyster embryos were exposed to 4 nominal copper concentrations (0.1, 1, 10 and 20 μg L^-1 Cu²⁺) during early development assays. Embryotoxicity was monitored through the oyster embryo-larval bioassay at the D-larva stage 24 h post fertilization (hpf) and genotoxicity at gastrulation 7 hpf. In parallel, the relative expression of 15 genes encoding putative homeotic, biomineralization and DNA methylation proteins was measured at three developmental stages (3 hpf morula stage, 7 hpf gastrula stage, 24 hpf D-larvae stage) using RT-qPCR. Global DNA content in methylcytosine and hydroxymethylcytosine were measured by HPLC and gene-specific DNA methylation levels were monitored using MeDIP-qPCR. A significant increase in larval abnormalities was observed from copper concentrations of 10 μg L^-1, while significant genotoxic effects were detected at 1 μg L^-1 and above. All the selected genes presented a stage-dependent expression pattern, which was impaired for some homeobox and DNA methylation genes (Notochord, HOXA1, HOX2, Lox5, DNMT3b and CXXC-1) after copper exposure. While global DNA methylation (5-methylcytosine) at gastrula stage didn't show significant changes between experimental conditions, 5-hydroxymethylcytosine, its degradation product, decreased upon copper treatment. The DNA methylation of exons and the transcript levels were correlated in control samples for HOXA1 but such a correlation was diminished following copper exposure. The methylation level of some specific gene regions (HoxA1, Hox2, Engrailed2 and Notochord) displayed changes upon copper exposure. Such changes were gene and exon-specific and no obvious global trends could be identified. Our study suggests that the embryotoxic effects of copper in oysters could involve homeotic gene expression impairment possibly by changing DNA methylation levels.

Epigenetics: DNA Methylation Analysis in Esophageal Adenocarcinoma

The aberrant DNA methylation has been noted to occur at promoter of tumor suppressor, cell adhesion, DNA repair, and other growth regulating genes during the progression of nonneoplastic esophageal mucosa to Barrett esophagus to esophageal adenocarcinoma. Methylation-mediated silencing of individual gene or concurrent loss of a number of genes plays crucial roles in dysplasia-metaplasia-neoplasia sequence of esophageal adenocarcinoma. In addition, promoter methylation of genes had shown significant prognostic potential in patients with esophageal adenocarcinoma. Thus, determination of methylation status of genes of interest can be used as a molecular marker for risk stratification and/or better prognosis of patients with esophageal adenocarcinoma. There are a number of methods including bead array, PCR and sequencing, pyrosequencing, methylation-specific PCR, and PCR with high-resolution melt curve available to determine the methylation status of particular gene of interest. Herein, we describe the polymerase chain reaction followed by sequencing-based protocol for identifying DNA methylation status in esophageal adenocarcinoma.

Reversible DNA-Protein Cross-Linking at Epigenetic DNA Marks

5-Formylcytosine (5fC) is an endogenous DNA modification frequently found within regulatory elements of mammalian genes. Although 5fC is an oxidation product of 5-methylcytosine (5mC), the two epigenetic marks show distinct genome-wide distributions and protein affinities, suggesting that they perform different functions in epigenetic signaling. A unique feature of 5fC is the presence of a potentially reactive aldehyde group in its structure. Herein, we show that 5fC bases in DNA readily form Schiff-base conjugates with Lys side chains of nuclear proteins in vitro and in vivo. These covalent protein-DNA complexes are reversible (t1/2 =1.8 h), suggesting that they contribute to transcriptional regulation and chromatin remodeling. On the other hand, 5fC-mediated DNA-protein cross-links, if present at replication forks or actively transcribed regions, may interfere with DNA replication and transcription.

APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA

AID/APOBEC family enzymes are best known for deaminating cytosine bases to uracil in single-stranded DNA, with characteristic sequence preferences that can produce mutational signatures in targets such as retroviral and cancer cell genomes. These deaminases have also been proposed to function in DNA demethylation via deamination of either 5-methylcytosine (mC) or TET-oxidized mC bases (ox-mCs), which include 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. One specific family member, APOBEC3A (A3A), has been shown to readily deaminate mC, raising the prospect of broader activity on ox-mCs. To investigate this claim, we developed a novel assay that allows for parallel profiling of activity on all modified cytosines. Our steady-state kinetic analysis reveals that A3A discriminates against all ox-mCs by >3700-fold, arguing that ox-mC deamination does not contribute substantially to demethylation. A3A is, by contrast, highly proficient at C/mC deamination. Under conditions of excess enzyme, C/mC bases can be deaminated to completion in long DNA segments, regardless of sequence context. Interestingly, under limiting A3A, the sequence preferences observed with targeting unmodified cytosine are further exaggerated when deaminating mC. Our study informs how methylation, oxidation, and deamination can interplay in the genome and suggests A3A's potential utility as a biotechnological tool to discriminate between cytosine modification states.

Structure and Function of TET Enzymes

Mammalian DNA methylation mainly occurs at the carbon-C5 position of cytosine (5mC). TET enzymes were discovered to successively oxidize 5mC to 5-hydromethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). TET enzymes and oxidized 5mC derivatives play important roles in various biological and pathological processes, including regulation of DNA demethylation, gene transcription, embryonic development, and oncogenesis. In this chapter, we will discuss the discovery of TET-mediated 5mC oxidation and the structure, function, and regulation of TET enzymes.

Oxidized C5-methyl cytosine bases in DNA: 5-Hydroxymethylcytosine; 5-formylcytosine; and 5-carboxycytosine

Recent reports suggest that the Tet enzyme family catalytically oxidize 5-methylcytosine in mammalian cells. The oxidation of 5-methylcytosine can result in three chemically distinct species - 5-hydroxymethylcytsine, 5-formylcytosine, and 5-carboxycytosine. While the base excision repair machinery processes 5-formylcytosine and 5-carboxycytosine rapidly, 5-hydroxymethylcytosine is stable under physiological conditions. As a stable modification 5-hydroxymethylcytosine has a broad range of functions, from stem cell pluriopotency to tumorigenesis. The subsequent oxidation products, 5-formylcytosine and 5-carboxycytosine, are suggested to be involved in an active DNA demethylation pathway. This review provides an overview of the biochemistry and biology of 5-methylcytosine oxidation products.

Raman spectroscopy and quantum-mechanical analysis of tautomeric forms in cytosine and 5-methylcytosine on gold surfaces

Spectral differences between cytosine (Cyt) and 5-methylcytosine (5MC) were investigated by means of Raman spectroscopy with a combination of density functional theory (DFT) calculations. Surface-enhanced Raman scattering (SERS) revealed discriminating peaks of 5MC from those of Cyt upon adsorption on gold nanoparticles (AuNPs). Among the notable features, the multiple bands between 850 and 700cm^-1 for the ring-breathing modes of 5MC and Cyt could be correlated well with the simulated spectra based on the DFT calculations of the adsorbates on the gold cluster atoms. The relative energetic stabilities of the enol/keto and the amino/imino tautomeric forms of Cyt and 5MC have been estimated using DFT calculations, before and after binding six atom gold clusters. Among the six tautomeric forms, the 7H keto amino and the 4H imino trans forms are expected to be predominant in binding gold atoms, whereas the enol trans/cis conformers would coexist in the free gas phase. Our approach may provide useful theoretical guidelines for identifying 5MC from Cyt by analyzing Raman spectra on gold surfaces on the basis of quantum-mechanical calculations.

Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

BACKGROUND

Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes.

RESULTS

We have carried out an unbiased global analysis of m5C in total and nuclear poly(A) RNA of mouse embryonic stem cells and murine brain. We show that there are intriguing differences in these samples and cell compartments with respect to the degree of methylation, functional classification of methylated transcripts, and position bias within the transcript. Specifically, we observe a pronounced accumulation of m5C sites in the vicinity of the translational start codon, depletion in coding sequences, and mixed patterns of enrichment in the 3' UTR. Degree and pattern of methylation distinguish transcripts modified in both embryonic stem cells and brain from those methylated in either one of the samples. We also analyze potential correlations between m5C and micro RNA target sites, binding sites of RNA binding proteins, and N6-methyladenosine.

CONCLUSION

Our study presents the first comprehensive picture of cytosine methylation in the epitranscriptome of pluripotent and differentiated stages in the mouse. These data provide an invaluable resource for future studies of function and biological significance of m5C in mRNA in mammals.

Transcriptome-Wide Detection of 5-Methylcytosine by Bisulfite Sequencing

While low-throughput RNA bisulfite sequencing is the method of choice to assess the methylation status of specific cytosines in candidate RNAs, the combination of bisulfite treatment of RNA with today's high-throughput sequencing techniques opens the door to methylation studies at nucleotide resolution on a transcriptome-wide scale. Below we describe a protocol for the transcriptome-wide analysis of total or fractionated poly(A)RNA in cells and tissues. Although the nature of the bisulfite sequencing protocol makes it comparably easy to translate from a low to a high-throughput approach, several critical points require attention before starting such a project. We describe a step-by-step protocol for planning and performing the experiment and analyzing the data.

Automated Chemical Solid-Phase Synthesis and Deprotection of 5-Hydroxymethylcytosine-Containing RNA

5-Hydroxymethylcytosine is an epigenetic base modification that is part of the demethylation pathway of 5-methylcytosine in DNA. 5-Methylcytosine is iteratively oxidized to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine by enzymes of the TET protein family. Since the discovery of 5-hydroxymethylcytosine also in RNA its role in regulatory processes and metabolism remains elusive. To gain more insight into the function of RNA containing 5-hydroxymethylcytidine, innovative and interdisciplinary approaches are required. In this context, synthetic oligoribonucleotides containing 5-hyroxymethylcytidine are an inevitable tool. Therefore, in this chapter, we present the efficient synthesis of RNA oligonucleotides containing 5-hydroxymethylcytosine by solid-phase synthesis. The incorporation of the modified cytosine derivative into RNA is compatible with standard phosphoramidite-based synthesis procedures of oligoribonucleotides.

Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions

5-Hydroxymethylcytosine (5hmC) is an epigenetic marker that has recently been shown to promote homologous recombination (HR). In this study, we determine the effects of 5hmC on the structure, thermodynamics, and conformational dynamics of the Holliday junction (the four-stranded DNA intermediate associated with HR) in its native stacked-X form. The hydroxymethyl and the control methyl substituents are placed in the context of an amphimorphic GxCC trinucleotide core sequence (where xC is C, 5hmC, or the methylated 5mC), which is part of a sequence also recognized by endonuclease G to promote HR. The hydroxymethyl group of the 5hmC junction adopts two distinct rotational conformations, with an in-base-plane form being dominant over the competing out-of-plane rotamer that has typically been seen in duplex structures. The in-plane rotamer is seen to be stabilized by a more stable intramolecular hydrogen bond to the junction backbone. Stabilizing hydrogen bonds (H-bonds) formed by the hydroxyl substituent in 5hmC or from a bridging water in the 5mC structure provide approximately 1.5-2 kcal/mol per interaction of stability to the junction, which is mostly offset by entropy compensation, thereby leaving the overall stability of the G5hmCC and G5mCC constructs similar to that of the GCC core. Thus, both methyl and hydroxymethyl modifications are accommodated without disrupting the structure or stability of the Holliday junction. Both 5hmC and 5mC are shown to open the structure to make the junction core more accessible. The overall consequences of incorporating 5hmC into a DNA junction are thus discussed in the context of the specificity in protein recognition of the hydroxymethyl substituent through direct and indirect readout mechanisms.

Preferential 5-Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein

Tet (ten-eleven translocation) family proteins oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), and are suggested to be involved in the active DNA demethylation pathway. In this study, we reconstituted positioned mononucleosomes using CpG-methylated 382 bp DNA containing the Widom 601 sequence and recombinant histone octamer, and subjected the nucleosome to treatment with Tet1 protein. The sites of oxidized methylcytosine were identified by bisulfite sequencing. We found that, for the oxidation reaction, Tet1 protein prefers mCs located in the linker region of the nucleosome compared with those located in the core region.

MEK inhibitor PD0325901 and vitamin C synergistically induce hypomethylation of mouse embryonic stem cells

A rationally selected combination of small-molecule chemicals can affect cell plasticity and fate, suggesting an open chemistry way to manipulate cells to achieve a specific goal. Here we for the first time demonstrate that a combination of vitamin C (Vc) and PD0325901 can achieve about 90% erasure of 5-methylcytosine (5mC) within 5 days (decreasing from 3.2 to ~ 0.3 5mC per 100 C) in mouse embryonic stem cells (ESCs). The hypomethylated level is comparable to that of gonadal primordial germ cells (PGCs), whose pluripotency is closely associated with the global DNA hypomethylation. In contrast, Vc or PD0325901 alone only induces a moderately reduced level of global DNA methylation. Our mechanistic study suggested that PD0325901 elevated expression of Prdm14, which repressed de novo methyltransferase Dnmt3b and its cofactor Dnmt3l at levels of protein, via the mode to eliminate 5mC from de novo synthesis. By further addition of Vc, the oxidation of 5mC as catalyzed by Tet1/Tet2 dioxygenases was significantly increased as manifested by the elevated level of 5-hydroxymethylcytosine. However, by the depletion of Tet1/Tet2, Vc failed to enhance PD0325901-stimulated hypomethylation of ESCs' genomic DNA. Furthermore, mouse ESCs in Vc/PD0325901-supplemented medium show great morphology and pluripotency. Therefore, we demonstrate a novel and synergistic chemical approach for promoting hypomethylation and sustaining pluripotency of ESCs.

Spontaneous Oligomerization of Nucleotide Alternatives in Aqueous Solutions

On early Earth, a primitive polymer that could spontaneously form from likely available precursors may have preceded both RNA and DNA as the first genetic material. Here, we report that heated aqueous solutions containing 5-hydroxymethyluracil (HMU) result in oligomers of uracil, heated solutions containing 5-hydroxymethylcytosine (HMC) result in oligomers of cytosine, and heated solutions containing both HMU and HMC result in mixed oligomers of uracil and cytosine. Oligomerization of hydroxymethylated pyrimidines, which may have been abundant on the primitive Earth, might have been important in the development of simple informational polymers.

Genetic Studies on Mammalian DNA Methyltransferases

Cytosine methylation at the C5-position, generating 5-methylcytosine (5mC), is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80 %) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation levels and patterns are associated with various human diseases, including cancer and developmental disorders. DNA methylation is mediated by three active DNA methyltransferases (Dnmts), namely, Dnmt1, Dnmt3a, and Dnmt3b, in mammals. Over the last two decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and X-chromosome inactivation.

A New Epigenetic Mechanism of Temozolomide Action in Glioma Cells

Temozolomide (TMZ) is an oral alkylating chemotherapeutic agent that prolongs the survival of patients with glioblastoma (GBM). Despite that high TMZ potential, progression of disease and recurrence are still observed. Therefore a better understanding of the mechanism of action of this drug is necessary and may allow more durable benefit from its anti-glioma properties. Using nucleotide post-labelling method and separation on thin-layer chromatography we measured of global changes of 5-methylcytosine (m5C) in DNA of glioma cells treated with TMZ. Although m5C is not a product of TMZ methylation reaction of DNA, we analysed the effects of the drug action on different glioma cell lines through global changes at the level of the DNA main epigenetic mark. The first effect of TMZ action we observed is DNA hypermethylation followed by global demethylation. Therefore an increase of DNA methylation and down regulation of some genes expression can be ascribed to activation of DNA methyltransferases (DNMTs). On the other hand hypomethylation is induced by oxidative stress and causes uncontrolled expression of pathologic protein genes. The results of brain tumours treatment with TMZ suggest the new mechanism of modulation epigenetic marker in cancer cells. A high TMZ concentration induced a significant increase of m5C content in DNA in the short time, but a low TMZ concentration at longer time hypomethylation is observed for whole range of TMZ concentrations. Therefore TMZ administration with low doses of the drug and short time should be considered as optimal therapy.

The hypomethylating agent Decitabine causes a paradoxical increase in 5-hydroxymethylcytosine in human leukemia cells

The USFDA approved "epigenetic drug", Decitabine, exerts its effect by hypomethylating DNA, demonstrating the pivotal role aberrant genome-wide DNA methylation patterns play in cancer ontology. Using sensitive technologies in a cellular model of Acute Myeloid Leukemia, we demonstrate that while Decitabine reduces the global levels of 5-methylcytosine (5mC), it results in paradoxical increase of 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) levels. Hitherto, the only biological mechanism known to generate 5hmC, 5fC and 5caC, involving oxidation of 5mC by members of Ten-Eleven-Translocation (TET) dioxygenase family, was not observed to undergo any alteration during DAC treatment. Using a multi-compartmental model of DNA methylation, we show that partial selectivity of TET enzymes for hemi-methylated CpG dinucleotides could lead to such alterations in 5hmC content. Furthermore, we investigated the binding of TET1-catalytic domain (CD)-GFP to DNA by Fluorescent Correlation Spectroscopy in live cells and detected the gradual increase of the DNA bound fraction of TET1-CD-GFP after treatment with Decitabine. Our study provides novel insights on the therapeutic activity of DAC in the backdrop of the newly discovered derivatives of 5mC and suggests that 5hmC has the potential to serve as a biomarker for monitoring the clinical success of patients receiving DAC.