Base-Flipping Propensities of Unmethylated, Hemimethylated, and Fully Methylated CpG Sites

Base Dynamics in the HhaI Protein Binding Site

Protein-DNA interactions play an important role in numerous biological functions within the living cell. In many of these interactions, the DNA helix is significantly distorted upon protein-DNA complex formation. The HhaI restriction-modification system is one such system, where the methylation target is flipped out of the helix when bound to the methyltransferase. However, the base flipping mechanism is not well understood. The dynamics of the binding site of the HhaI methyltransferase and endonuclease (underlined) within the DNA oligomer [d(G1A2T3A4G5C6G7C8T9A10T11C12)]2 are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs deuterated on the base of nucleotides within and flanking the [5'-GCGC-3']2 sequence indicate that all of these positions are structurally flexible. Previously, conformational flexibility within the phosphodiester backbone and furanose ring within the target sequence has been observed and hypothesized to play a role in the distortion mechanism. However, whether that distortion was occurring through an active or passive mechanism remained unclear. These NMR data demonstrate that although the [5'-GCGC-3']2 sequence is dynamic, the target cytosine is not passively flipping out of the double-helix on the millisecond-picosecond time scale. Additionally, although previous studies have shown that both the furanose ring and phosphodiester backbone experience a change in dynamics upon methylation, which may play a role in recognition and cleavage by the endonuclease, our observations here indicate that methylation has no effect on the dynamics of the base itself.

All-or-None Selectivity in Probing Polarity-Determined Trinucleotide Repeat Foldings with a Parity Resolution by a Beyond-Size-Matching Ligand

Abnormal amplification of trinucleotide repeats (TNRs) is associated with neurodegenerative diseases by forming a particular hairpin bulge. It is well known that the polarity and parity of TNRs can regulate the formed hairpin structures. Therefore, there is a great challenge to efficiently discriminate the hairpin structures of TNRs with substantial selectivity. Herein, we developed a fluorescent ligand of pseudohypericin (Pse) with a beyond-size-matching (BSM) geometry to selectively sense hairpin structures of GTC and CTG TNRs. The GTC hairpin structures can bind with Pse dominantly at extreme T-T mismatches by the virtue of their most extrahelical conformations, while there is no binding event to occur with the polarity-inverted counterpart CTG hairpin structures because of the limited space provided by their intrahelical T-T mismatches. In addition, this all-or-none response with the polarity-dependent folding (PoDF) is independent of the length of these TNRs. Interestingly, the parity-dependent folding (PaDF) of GTC hairpin structures can also be resolved. Besides pure TNRs, the competency of this BSM ligand to sense the PoDF and PaDF effects was also generalized to DNAs with TNRs occurring at loop and stem end regions. To our knowledge, this is the first experimental observation with the state-of-the-art performance over the fluorescence measurement of PoDF and PaDF in TNRs. Our work provides an expedient way to elucidate the TNR folding by designing ligands having BSM features.

LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data

BACKGROUND

DNA methylation plays an important role in multiple biological processes that are closely related to human health. The study of DNA methylation can provide an insight into the mechanism behind human health and can also have a positive effect on the assessment of human health status. However, the available sequencing technology is limited by incomplete CpG coverage. Therefore, it is crucial to discover an efficient and convenient method capable of distinguishing between the states of CpG sites. Previous studies focused on identifying methylation states of the CpG sites in single cell, which only evaluated sequence information or structural information.

RESULTS

In this paper, we propose a novel model, LightCpG, which combines the positional features with the sequence and structural features to provide information on the CpG sites at two stages. Next, we used the LightGBM model for training of the CpG site identification, and further utilized sample extraction and merged features to reduce the training time. Our results indicate that our method achieves outstanding performance in recognition of DNA methylation. The average AUC values of our method using the 25 human hepatocellular carcinoma cells (HCC) cell datasets and six human heptoplastoma-derived (HepG2) cell datasets were 0.9616 and 0.9213, respectively. Moreover, the average training times for our method on the HCC and HepG2 datasets were 8.3 and 5.06 s, respectively. Furthermore, the computational complexity of our model was much lower compared with other available methods that detect methylation states of the CpG sites.

CONCLUSIONS

In summary, LightCpG is an accurate model for identifying the DNA methylation status of CpG sites in single cells. Furthermore, three types of feature extraction methods and two strategies used in LightCpG are helpful for other prediction problems.

Deinococcus radiodurans' SRA-HNH domain containing protein Shp (Dr1533) is involved in faithful genome inheritance maintenance following DNA damage

BACKGROUND

Deinococcus radiodurans R1 (DR) survives conditions of extreme desiccation, irradiation and exposure to genotoxic chemicals, due to efficient DNA breaks repair, also through Mn²⁺ protection of DNA repair enzymes.

METHODS

Possible annotated domains of the DR1533 locus protein (Shp) were searched by bioinformatic analysis. The gene was cloned and expressed as fusion protein. Band-shift assays of Shp or the SRA and HNH domains were performed on oligonucleotides, genomic DNA from E. coli and DR. shp knock-out mutant was generated by homologous recombination with a kanamycin resistance cassette.

RESULTS

DR1533 contains an N-terminal SRA domain and a C-terminal HNH motif (SRA-HNH Protein, Shp). Through its SRA domain, Shp binds double-strand oligonucleotides containing 5mC and 5hmC, but also unmethylated and mismatched cytosines in presence of Mn²⁺. Shp also binds to Escherichia coli dcm⁺ genomic DNA, and to cytosine unmethylated DR and E. coli dcm^- genomic DNAs, but only in presence of Mn²⁺. Under these binding conditions, Shp displays DNAse activity through its HNH domain. Shp KO enhanced >100 fold the number of spontaneous mutants, whilst the treatment with DNA double strand break inducing agents enhanced up to 3-log the number of survivors.

CONCLUSIONS

The SRA-HNH containing protein Shp binds to and cuts 5mC DNA, and unmethylated DNA in a Mn²⁺ dependent manner, and might be involved in faithful genome inheritance maintenance following DNA damage.

GENERAL SIGNIFICANCE

Our results provide evidence for a potential role of DR Shp protein for genome integrity maintenance, following DNA double strand breaks induced by genotoxic agents.

Dynamics of a DNA Mismatch Site Held in Confinement Discriminate Epigenetic Modifications of Cytosine

The identification and discrimination of four epigenetic modifications to cytosine in the proposed active demethylation cycle is demonstrated at the single-molecule level, without the need for chemical pretreatment or labeling. The wild-type protein nanopore α-hemolysin is used to capture individual DNA duplexes containing a single cytosine-cytosine mismatch. The mismatch is held at the latch constriction of α-hemolysin, which is used to monitor the kinetics of base-flipping at the mismatch site. Base-flipping and the subsequent interactions between the DNA and the protein are dramatically altered when one of the cytosine bases is replaced with methyl-, hydroxymethyl-, formyl-, or carboxylcytosine. As well as providing a route to single-molecule analysis of important epigenetic markers in DNA, our results provide important insights into how the introduction of biologically relevant, but poorly understood, modifications to cytosine affect the local conformational dynamics of a DNA duplex in a confined environment.

Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors

C5-methylation of cytosines is strongly correlated with UV-induced mutations detected in skin cancers. Mutational hot-spots appearing at TCG sites are due to the formation of pyrimidine cyclobutane dimers (CPDs). The present study, performed for the model DNA duplex (TCGTA)3·(TACGA)3 and the constitutive single strands, examines the factors underlying the effect of C5-methylation on pyrimidine dimerization at TCG sites. This effect is quantified for the first time by quantum yields ϕ. They were determined following irradiation at 255, 267, and 282 nm and subsequent photoproduct analysis using HPLC coupled to mass spectrometry. C5-methylation leads to an increase of the CPD quantum yield up to 80% with concomitant decrease of that of pyrimidine(6-4) pyrimidone adducts (64PPs) by at least a factor of 3. The obtained ϕ values cannot be explained only by the change of the cytosine absorption spectrum upon C5-methylation. The conformational and electronic factors that may affect the dimerization reaction are discussed in light of results obtained by fluorescence spectroscopy, molecular dynamics simulations, and quantum mechanical calculations. Thus, it appears that the presence of an extra methyl on cytosine affects the sugar puckering, thereby enhancing conformations of the TC step that are prone to CPD formation but less favorable to 64PPs. In addition, C5-methylation diminishes the amplitude of conformational motions in duplexes; in the resulting stiffer structure, ππ* excitations may be transferred from initially populated exciton states to reactive pyrimidines giving rise to CPDs.

Relaxed specificity of prokaryotic DNA methyltransferases results in DNA site-specific modification of RNA/DNA heteroduplexes

RNA/DNA hybrid duplexes regularly occur in nature, for example in transcriptional R loops. Their susceptibility to modification by DNA-specific or RNA-specific enzymes is, thus, a biologically relevant question, which, in addition, has possible biotechnological implications. In this study, we investigated the activity of four isospecific DNA methyltransferases (M.EcoVIII, M.LlaCI, M.HindIII, M.BstZ1II) toward an RNA/DNA duplex carrying one 5'-AAGCUU-3'/3'-TTCGAA-5' target sequence. The analyzed enzymes belong to the β-group of adenine N6-methyltransferases and recognize the palindromic DNA sequence 5'-AAGCTT-3'/3'-TTCGAA-5'. Under standard conditions, none of these isospecific enzymes could detectibly methylate the RNA/DNA duplex. However, the addition of agents that generally relax specificity, such as dimethyl sulfoxide (DMSO) and glycerol, resulted in substantial methylation of the RNA/DNA duplex by M.EcoVIII and M.LlaCI. Only the DNA strand of the RNA/DNA duplex was methylated. The same was not observed for M.HindIII or M.BstZ1II. This is, to our knowledge, the first report that demonstrates such activity by prokaryotic DNA methyltransferases. Possible applications of these findings in a laboratory practice are also discussed.

Dual base-flipping of cytosines in a CpG dinucleotide sequence

Simultaneous flipped-out conformation of two neighboring bases on opposite strands of DNAs has been observed in several X-ray structures. It has also been detected for two cytosines on opposite strands in different contexts of CpG sites. In this paper, we study by MD simulations the dual base flipping of the two cytosines in hemi-methylated CpG site. We calculate the potential of mean force of flipping-out the unmethylated cytosine in three model systems. The first is for DNA bound to the regulatory protein UHRF1. In this case, the methyl-cytosine on the complementary strand is flipped-out into the binding pocket of the SRA domain of the protein. The other two systems are for unbound DNAs in which the methyl-cytosine is either intra-helical or extra-helical. We find that when the methyl-cytosine is flipped-out it is easier to flip-out the other (unmethylated) cytosine on the opposite strand by about 14-16kJ/mol. This lower penalty for dual-base flipping is observed for both the bound and unbound states of the DNA. Analyses of the hydrogen bond network and stacking interactions within the CpG site indicate that the lower penalty is due to stabilization of the dual-base flipped-out conformation via interactions involving the orphan guanines. The results presented in this paper suggest that the extra-helical conformation of the methyl-cytosine recognized by UHRF1 can facilitate the base-flipping process of the target cytosine to be methylated by Dnmt1.