Journal: Osteoarthritis and Cartilage Open

Article Title: Peripheral blood DNA methylation changes are predictive of incident radiographic osteoarthritis development: Data and biospecimens from the osteoarthritis initiative

doi: 10.1016/j.ocarto.2025.100692

Figure Lengend Snippet: Receiver operator characteristic curves for 40 cycles of Monte Carlo cross validation of generalized logistic models. (A) Models developed using imputed peripheral blood cellular composition data alone; (B) Full methylation models trained on the entire DNA methylation dataset; results from model testing of each round of cross-validation, tested on validation data unseen during model development (C) Parsimonious model performance after dataset reduced to 21 CpG sites most frequently chosen during full model development, tested on validation data. (D) Relative contributions to model predictions of each of the 21 CpG sites included in parsimonious models. (E) Model accuracy by time to incident radiographic OA development.

Article Snippet: For methylation analysis, 500 ng of DNA was treated with sodium bisulfite (EZ DNA methylation kit, Zymo) and loaded onto Illumina Infinium EPICv2 methylation arrays.

Techniques: Biomarker Discovery, Methylation, DNA Methylation Assay

Journal: EMBO Reports

Article Title: DNA methylation at retrotransposons protects the germline by preventing NRF1-mediated activation

doi: 10.1038/s44319-025-00526-1

Figure Lengend Snippet: ( A ) Scheme showing percentage of mice testes cells with different age classified into developmental stages of Spg, Spc, spermatids and somatic cells. Meiosis I with Leptotene (L), Zygotene (Z), Pachytene (P) and Diplotene stages as well as Meiosis II are depicted in Spc. This image is modified from (Ernst et al, ). ( B ) Scheme showing the DNA methylation dynamics of wild-type and Dnmt3C KO/KO mouse germ cells across spermatogenesis. ( C ) Representative immunostaining from biological duplicates of LINE1-ORF1p and TRA98 (germ cell marker) on cryosections of wild-type (WT) and Dnmt3C KO/KO testes at specific developmental time points centered on one representative germ cell nucleus. Zoom10, Scale bar, 5 µm. ( D ) Box plots displaying the mean intensity of LINE1-ORF1p quantification from three nuclei as in ( C ). Error bars represent 1.5 times the interquartile range (IQR) above and below the median, where IQR is defined as the difference between the third and first quartiles.

Article Snippet: Methylation levels were checked by bisulfite conversion (EZ DNA Methylation Quick kit, D5005), amplification, cloning into pMiniTTM 2.0 Vectors (NEB, E1203S), followed by transformation and Sanger sequencing of ten clones per probe (Fig. ).

Techniques: Modification, DNA Methylation Assay, Immunostaining, Marker

Journal: EMBO Reports

Article Title: DNA methylation at retrotransposons protects the germline by preventing NRF1-mediated activation

doi: 10.1038/s44319-025-00526-1

Figure Lengend Snippet: ( A ) Illustration of the bait sequence used from the IAP LTR1a promoter, and the corresponding scrambled control used in the DNA-pulldown experiment. CpG sites, which are identical between IAP LTR1a and the scrambled control, are highlighted with a yellow frame. The sequences corresponding to random primers used for amplification and biotinylation, are shown in gray. ( B ) as in ( A ) for the LINE1MdT promoter and its scrambled control. ( C ) Bisulfite cloning results for IAPme, IAPnon, CONTme, and CONTnon, represented as black/white circle diagrams, with black circles indicating methylated cytosines and white I indicating unmethylated. Each column is a CpG site, and each row represents a biological replicate (n=10). Average methylation percentages and bisulfite conversion rates are indicated at the bottom. ( D ) As in ( C ) for LINE1me, LINE1non, CONTme and CONTnon. ( E ) Representative track example of CREB1 and NRF1 CUT&Tag example at bona fide targets Pdgfb and Ccdc155 , respectively. ( F ) Heatmaps displaying normalized coverage and metaplots showing mean enrichment of CREB1 and NRF1 at DNMT3C targets in wild-type and Dnmt3C KO/KO Spermatogonia (Spg) merged from two biological replicates.

Article Snippet: Methylation levels were checked by bisulfite conversion (EZ DNA Methylation Quick kit, D5005), amplification, cloning into pMiniTTM 2.0 Vectors (NEB, E1203S), followed by transformation and Sanger sequencing of ten clones per probe (Fig. ).

Techniques: Sequencing, Control, Amplification, Cloning, Methylation

Journal: EMBO Reports

Article Title: DNA methylation at retrotransposons protects the germline by preventing NRF1-mediated activation

doi: 10.1038/s44319-025-00526-1

Figure Lengend Snippet: ( A ) Schematic representation of LINE1 and IAP expression dynamics in Dnmt3C KO/KO (green) and Dnmt3C WT/WT (gray) throughout spermatogenesis. ( B ) A chromatin switch from bivalent H3K27me3-H3K4me3 (spermatogonia) to active H3K27ac-H3K4me3 (spermatocytes). Unmethylated LINE1 elements switch from a bivalent state (low transcriptional, poised for reactivation in meiosis) to an active state in spermatocytes (high transcriptional output). ( C ) Model of IAP regulation in spermatogonia. In Dnmt3C WT/WT , IAPs are silenced by DNA methylation and H3K9me3; Low/No NRF1 occupancy; No IAP transcription and translation. In Dnmt3C KO/KO , IAPs are activated by the absence of DNA methylation and presence of H3K4me3; Higher NRF1 occupancy; High IAP transcription and translation. In dKO ( Dnmt3C KO/KO ; Nrf1 cKO/KO ), unmethylated IAPs are silenced by the loss of NRF1 trans-activator; Low/No IAP transcription no IAP translation.

Article Snippet: Methylation levels were checked by bisulfite conversion (EZ DNA Methylation Quick kit, D5005), amplification, cloning into pMiniTTM 2.0 Vectors (NEB, E1203S), followed by transformation and Sanger sequencing of ten clones per probe (Fig. ).

Techniques: Expressing, DNA Methylation Assay