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Dynamic DNA methylation changes during colorectal oncogenesis with insights from adenoma stages
Overs A, et al.
The dynamics of colorectal epigenetics within the adenoma stages of oncogenesis remain undocumented. In this study, we investigated DNA methylation dynamics in colorectal cancer oncogenesis from non-tumor colon tissue to low-grade, high-grade adenoma and adenocarcinoma. The methylome of 12 low-grade and 19 high-gr...

Independent evaluation of an 11-CpG panel for age estimation in blood
Mie Rath Refn et al.
Highlights A set of 11 CpGs for age prediction was investigated in 148 Danish blood samples. Assay optimization improved coverage and reliability in DNA methylation quantification. The original model developed for UK individuals showed a bias in age predictions in Danes, underestimating ...

COL25A1 and METAP1D DNA methylation are promising liquid biopsy epigenetic biomarkers of colorectal cancer using digital PCR
Alexis Overs et al.
Background Colorectal cancer is a public health issue and was the third leading cause of cancer-related death worldwide in 2022. Early diagnosis can improve prognosis, making screening a central part of colorectal cancer management. Blood-based screening, diagnosis and follow-up of colorectal cancer patients are po...

Direct enzymatic sequencing of 5-methylcytosine at single-baseresolution.
Wang T. et al.
5-methylcytosine (5mC) is the most important DNA modification in mammalian genomes. The ideal method for 5mC localization would be both nondestructive of DNA and direct, without requiring inference based on detection of unmodified cytosines. Here we present direct methylation sequencing (DM-Seq), a bisulfite-free me...

Transfer of blocker-based qPCR reactions for DNA methylation analysisinto a microfluidic LoC system using thermal modeling.
Kärcher J.et al.
Changes in the DNA methylation landscape are associated with many diseases like cancer. Therefore, DNA methylation analysis is of great interest for molecular diagnostics and can be applied, e.g., for minimally invasive diagnostics in liquid biopsy samples like blood plasma. Sensitive detection of local methylation,...

Development of a quantitative methylation-specific droplet digital PCRassay for detecting Dickkopf-related protein 3.
Araki K. et al.
OBJECTIVE: The detection and monitoring of DNA methylation status in circulating tumor cell DNA (ctDNA) provides critical insights into cancer diagnosis and progression. The methylation status of the Dickkopf-related protein 3 (DKK3) promoter region is correlated with the metastasis and recurrence of multiple cancer...

Development and inter-laboratory validation of the VISAGE enhanced toolfor age estimation from semen using quantitative DNA methylationanalysis.
Heidegger A. et al.
The analysis of DNA methylation has become an established method for chronological age estimation. This has triggered interest in the forensic community to develop new methods for age estimation from biological crime scene material. Various assays are available for age estimation from somatic tissues, the majority f...

Differential epigenetic regulation between the alternative promoters,PRDM1α and PRDM1β, of the tumour suppressor gene PRDM1 in humanmultiple myeloma cells.
Romero-García, Raquel and Gómez-Jaramillo, Laura and Mateos, Rosa Maríaand Jiménez-Gómez, Gema and Pedreño-Horrillo, Nuria and Foncubierta,Esther and Rodríguez-Gutiérrez, Juan Francisco and Garzón, Sebastiánand Mora-López, Francisco and Rodríguez, Carm
Multiple myeloma (MM) is a B-cell neoplasm that is characterized by the accumulation of malignant plasma cells in the bone marrow. The transcription factor PRDM1 is a master regulator of plasma cell development and is considered to be an oncosuppressor in several lymphoid neoplasms. The PRDM1β isoform is an alt...

Recombination may occur in the absence of transcription in the immunoglobulin heavy chain recombination centre.
Oudinet C, Braikia FZ, Dauba A, Khamlichi AA
Developing B cells undergo V(D)J recombination to generate a vast repertoire of Ig molecules. V(D)J recombination is initiated by the RAG1/RAG2 complex in recombination centres (RCs), where gene segments become accessible to the complex. Whether transcription is the causal factor of accessibility or whether it is a ...

Developmental regulation of DNA cytosine methylation at the immunoglobulin heavy chain constant locus.
Oudinet C, Braikia FZ, Dauba A, Santos JM, Khamlichi AA
DNA cytosine methylation is involved in the regulation of gene expression during development and its deregulation is often associated with disease. Mammalian genomes are predominantly methylated at CpG dinucleotides. Unmethylated CpGs are often associated with active regulatory sequences while methylated CpGs are of...

Reproducibility of methylated CpG typing with the Illumina MiSeq
Kampmann M.L. et al.
DNA methylation patterns may be used for identification of body fluids and for age estimation of human individuals. We evaluated some of the challenges and pitfalls of studying methylated CpG sites. We compared the methylated CpG analysis of two different methods 1) massively parallel sequencing (MPS) using the Il...

Faithful SGCE imprinting in iPSC-derived cortical neurons: an endogenous cellular model of myoclonus-dystonia
Grütz K. et al.
In neuropathology research, induced pluripotent stem cell (iPSC)-derived neurons are considered a tool closely resembling the patient brain. Albeit in respect to epigenetics, this concept has been challenged. We generated iPSC-derived cortical neurons from myoclonus-dystonia patients with mutations (W100G and R102X)...

Regulation of Hox orthologues in the oyster Crassostrea gigas evidences a functional role for promoter DNA methylation in an invertebrate.
Saint-Carlier E, Riviere G
DNA methylation within promoter regions (PRDM) controls vertebrate early gene transcription and thereby development, but is neglected outside this group. However, epigenetic features in the oyster Crassostrea gigas suggest functional significance of PDRM in invertebrates. To investigate this, reporter constructs con...