Emerging methylation-based approaches in microbiome engineering

C Won, SS Yim - Biotechnology for Biofuels and Bioproducts, 2024 - Springer
Bacterial epigenetics, particularly through DNA methylation, exerts significant influence over
various biological processes such as DNA replication, uptake, and gene regulation in …

The epigenetic landscape in intestinal stem cells and its deregulation in colorectal cancer

AEM Larue, Y Atlasi - Stem Cells, 2024 - academic.oup.com
Epigenetic mechanisms play a pivotal role in controlling gene expression and cellular
plasticity in both normal physiology and pathophysiological conditions. These mechanisms …

Spatial multi-omics in whole skeletal muscle reveals complex tissue architecture

C Martínez Mir, P Pisterzi, I De Poorter, M Rilou… - Communications …, 2024 - nature.com
Myofibers are large multinucleated cells that have long thought to have a rather simple
organization. Single-nucleus transcriptomics, spatial transcriptomics and spatial …

[HTML][HTML] Paraburkholderia tropica Primes a Multilayered Transcriptional Defense Response to the Nematode Meloidogyne spp. in Tomato

C González-Cardona, WR López, J Jovel… - International Journal of …, 2024 - mdpi.com
Meloidogyne causes a devastating disease known as root-knot that affects tomatoes and
other cash crops worldwide. Conversely, Paraburkholderia tropica has proven beneficial in …

Methylome profiling of cell-free DNA during the early life course in (un) complicated pregnancies using MeD-seq: Protocol for a cohort study embedded in the …

MM van Vliet, S Schoenmakers, RG Boers… - PloS one, 2025 - journals.plos.org
Introduction Placental DNA methylation differences have been associated with timing in
gestation and pregnancy complications. Maternal cell-free DNA (cfDNA) partly originates …

[HTML][HTML] Toward DNA-Based Recording of Biological Processes

H Jang, SS Yim - International Journal of Molecular Sciences, 2024 - mdpi.com
Exploiting the inherent compatibility of DNA-based data storage with living cells, various
cellular recording approaches have been developed for recording and retrieving biologically …

Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation

S Kefalopoulou, PMJ Rullens, KL de Luca, SS de Vries… - BioRxiv, 2023 - biorxiv.org
The regulation of gene expression is governed at multiple levels of chromatin organization.
However, how coordination is achieved remains relatively unexplored. Here we present …

[HTML][HTML] From Genotype to Phenotype: How Enhancers Control Gene Expression and Cell Identity in Hematopoiesis

R Mulet-Lazaro, R Delwel - HemaSphere, 2023 - journals.lww.com
Blood comprises a wide array of specialized cells, all of which share the same genetic
information and ultimately derive from the same precursor, the hematopoietic stem cell …

From Background to Signal: Simultaneously derived Copy Numbers from Methylation-Dependent Sequencing cell-free DNA

DM Hazelaar, RG Boers, JB Boers, V de Weerd… - bioRxiv, 2025 - biorxiv.org
Cell-free DNA (cfDNA) analysis offers a powerful, non-invasive approach to cancer
diagnostics and monitoring by revealing tumor-specific genomic and epigenetic alterations …

The Cellular Origin of the Pulmonary Pericyte

R Rottier, I Sreeram, R Boers, J Boers, B Tan… - 2024 - researchsquare.com
Emerging evidence suggests pericytes play a significant role in various lung diseases.
However, characterizing pericytes remains challenging, impeding our understanding of their …