3-D Chromatin Remodeling & Replication

Our lab investigates local and spatial re-organization of chromatinized replication forks in response to replication stress. We use a combination of super-resolution

imaging, genomics and proteomics based approaches to understand the complex mechanisms of chromatin regulation in maintaining replication fork stability in normal as well as cancer cells.

We uses mammalian system (human/mouse cell lines, tumor organoids and patient tumor samples including PDX) to study chromatin organization upon replication stress.

Our study unveils the hidden truth: de novo heterochromatin forms at all replication forks during replication stress, all thanks to our incredible single molecule ChromStretch technology to unveil this incredible phenomenon. This study uncoveres a checkpoint-regulated pathway where the "writers" EHMT2/G9a & Suv39h1 were revealed as key players in de novo priming of H3K9me marks at stressed forks. Chromatin compaction becomes the guardian shield of underlying DNA upon replication stress. Furthermore, upon stress release, the "eraser" JMJD1A/KDM3A steps in, facilitating heterochromatin disassembly from the replication forks. Canonical fork restart accelerates, preserving genome stability.

Dynamic de novo heterochromatin assembly & disassembly at replication forks upon replication stress

Gaggioli et al, 2023, Nature Cell Biology

Innovative technology development to study the dynamics of histone modifications at forks

We are further investigating the role of epigenetic signatures and chromatin modifiers in initiating the chromatin signaling cascade in response to replication stress and their checkpoint-dependent regulation in distinguishing the two states of fork dynamics, using our innovative super-resolution microscopy-based and proteomics technologies

(ChromStretch technology INTERNATIONAL PATENT #PCT/NL2023/050120)

3-D chromatin re-organization upon replication stress

Spatial re-organization of replication forks: We are investigating how local and spatial re-organization of replicating chromatin regulates replication stress response in cells. We are continuously developing novel tools to observe the 3-D chromatin organization using specialized single molecule to next-generation deep sequencing-based technologies.

R-loop homeostasis in vicinity of forks

We are studying the enigmatic role of RNA:DNA hybrids in facilitating epigenetic landscape and the potential role of replication fork preservation pathways, and the assisting Chro-Mates (chromatin modifiers and remodelers) in their removal further avoiding replication‐transcription conflicts (Review: Uruci et al. 2021, International Journal of Molecular Sciences).

Lo et al, 2021, Science Advances

Uruci et al. 2021, IJMS

Nucleosome remodeling at forks

We have described a hitherto unknown mechanism, by which the SWI/SNF chromatin remodeler, SMARCAD1 stabilizes active replication forks, independently of its role in DNA repair, that is essential to maintaining resistance towards replication poisons. We further show how fork protection-challenged BRCA1-deficient naïve- or chemoresistant tumors require SMARCAD1-mediated active fork stabilization to maintain unperturbed fork progression essential for tumor (cells and organoids) viability (Lo et al. 2021, Science Advances). We are investigating role of different nucleosome remodelers that act specifically either at active vs stalled replication forks to maintain fork stability.

Positions available

- we are looking for highly motivated PhDs and Postdoc candidates

Recquirement  : background of molecular biology / life sciences or equivalent Masters program

Postdoc candidates preferably skilled with genomics and cell biology approaches