Biology subjects

Bergamin, E.

Publications and source records attributed to Bergamin, E..

3 recordsLinked to original sources

bioRxiv2026

The DNA demethylase TET1 recognises chromatin via nucleosome engagement of its N-terminal region

TET1 is a DNA demethylase critical for mammalian embryonic development, yet how it is recruited to its chromatin substrate remains poorly understood. Here we identify a previously uncharacterized N-terminal region of TET1 that directly binds nucleosomes and promotes chromatin binding in mouse embryonic stem cells. Robust chromatin association was evidenced by fluorescence recovery after photobleaching during interphase and chromosome retention throughout mitosis. A 2.47 angstroms cryo-EM structure of the TET1-nucleosome complex reveals recognition of the nucleosome acidic patch through a canonical arginine anchor centred on R75, with additional contacts extending along the H2B surface. Biochemical and cellular analyses validate this interaction and demonstrate its contribution to TET1 chromatin engagement. The region is absent from TET2 and TET3 and displays strong conservation within mammals, indicating that direct nucleosome recognition is a specialized feature of TET1. Together, these findings uncover a previously unknown chromatin-binding module in TET1 and establish a structural basis for its interaction with nucleosomes.

molecular biology↗

bioRxiv2025

Stress-Induced Nuclear Import Governs Transcription Recovery after DNA Damage

Genotoxic stress inhibits transcription, generating RNA-DNA hybrid intermediates that promote toxic transcription-replication conflicts (TRCs). Here, we show that genotoxic stress triggers transient Importin-/{beta}1-dependent nuclear import of the mitochondrial exonuclease EXD2 to resolve these conflicts and maintain genome stability. Mechanistically, once imported into the nucleus, EXD2 is recruited to elongation-arrested RNA polymerase II (RNAPII) associated with RNA-DNA hybrids, and its exonuclease activity limits their accumulation, thereby suppressing TRCs. Mutation of a putative EXD2 nuclear localization signal phenocopies disruption of nuclear import, whereas forced nuclear targeting of EXD2 bypasses it. However, sustained nuclear localization of EXD2 leads to mitotic defects, underscoring the importance of its tight spatial regulation. Consistent with a direct role for EXD2 in RNA-DNA hybrid resolution, overexpression of the ribonuclease RNaseH1 compensates for its depletion following DNA damage. Together, our findings introduce the concept of a trafficking-dependent checkpoint that transiently licenses EXD2 nuclease activity in the nucleus in response to genotoxic stress to resolve RNA-DNA hybrid intermediates at stalled RNAPII complexes TeaserStress-triggered nuclear import of EXD2 resolves harmful RNA-DNA hybrids to protect genome stability after DNA damage.

molecular biology↗

bioRxiv2023

BCL7 proteins, metazoan-specific subunits of the mammalian SWI/SNF complex, bind the nucleosome core particle

BCL7 proteins are among the most recently identified subunits of the mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complex and are absent from the unicellular version of the complex. Mutations in BCL7 proteins are associated with different kind of cancers including blood malignancies. The information on the molecular function and on the structure of BCL7 proteins is to date very limited. Here we report that BCL7 proteins directly bind the nucleosome core particle (NCP) and free DNA with high affinity. We demonstrate that BCL7 proteins form defined complexes with the NCP and we identify the conserved N-terminal part of BCL7 proteins as sufficient to nucleosome binding. We further characterize the impact of BCL7 protein mutations reported in cancer patients on NCP binding and show that the R11S driver mutation reduces the affinity for the nucleosome. Our findings clarify the molecular function of BCL7 proteins and help rationalize the impact of cancer-associated mutations.

biochemistry↗