Biology subjects

Wapenaar, H.

Publications and source records attributed to Wapenaar, H..

3 recordsLinked to original sources

bioRxiv2023

The N-terminal region of DNMT3A combines multiple chromatin reading motifs to guide recruitment.

DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns. However, the mechanisms underlying DNMT3A recruitment to and function within different chromatin environments remain unclear. Using a combination of biochemical and structural approaches we find that DNMT3A interacts using multiple interfaces with chromatin; directly binding generic nucleosome features as well as site-specific post-translational histone modifications. The N-terminal region, unique to the DNMT3A1 isoform, is essential for these interactions and stabilises H3K36me2-nucleosome recruitment. Intriguingly, in the same region critical for nucleosome binding we also map a ubiquitylation-dependent recruitment motif (UDR). The UDR binds specifically to ubiquitylated H2AK119, explaining the previously observed recruitment to Polycomb-occupied heterochromatin. A cryo-EM structure of DNMT3A1-DNMT3L with a modified nucleosome reveals that the UDR interacts with the nucleosome surface including the acidic patch. Previously unexplained disease-associated mutations are present in the UDR and ablate nucleosome interactions. This leads to an increased understanding of how DNMT3A1 recruitment occurs in the genome and highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome.

biochemistry↗

bioRxiv2023

Histone divergence in Trypanosoma brucei results in unique alterations to nucleosome structure

Eukaryotes have a multitude of diverse mechanisms for organising and using their genomes, but the histones that make up chromatin are highly conserved. Unusually, histones from kinetoplastids are highly divergent. The structural and functional consequences of this variation are unknown. Here, we have biochemically and structurally characterised nucleosome core particles (NCPs) from the kinetoplastid parasite Trypanosoma brucei. A structure of the T. brucei NCP reveals that global histone architecture is conserved, but specific sequence alterations lead to distinct DNA and protein interaction interfaces. The T. brucei NCP is unstable and has weakened overall DNA binding. However, dramatic changes at the H2A-H2B interface introduce local reinforcement of DNA contacts. The T. brucei acidic patch has altered topology and is refractory to known binders, indicating that the nature of chromatin interactions in T. brucei may be unique. Overall, our results provide a detailed molecular basis for understanding evolutionary divergence in chromatin structure.

biochemistry↗

bioRxiv2022

DNMT3B PWWP mutations cause hypermethylation of heterochromatin

The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved largely by the de novo DNA methyltransferases DNMT3A and DNMT3B. Mutations in DNMT3B can cause immunodeficiency-centromeric instability-facial anomalies type 1 (ICF1) syndrome which is characterised by hypomethylated heterochromatin. However, in the genome, DNMT3B primarily localises to actively transcribing gene bodies through the interaction of its PWWP domain with the histone modification H3K36me3 and it is unclear how it is recruited to heterochromatin. Here we show that in DNMT3B knockout cells, loss of DNA methylation predominantly occurs in heterochromatic domains marked by H3K9me3. We also find that PWWP domain mutations which disrupt DNMT3Bs interaction with H3K36me3 result in striking increases of DNA methylation in H3K9me3-marked heterochromatin. Gains of methylation are also observed when the PWWP domain of DNMT3B is deleted. In contrast, we find that the ICF1 syndrome-causing PWWP mutation, S270P, does not result in hypermethylation of heterochromatin and destabilises the protein. We also show that removal of the N-terminus region of DNMT3B affects its recruitment to chromatin and ability to methylate H3K9me3 marked regions. Our results suggest that DNMT3B is recruited to H3K9me3 marked heterochromatin in a PWWP-independent manner and that this recruitment is facilitated by the proteins N-terminus. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in ICF syndrome, cancer and aging.

genetics↗