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Phosphorylation of BAF alters its dynamics and interaction with DNA but not its contacts with the nuclear envelope

A structural and biophysical study by researchers from I2BC department shows in vitro that mitotic phosphorylation of the BAF protein significantly shifts the conformation of BAF towards a more rigid structure, leads to its dissociation from DNA, but unexpectedly does not alter its binding to the nuclear envelope proteins emerin and laminin. This study paves the way for a broader exploration of the impact of mitotic phosphorylations on genome organization and on the mechanisms responsible for progeroid syndromes. 

Published on 29 March 2021

​Chromatin organization, BAF protein and accelerated aging


The chromatin of eukaryotic cells is extremely polymorphic during cell cycle. This is due to a complex orchestration of intermolecular interactions within chromatin and between chromatin and its environment, notably the nuclear membrane. The lamina, a dense network of proteins (lamins A, B and C) covering the internal face of the inner nuclear membrane, constitutes a site of anchoring of chromatin at the periphery of the nucleus, either by direct interaction of lamins with DNA or histones, or via different proteins binding to lamins. Mutations in lamins are responsible for pathologies, particularly rare forms of premature aging. In 2018, researchers from the team "Nuclear envelope, telomere and DNA repair" (I2BC), in collaboration with Brigitte Buendia's group (Université Paris Diderot), solved the structure of a complex bringing together lamin A/C, the DNA-binding protein BAF, and emerin, anchored in the nuclear wall. In this complex, a BAF dimer binds emerin on one side (via its LEM domain) and lamin A/C on the other (via the globular domain). They have shown that the interaction between BAF and lamin A/C is defective in patients with progeroid syndromes linked to mutations in lamin or BAF. Their study suggests that a defect in the interaction between these proteins could lead to a deregulation of chromatin organization and gene expression, causing the accelerated aging observed in patients with these syndromes (see news 2018). 

A matter of phosphorylation?

It is known that the phosphorylation of BAF by the VRK1 kinase and its dephosphorylation by PP2A regulate its localization and function. For example, phosphorylation of BAF (in its N-terminal region) prevents it from binding to DNA. Overexpression of VRK1 partially releases BAF from chromatin and relocates the protein from the nucleus to the cytoplasm. Conversely, depletion of VRK1 prevents the necessary release of BAF from chromosomes during mitosis. To better understand the role of BAF phosphorylation in the assembly and disassembly of the BAF/lamine/emerin complex during the cell cycle, the team, in collaboration with researchers from SIMoS (MTS Department) and EMBL (Grenoble), conducted a comparative analysis of BAF before and after phosphorylation. They solved the three-dimensional structure of phosphorylated BAF, described its dynamics in solution, and identified the impact of phosphorylation on the interactions of BAF with DNA on one side and lamin A/C and emerin on the other. Their results were published in Nucleic Acids Research.

Specifically, the researchers were able to reproduce in vitro the phosphorylation of the BAF protein by the mitotic kinase VRK1. They confirmed that BAF is doubly phosphorylated by VRK1 kinase, first on its serine 4, then on its threonine 3. The crystal structures of BAF before and after phosphorylation are very similar. However, in solution, the high flexibility of the N-terminus of BAF is strongly reduced after bi-phosphorylation. This stiffening is related to the establishment of interactions between the phosphorylated residues and the positively charged C-terminus of BAF. These regions are involved in interactions with DNA and with lamin A/C. Phosphorylation by VRK1 results in a 5000-fold decrease in the affinity of BAF for DNA, but unexpectedly, phosphorylated BAF remains bound not only to emerin but also to lamin (Figure).

This study paves the way for a broader exploration of the impact of mitotic phosphorylations on genome organization.


© S. Zinn-Justin/CEA

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