Cryo-EM Structures of the BAF-Lamin A/C Complex Bound to Nucleosomes

Overview

Journal Nat Commun

Date 2025 Feb 10

PMID 39929866

Authors

Naoki Horikoshi

Ryosuke Miyake

Chizuru Sogawa-Fujiwara

Mitsuo Ogasawara

Yoshimasa Takizawa

Hitoshi Kurumizaka

Affiliations

Soon will be listed here.

Abstract

Barrier-to-autointegration factor (BAF) associates with mitotic chromosomes and promotes nuclear envelope assembly by recruiting proteins, such as Lamins, required for the reconstruction of the nuclear envelope and lamina. BAF also mediates chromatin anchoring to the nuclear lamina via Lamin A/C. However, the mechanism by which BAF and Lamin A/C bind chromatin and affect the chromatin organization remains elusive. Here we report the cryo-electron microscopy structures of BAF-Lamin A/C-nucleosome complexes. We find that the BAF dimer complexed with the Lamin A/C IgF domain occupies the nucleosomal dyad position, forming a tripartite nucleosomal DNA binding structure. We also show that the Lamin A/C Lys486 and His506 residues, which are reportedly mutated in lipodystrophy patients, directly contact the DNA at the nucleosomal dyad. Excess BAF-Lamin A/C complexes symmetrically bind other nucleosomal DNA sites and connect two BAF-Lamin A/C-nucleosome complexes. Although the linker histone H1 competes with BAF-Lamin A/C binding at the nucleosomal dyad region, the two BAF-Lamin A/C molecules still bridge two nucleosomes. These findings provide insights into the mechanism by which BAF, Lamin A/C, and/or histone H1 bind nucleosomes and influence chromatin organization within the nucleus.

References

Kouzarides T . Chromatin modifications and their function. Cell. 2007; 128(4):693-705. DOI: 10.1016/j.cell.2007.02.005. View

Kastner B, Fischer N, Golas M, Sander B, Dube P, Boehringer D . GraFix: sample preparation for single-particle electron cryomicroscopy. Nat Methods. 2007; 5(1):53-5. DOI: 10.1038/nmeth1139. View

Machida S, Hayashida R, Takaku M, Fukuto A, Sun J, Kinomura A . Relaxed Chromatin Formation and Weak Suppression of Homologous Pairing by the Testis-Specific Linker Histone H1T. Biochemistry. 2016; 55(4):637-46. DOI: 10.1021/acs.biochem.5b01126. View

Loi M, Cenni V, Duchi S, Squarzoni S, Lopez-Otin C, Foisner R . Barrier-to-autointegration factor (BAF) involvement in prelamin A-related chromatin organization changes. Oncotarget. 2015; 7(13):15662-77. PMC: 4941268. DOI: 10.18632/oncotarget.6697. View

Margueron R, Reinberg D . Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet. 2010; 11(4):285-96. PMC: 3760772. DOI: 10.1038/nrg2752. View

Kimanius D, Dong L, Sharov G, Nakane T, Scheres S . New tools for automated cryo-EM single-particle analysis in RELION-4.0. Biochem J. 2021; 478(24):4169-4185. PMC: 8786306. DOI: 10.1042/BCJ20210708. View

Croll T . ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D Struct Biol. 2018; 74(Pt 6):519-530. PMC: 6096486. DOI: 10.1107/S2059798318002425. View

Gorjanacz M, Klerkx E, Galy V, Santarella R, Lopez-Iglesias C, Askjaer P . Caenorhabditis elegans BAF-1 and its kinase VRK-1 participate directly in post-mitotic nuclear envelope assembly. EMBO J. 2006; 26(1):132-43. PMC: 1782363. DOI: 10.1038/sj.emboj.7601470. View

Zhou B, Feng H, Kale S, Fox T, Khant H, de Val N . Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. Mol Cell. 2020; 81(1):166-182.e6. PMC: 7796963. DOI: 10.1016/j.molcel.2020.10.038. View

10.

Bereziat V, Cervera P, Le Dour C, Verpont M, Dumont S, Vantyghem M . LMNA mutations induce a non-inflammatory fibrosis and a brown fat-like dystrophy of enlarged cervical adipose tissue. Am J Pathol. 2011; 179(5):2443-53. PMC: 3204020. DOI: 10.1016/j.ajpath.2011.07.049. View

11.

Zheng R, Ghirlando R, Lee M, Mizuuchi K, Krause M, Craigie R . Barrier-to-autointegration factor (BAF) bridges DNA in a discrete, higher-order nucleoprotein complex. Proc Natl Acad Sci U S A. 2000; 97(16):8997-9002. PMC: 16810. DOI: 10.1073/pnas.150240197. View

12.

Furukawa K, Sugiyama S, Osouda S, Goto H, Inagaki M, Horigome T . Barrier-to-autointegration factor plays crucial roles in cell cycle progression and nuclear organization in Drosophila. J Cell Sci. 2003; 116(Pt 18):3811-23. DOI: 10.1242/jcs.00682. View

13.

Buchwalter A, Kaneshiro J, Hetzer M . Coaching from the sidelines: the nuclear periphery in genome regulation. Nat Rev Genet. 2018; 20(1):39-50. PMC: 6355253. DOI: 10.1038/s41576-018-0063-5. View

14.

Haraguchi T, Kojidani T, Koujin T, Shimi T, Osakada H, Mori C . Live cell imaging and electron microscopy reveal dynamic processes of BAF-directed nuclear envelope assembly. J Cell Sci. 2008; 121(Pt 15):2540-54. DOI: 10.1242/jcs.033597. View

15.

Zhuang X, Semenova E, Maric D, Craigie R . Dephosphorylation of barrier-to-autointegration factor by protein phosphatase 4 and its role in cell mitosis. J Biol Chem. 2013; 289(2):1119-27. PMC: 3887179. DOI: 10.1074/jbc.M113.492777. View

16.

Rohou A, Grigorieff N . CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J Struct Biol. 2015; 192(2):216-21. PMC: 6760662. DOI: 10.1016/j.jsb.2015.08.008. View

17.

Marcelot A, Petitalot A, Ropars V, Le Du M, Samson C, Dubois S . Di-phosphorylated BAF shows altered structural dynamics and binding to DNA, but interacts with its nuclear envelope partners. Nucleic Acids Res. 2021; 49(7):3841-3855. PMC: 8053085. DOI: 10.1093/nar/gkab184. View

18.

Samson C, Petitalot A, Celli F, Herrada I, Ropars V, Le Du M . Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies an interface disrupted in autosomal recessive progeroid diseases. Nucleic Acids Res. 2018; 46(19):10460-10473. PMC: 6212729. DOI: 10.1093/nar/gky736. View

19.

Chen V, Arendall 3rd W, Headd J, Keedy D, Immormino R, Kapral G . MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 1):12-21. PMC: 2803126. DOI: 10.1107/S0907444909042073. View

20.

Snyers L, Lohnert R, Weipoltshammer K, Schofer C . Emerin prevents BAF-mediated aggregation of lamin A on chromosomes in telophase to allow nuclear membrane expansion and nuclear lamina formation. Mol Biol Cell. 2022; 33(14):ar137. PMC: 9727812. DOI: 10.1091/mbc.E22-01-0007. View