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Instruments / Technical Area	Publication Details	Published
Krios I-Titan Krios I at Diamond Krios II-Titan Krios II at Diamond	A tail-based mechanism drives nucleosome demethylation by the LSD2/NPAC multimeric complex Chiara Marabelli , Biagina Marrocco , Simona Pilotto , Sagar Chittori , Sarah Picaud , Sara Marchese , Giuseppe Ciossani , Federico Forneris , Panagis Filippakopoulos , Guy Schoehn , Daniela Rhodes , Sriram Subramaniam , Andrea Mattevi Cell Reports 27, 387 - 399.e7 DOI: 10.1016/j.celrep.2019.03.061 Diamond Proposal Number(s): [16082] Open Access Show Abstract ▼ Abstract: LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase activity relies on a specific linker peptide from the multidomain protein NPAC. We used single-particle cryoelectron microscopy (cryo-EM), in combination with kinetic and mutational analysis, to analyze the mechanisms underlying the function of the human LSD2/NPAC-linker/nucleosome complex. Weak interactions between LSD2 and DNA enable multiple binding modes for the association of the demethylase to the nucleosome. The demethylase thereby captures mono- and dimethyl Lys4 of the H3 tail to afford histone demethylation. Our studies also establish that the dehydrogenase domain of NPAC serves as a catalytically inert oligomerization module. While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes.	Apr 2019
	Exploring TRF2-dependent DNA distortion through single-DNA manipulation studies Xiaodan Zhao , Vinod Kumar Vogirala , Meihan Liu , Yu Zhou , Daniela Rhodes , Sara Sandin , Jie Yan Communications Biology 7 DOI: 10.1038/s42003-024-05838-x Open Access Show Abstract ▼ Abstract: TRF2 is a component of shelterin, a telomere-specific protein complex that protects the ends of mammalian chromosomes from DNA damage signaling and improper repair. TRF2 functions as a homodimer and its interaction with telomeric DNA has been studied, but its full-length DNA-binding properties are unknown. This study examines TRF2’s interaction with single-DNA strands and focuses on the conformation of the TRF2-DNA complex and TRF2’s preference for DNA chirality. The results show that TRF2-DNA can switch between extended and compact conformations, indicating multiple DNA-binding modes, and TRF2’s binding does not have a strong preference for DNA supercoiling chirality when DNA is under low tension. Instead, TRF2 induces DNA bending under tension. Furthermore, both the N-terminal domain of TRF2 and the Myb domain enhance its affinity for the telomere sequence, highlighting the crucial role of multivalent DNA binding in enhancing its affinity and specificity for telomere sequence. These discoveries offer unique insights into TRF2’s interaction with telomeric DNA.	Feb 2024
I24-Microfocus Macromolecular Crystallography	The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle Nadia Arnaudo , Israel S. Fernandez , Stephen H. Mclaughlin , Sew Y. Peak-Chew , Daniela Rhodes , Fabrizio Martino Nature Structural & Molecular Biology DOI: 10.1038/nsmb.2641 PMID: 23934150 Show Abstract ▼ Abstract: The N-terminal acetylation of Sir3 is essential for heterochromatin establishment and maintenance in yeast, but its mechanism of action is unknown. The crystal structure of the N-terminally acetylated BAH domain of Saccharomyces cerevisiae Sir3 bound to the nucleosome core particle reveals that the N-terminal acetylation stabilizes the interaction of Sir3 with the nucleosome. Additionally, we present a new method for the production of proteinnucleosome complexes for structural analysis.	Aug 2013

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