January 23 @ 11:00 AM – 12:00 PM
Dr. Yasuhiro Arimura
Assistant Professor, Basic Sciences Division
Fred Hutchinson Cancer Center
“Toward Sub-Nanometer Visualization of Endogenous Chromatin-Associated Complexes in Action”
Abstract: Eukaryotic chromatin dynamically changes its structure during the cell cycle and cellular differentiation. The structures of these chromatin and chromatin-related complexes are considered instrumental in regulating numerous biological events on chromosomes. Nevertheless, we have yet to visualize these structures at sub-nanometer resolution and thus are far from understanding the structural basis of these events. To address this, I have been developing cryo-EM-based methods to analyze sub-nanometer-resolution chromatin structures formed in cellular environments. One method involves isolating the intact chromosome-associated complexes, suitable for cryo-EM analysis, from the interphase and metaphase chromosomes in Xenopus egg extract (Arimura Mol Cell, 2021). However, with this method, although mass spectrometry detected approximately 1000 proteins in the samples prepared for the structural analysis, the cryo-EM structures of these nucleosome-bound proteins, except for the most abundant H1.8 and nucleosome could not be detected. To overcome this limitation, Magnetic Isolation and Concentration (MagIC)-cryo-EM, a technique enabling the direct structural analysis of targets captured on nanomagnetic beads (Arimura elife, 2024) was developed. MagIC-cryo-EM, which enables the isolation and cryo-EM structural determination of < 0.0005 mg/ml target protein complexes in heterogeneous samples, was able to characterize the structural variations of nucleosomes associated with the oocyte-specific linker histone H1.8, that were isolated from interphase and metaphase chromosomes in Xenopus egg extract. These two methods successfully provided structural insights into how the association of H1.8 with nucleosomes is regulated in a cell cycle-dependent manner. I believe that this method is highly beneficial for the chromatin biology field as it enables the sub-nanometer resolution structural analyses of native chromatin-related complexes. The required sample for MagIC-cryo-EM is heterogeneous liquid that contains the target molecules at a < 0.0005 mg/ml concentration, which is 100 to 1000-fold lower than conventional cryo-EM methods. The sample amount required (~2 ng of DNA) is comparable to, or even less than, what is typically used in the widely adopted ChIP-seq method, suggesting that numerous chromatin-related complexes that have been analyzed by ChIP-seq might be ideal targets for MagIC-cryo-EM. My newly established lab will further advance these methods to elucidate the structural basis of chromosomal events by enabling the sub-nanometer visualization of endogenous chromatin-associated complexes in action.
Host: Ken Cho
Seminar will be held in person only.
Developmental & Cell Biology Fall 2024 Seminar Series
Each quarter the Department of Developmental and Cell Biology hosts a weekly seminar. The purpose of these seminars is to enable experts from around the country to share their newest discoveries and ideas with our students and faculty. Seminars are held on Thursdays at 11:00 a.m., in Natural Sciences II room 4201.
For questions about this event, please contact Mayra Rubio at mrubio3@uci.edu.