Access to genetic information within the cell nucleus is regulated by the distribution of nucleosomes, which are the basic unit of chromatin. Local access to specific genomic regions is facilitated by repositioning nucleosomes to enable transcription and other nuclear processes. Nucleosome positioning is primarily regulated by ATP-dependent chromatin remodeling enzymes (CRs) that belong to the Snf2-type helicase family. These enzymes disrupt histone-DNA contacts by consuming ATP. The functions of CRs can be redundant or essential, complicating their study in vivo. To address this, we employ a unique bottom-up approach, in which we reconstitute chromatin in vitro using purified proteins and a yeast genomic plasmid library. To elucidate the diverse remodeling functions of CRs, we add purified CRs in combination with various transcription factors to the in vitro reconstituted chromatin. The resulting changes in nucleosome positioning are monitored using MNase-seq. Depending on the type of CR used, we observe distinct nucleosome positioning patterns. Furthermore, we have expanded our in vitro reconstitution approach to explore the 3D genome organization of reconstituted chromatin, discovering a role for CRs in the 3D genome organization of S. cerevisiae.
","image_description":"","creation_date":"2026-01-23T09:41:37","last_modification_date":"2026-03-10T12:18:20","link_label":"","link_url":"","canceled":"False","cancel_reason":"","place_and_room":"BCH 2218","url_place_and_room":"https://plan.epfl.ch/?room==BCH%202218","url_online_room":"","spoken_languages":["https://memento.epfl.ch/api/v1/spoken_languages/2/?format=json"],"speaker":"Elisa Oberbeckmann (University of Goettingen)","organizer":"Professeur Beat Fierz","contact":"Marie Munoz","is_internal":"False","theme":"","vulgarization":{"id":2,"fr_label":"Public averti","en_label":"Informed public"},"registration":{"id":3,"fr_label":"Entrée libre","en_label":"Free"},"keywords":"CBseminar","file":null,"icalendar_url":"https://memento.epfl.ch/event/export/119413/","category":{"id":1,"code":"CONF","fr_label":"Conférences - Séminaires","en_label":"Conferences - Seminars","activated":true},"academic_calendar_category":null,"domains":[],"mementos":["https://memento.epfl.ch/api/v1/mementos/1/?format=json","https://memento.epfl.ch/api/v1/mementos/14/?format=json","https://memento.epfl.ch/api/v1/mementos/6/?format=json"]},{"id":70936,"title":"Probing and Modulating Transcription Factor–DNA Interactions via Chemically Modified Proteins","slug":"probing-and-modulating-transcription-factordna-i-2","event_url":"https://memento.epfl.ch/event/probing-and-modulating-transcription-factordna-i-2","visual_url":"https://memento.epfl.ch/image/32324/200x112.jpg","visual_large_url":"https://memento.epfl.ch/image/32324/720x405.jpg","visual_maxsize_url":"https://memento.epfl.ch/image/32324/max-size.jpg","lang":"en","start_date":"2026-05-19","end_date":"2026-05-19","start_time":"16:15:00","end_time":"17:45:00","description":"Chemical protein synthesis provides a powerful means to prepare novel, modified proteins with atomic-level precision, offering unprecedented opportunities to understand fundamental biological processes.1 Of particular interest is gene expression, which is controlled through interactions between transcription factors (TFs) and DNA. This presentation will highlight the power of combining total synthesis and late-stage transformations to generate complex, modified proteins for deciphering the molecular roles of post-translational modifications (PTMs) in TFs regulation. Specific examples will focus on the synthesis of site-specifically phosphorylated and acetylated TFs, such as the Myc/Max system.2, 3 Remarkably, these studies revealed that phosphorylation and acetylation patterns modulate Max–DNA interactions by altering DNA binding affinity and sequence specificity. Importantly, such mechanistic insights led to the development of novel bioactive miniproteins derived from Max (μMax), capable of inhibiting oncogene expression and cancer cell proliferation through antagonistic binding to target genes in cancer cells, paving the way for the development of new therapeutic proteins targeting oncogene expression.4-6
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\r\n1. O. Harel, M. Jbara, Angew. Chem. Int. Ed., 2023, 62, e202217716
\r\n2. R. Nithun, Y. Yao, X. Lin, S. Habiballah, A. Afek, M. Jbara, Angew. Chem. In. Ed., 2023, 62, e202310913
\r\n3. R. Nithun, Y. Yao, O. Harel, S. Habiballah, A. Afek, M. Jbara, ACS Central Science, 2024, 10, 1295–1303
\r\n4. X. Lin, S. Mandal, R. Nithun, R. Kolla, B. Bouri, H. Lashuel, M. Jbara, JACS, 2024, 146, 25788
\r\n5. X. Lin, O. Harel, M. Jbara, Angew. Chem. In. Ed., 2024, 63, e202317511
\r\n6. O. Harel, F. Nadal-Bufi, R. Nithun, Y. Yao, A. Afek, M. Vendrell, M. Jbara, JACS, 2025, 147, 46, 42647
Thesis Director: Prof. A. L. A. Persat,
\r\nBiotechnology and Bioengineering doctoral program
\r\nThesis Nr. 11340
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\r\nTo take part in the public defense, please contact directly the speaker