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oai:dspace.mit.edu:1721.1/1541542024-04-17T03:56:55Zcom_1721.1_7582com_1721.1_7581col_1721.1_131022

Cissé, Ibrahim I. Lee, Choongman Massachusetts Institute of Technology. Department of Physics 2024-04-16T19:04:09Z 2024-04-16T19:04:09Z 2023-02 2023-05-10T19:59:44.487Z https://hdl.handle.net/1721.1/154154 https://orcid.org/0000-0003-3825-7605 Biomolecular condensates are membraneless compartments composed of selectively concentrated biomolecules with liquid-like properties. In this thesis, we discuss our discoveries showing that biomolecular condensates are associated with transcription. However, tools to study transcriptional condensates in living cells are limited due to the size of the condensates (tens to hundreds of nanometers) and the dynamics of the condensates in living cells. Therefore, we develop optogenetic tools to target and manipulate endogenous transcriptional condensates. We find that intrinsically disordered regions of transcription factors can be used to direct cargo to the condensates. Combined with an improved light-induced dimer and its binding partner allow us to generate a quick response with high insertion efficiency. We adopt a proximity-based modification to biotinylate proteins inside of the condensates upon blue light exposure. This helps to determine the constituent of the condensates using mass spectrometry. Our approach opens the road to the proteome-wide investigation of the transcriptional condensates. In this thesis, we discuss the development and future outlook of the technique. Ph.D. Massachusetts Institute of Technology In Copyright - Educational Use Permitted Copyright MIT http://rightsstatements.org/page/InC-EDU/1.0/ Targeting and Manipulating Endogenous Transcriptional Condensates Thesis application/pdf Doctoral Doctor of Philosophy Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="26e0ba23-dcdb-48c7-99cb-d8dabc70a845"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Title>Targeting and Manipulating Endogenous Transcriptional Condensates</Title> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2023-02</PublicationDate> <Authors> <Author> <DisplayName>Lee, Choongman</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://rightsstatements.org/page/InC-EDU/1.0/</License> <Abstract>Biomolecular condensates are membraneless compartments composed of selectively concentrated biomolecules with liquid-like properties. In this thesis, we discuss our discoveries showing that biomolecular condensates are associated with transcription. However, tools to study transcriptional condensates in living cells are limited due to the size of the condensates (tens to hundreds of nanometers) and the dynamics of the condensates in living cells. Therefore, we develop optogenetic tools to target and manipulate endogenous transcriptional condensates. We find that intrinsically disordered regions of transcription factors can be used to direct cargo to the condensates. Combined with an improved light-induced dimer and its binding partner allow us to generate a quick response with high insertion efficiency. We adopt a proximity-based modification to biotinylate proteins inside of the condensates upon blue light exposure. This helps to determine the constituent of the condensates using mass spectrometry. Our approach opens the road to the proteome-wide investigation of the transcriptional condensates. In this thesis, we discuss the development and future outlook of the technique.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>