Nature Cell Biology
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St. Jude Bringing Chemistry to Medicine virtual symposium
Thursday, July 21, 2022
Nature
Increasing the resilience of plant immunity to a warming climate
Ankur Jain on Nucleic Acid Phase Separation
Wednesday, July 27, 2022
bioRxiv
Phase separation of Myc differentially regulates gene transcription
For Beginners
Must ReadNature chemical biology
Learning the chemical grammar of biomolecular condensates
Experimental & molecular medicine
LncRNA TMPO-AS1 promotes esophageal squamous cell carcinoma progression by forming biomolecular condensates with FUS and p300 to regulate TMPO transcription
Molecules and cells
Quantitative Frameworks for Multivalent Macromolecular Interactions in Biological Linear Lattice Systems
Science Advances
Phase separation of HRLP regulates flowering time in Arabidopsis
Nature communications
Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing
Frontiers in plant science
Editorial: Biology of Stress Granules in Plants
Jill Bouchard
Editor in Chief, Condensates.com
Here's the editorial introducing the Frontiers in Plant Science Research Topic on the Biology of Stress Granules in Plants . Make sure to check out all the articles with the FrontPlantSci Research Topic tag.
Nature reviews: Molecular cell biology
The Mediator complex as a master regulator of transcription by RNA polymerase II
Sidharth Sirdeshmukh
Research Associate, Dewpoint
The Mediator complex is basically a central regulator/ coordinating scaffold for enhancers that beckons Pol II to transcribe DNA to RNA, but doesn’t bind to DNA itself. I think of it as a rotating log that floats around, but doesn’t touch the DNA. This log has peg holes, and the peg holes can change size and position, leaving room for various enhancers (the pegs). The size and position of the peg holes will continue to change as new enhancers bind. When the peg holes are filled ‘favorably’ then Pol II is finally recruited to the DNA, initiating transcription. This review says that the Mediator complex is composed of protein modules that are flexible, and that the flexibility (ie. Peg holes that change size and position) is conferred by the IDRs within those modules. Transcription factors also have IDRs, particularly in the regions where they bind the Mediator. So, to go back to the log analogy, the pegs and the logs physically diffuse and concentrate between/ among each other. Some of theoretical open questions that Mediator IDRs suggest will be closed as better crystal structures of the Mediator complex and its modules are resolved and made available. Condensate biologists may also link colocalization/ kinetics experiments to transcriptional regulation experiments to say more about this. What’s interesting to me at this point, is the matrix representation of transcription and translation that one can picture: The Mediator-directed ‘scaffold’ exists around DNA and drives the production of RNA, which now either degrades, remains, or is translated into protein. These newly translated proteins may serve as enhancers themselves, now circling back to regulate the Mediator complex from which they came from. The cell is basically a meshwork/ soup/ jungle of RNA and protein that comes together and separates in real time, in response to unique cellular contexts. The Mediator complex encourages/ directs this cyclical cascade of RNA-protein interactions that support cells. What’s interesting to consider is whether Mediators in separate cells are ‘aware’ of each other, and coordinate processes to support neighboring cells? If these processes are coordinated through cells, are they coordinated to support the health of the cells, or the health of the Mediators themselves? Perhaps there are peripheral RNAs or proteins in the same cell, or neighboring cells, that are modulating the group-conformation of the Mediators within single cells or across microenvironments? Is there a way that diffusing the Mediator complex (or modules within it), which is highly disordered and displays a condensate phenotype according to this review, in one cell type, would produce favorable effects in a heterogenous environment?
Cells
The Association of MEG3 lncRNA with Nuclear Speckles in Living Cells
Frontiers in molecular biosciences
In vivo Proximity Labeling of Nuclear and Nucleolar Proteins by a Stably Expressed, DNA Damage-Responsive NONO-APEX2 Fusion Protein
Kitchen Table Talk
For Beginners
Must ReadVIDEO: Bede Portz on An Introduction to Biomolecular Condensates in Disease and to Dewpoint Therapeutics
bioRxiv
Cytoplasmic forces functionally reorganize nuclear condensates in oocytes
Cancers
Super-Enhancers, Phase-Separated Condensates, and 3D Genome Organization in Cancer
Science
Building the nuclear pore complex
Jill Bouchard
Editor in Chief, Condensates.com
Here's the introduction to Science's special issue on the nuclear pore complex. Make sure to check out all the incredible papers in the issue with our Science Special Issue tag.
Nature communications
Controlling synthetic membraneless organelles by a red-light-dependent singlet oxygen-generating protein
Plant physiology