We are analyzing https://link.springer.com/article/10.1007/s00018-024-05559-8.

Title:
Liquid condensates: a new barrier to loop extrusion? | Cellular and Molecular Life Sciences
Description:
Liquid–liquid phase separation (LLPS), driven by dynamic, low-affinity multivalent interactions of proteins and RNA, results in the formation of macromolecular condensates on chromatin. These structures are likely to provide high local concentrations of effector factors responsible for various processes including transcriptional regulation and DNA repair. In particular, enhancers, super-enhancers, and promoters serve as platforms for condensate assembly. In the current paradigm, enhancer-promoter (EP) interaction could be interpreted as a result of enhancer- and promoter-based condensate contact/fusion. There is increasing evidence that the spatial juxtaposition of enhancers and promoters could be provided by loop extrusion (LE) by SMC complexes. Here, we propose that condensates may act as barriers to LE, thereby contributing to various nuclear processes including spatial contacts between regulatory genomic elements.
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Keywords {🔍}

pubmed, article, google, scholar, cas, cohesin, central, condensates, cell, chromatin, nat, transcriptional, httpsdoiorgs, enhancers, transcription, phase, dna, separation, condensate, extrusion, ctcf, loop, mol, genome, biol, liquid, barrier, cells, gene, llps, promoters, sci, complexes, sites, tfs, rnapii, interactions, protein, regulation, genes, binding, loops, spatial, commun, complex, formation, enhancerpromoter, depletion, cohesinsa, assembly,

Topics {✒️}

chimeric protein dcas9-cry2-fusn double-strand break repair p53-mediated enhancer-promoter looping high-resolution single-gene imaging ews/fli1-bound sites form article download pdf unstructured c-terminal domain long-range chromatin interactions long-range ep contacts long-range enhancer action transcription decouples estrogen-dependent live-cell single-molecule dynamics phase-separated nuclear bodies enhancer–promoter entanglement explains promoter-based condensate contact/fusion enhancer-mediated gene activation liquid–liquid phase separation liquid-liquid phase separation abolishes enhancer-promoter looping tgfβ-dependent transcription activation enhancer-promoter contact frequencies yap-maml2 differentially regulates ews/fli1 occupied regions sequence-based grammar governing enhancer-mediated gene regulation ews/fli1-bound enhancers ews/fli mediated reprogramming unrelated structural/biochemical features facilitate promoter/enhancer contacts broad chip-seq peaks ews/fli1 condensates formed rna-mediated feedback control low-affinity multivalent interactions cohesin chip-seq profile laser-induced dna damage rao ssp chip-seq raw data enhancer-promoter communication c-terminal domain integrating multi-omics data sequence-dependent surface condensation auxin-induced proteolytic degradation cohesin chip-seq peaks changing growth/environmental conditions cohesin-mediated dna looping genome-wide functional organization enhancer–promoter interactions loop anchors genome-wide ctcf-mediated chromatin looping ews/fli1 disrupts

Questions {❓}

Are condensates highly permeable barriers for LE, and how do they affect LE velocity?
Can the rapid assembly and disassembly of transcriptional condensates account for the dynamics of EP looping?
Does cohesin-mediated juxtaposition ensure the specificity and selectivity of the condensate fusion?
How does paused and moving RNAPII affect the barrier function of transcriptional condensates?
Liquid condensates: a new barrier to loop extrusion?
Liquid condensates: a new barrier to loop extrusion?
Which properties of LLPS condensates contribute to their barrier activity and to what extent?

Schema {🗺️}

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         description:Liquid–liquid phase separation (LLPS), driven by dynamic, low-affinity multivalent interactions of proteins and RNA, results in the formation of macromolecular condensates on chromatin. These structures are likely to provide high local concentrations of effector factors responsible for various processes including transcriptional regulation and DNA repair. In particular, enhancers, super-enhancers, and promoters serve as platforms for condensate assembly. In the current paradigm, enhancer-promoter (EP) interaction could be interpreted as a result of enhancer- and promoter-based condensate contact/fusion. There is increasing evidence that the spatial juxtaposition of enhancers and promoters could be provided by loop extrusion (LE) by SMC complexes. Here, we propose that condensates may act as barriers to LE, thereby contributing to various nuclear processes including spatial contacts between regulatory genomic elements.
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            Macromolecule condensates
            Genome spatial organization
            Loop extrusion
            Cohesin
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      headline:Liquid condensates: a new barrier to loop extrusion?
      description:Liquid–liquid phase separation (LLPS), driven by dynamic, low-affinity multivalent interactions of proteins and RNA, results in the formation of macromolecular condensates on chromatin. These structures are likely to provide high local concentrations of effector factors responsible for various processes including transcriptional regulation and DNA repair. In particular, enhancers, super-enhancers, and promoters serve as platforms for condensate assembly. In the current paradigm, enhancer-promoter (EP) interaction could be interpreted as a result of enhancer- and promoter-based condensate contact/fusion. There is increasing evidence that the spatial juxtaposition of enhancers and promoters could be provided by loop extrusion (LE) by SMC complexes. Here, we propose that condensates may act as barriers to LE, thereby contributing to various nuclear processes including spatial contacts between regulatory genomic elements.
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         Liquid–liquid phase separation
         Macromolecule condensates
         Genome spatial organization
         Loop extrusion
         Cohesin
         Enhancer-promoter communication
         Cell Biology
         Biomedicine
         general
         Life Sciences
         Biochemistry
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      name:Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
      name:Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
      name:Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia

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