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LDB1 establishes multi-enhancer networks to regulate gene expression.
Mol Cell
January 2025
Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. Electronic address:
How specific enhancer-promoter pairing is established remains mostly unclear. Besides the CTCF/cohesin machinery, few nuclear factors have been studied for a direct role in physically connecting regulatory elements. Using a murine erythroid cell model, we show via acute degradation experiments that LDB1 directly and broadly promotes connectivity among regulatory elements.
View Article and Find Full Text PDFInducing Exit from Mitosis by Inactivating Cdk1/Cyclin B in Metaphase-Arrested Cells: A Tool to Study Mitotic Exit and Reestablishment of Interphase.
Methods Mol Biol
November 2024
Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, WI, USA.
Treatments which inhibit or inactivate Cdk1/cyclin B in metaphase-arrested mammalian cells and budding yeast are described. These treatments induce the cells to exit mitosis and return to interphase, though without chromosome segregation or cytokinesis, and they provide the basis for a method to identify enzymes or other proteins which act "downstream" from Cdk1 inactivation and to elucidate the roles of those proteins in mitotic exit. In this method, inactivation of Cdk1 is combined with inhibition or inactivation of a protein of interest and the effects are observed.
View Article and Find Full Text PDFLDB1 establishes multi-enhancer networks to regulate gene expression.
bioRxiv
August 2024
Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
How specific enhancer-promoter pairing is established is still mostly unclear. Besides the CTCF/cohesin machinery, only a few nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops.
View Article and Find Full Text PDFYY1-controlled regulatory connectivity and transcription are influenced by the cell cycle.
Nat Genet
September 2024
Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Few transcription factors have been examined for their direct roles in physically connecting enhancers and promoters. Here acute degradation of Yin Yang 1 (YY1) in erythroid cells revealed its requirement for the maintenance of numerous enhancer-promoter loops, but not compartments or domains. Despite its reported ability to interact with cohesin, the formation of YY1-dependent enhancer-promoter loops does not involve stalling of cohesin-mediated loop extrusion.
View Article and Find Full Text PDFQuantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle.
Open Biol
November 2023
Department of Chemistry, State University of New York at Stony Brook, Stony Brook, NY 11794, USA.
Cell cycle is known to be regulated by the underlying gene network. Chromosomes, which serve as the scaffold for gene expressions, undergo significant structural reorganizations during mitosis. Understanding the mechanism of the cell cycle from the chromosome structural perspective remains a grand challenge.
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