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1. Light Modulates Ethylene Synthesis, Signaling, and Downstream Transcriptional Networks to Control Plant Development

   https://doi.org/10.3389/fpls.2019.01094  

   Harkey, Alexandria F.; Yoon, Gyeong Mee; Seo, Dong Hye; DeLong, Alison; Muday, Gloria K. (September 2019, Frontiers in Plant Science)
2. Light Modulates Ethylene Synthesis, Signaling, and Downstream Transcriptional Networks to Control Plant Development

   Harkey, A; Yoon, GM; Seo, DH; DeLong, A; Muday, G (September 2019, Frontiers of plant science)

   The inhibition of hypocotyl elongation by ethylene in dark-grown seedlings was the basis of elegant screens that identified ethylene-insensitive Arabidopsis mutants, which remained tall even when treated with high concentrations of ethylene. This simple approach proved invaluable for identification and molecular characterization of major players in the ethylene signaling and response pathway, including receptors and downstream signaling proteins, as well as transcription factors that mediate the extensive transcriptional remodeling observed in response to elevated ethylene. However, the dark-adapted early developmental stage used in these experiments represents only a small segment of a plant’s life cycle. After a seedling’s emergence from the soil, light signaling pathways elicit a switch in developmental programming and the hormonal circuitry that controls it. Accordingly, ethylene levels and responses diverge under these different environmental conditions. In this review, we compare and contrast ethylene synthesis, perception, and response in light and dark contexts, including the molecular mechanisms linking light responses to ethylene biology. One powerful method to identify similarities and differences in these important regulatory processes is through comparison of transcriptomic datasets resulting from manipulation of ethylene levels or signaling under varying light conditions. We performed a meta-analysis of multiple transcriptomic datasets to uncover transcriptional responses to ethylene that are both light-dependent and light-independent. We identified a core set of 139 transcripts with robust and consistent responses to elevated ethylene across three root-specific datasets. This “gold standard” group of ethylene-regulated transcripts includes mRNAs encoding numerous proteins that function in ethylene signaling and synthesis, but also reveals a number of previously uncharacterized gene products that may contribute to ethylene response phenotypes. Understanding these light-dependent differences in ethylene signaling and synthesis will provide greater insight into the roles of ethylene in growth and development across the entire plant life cycle. 

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3. Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

   https://doi.org/10.1016/j.molcel.2019.08.016  

   Zamudio, Alicia V.; Dall’Agnese, Alessandra; Henninger, Jonathan E.; Manteiga, John C.; Afeyan, Lena K.; Hannett, Nancy M.; Coffey, Eliot L.; Li, Charles H.; Oksuz, Ozgur; Sabari, Benjamin R.; et al (December 2019, Molecular Cell)

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4. The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes

   https://doi.org/10.1038/s41467-022-28094-1  

   Asthana, Anushweta; Ramanan, Parameshwaran; Hirschi, Alexander; Guiley, Keelan Z; Wijeratne, Tilini U; Shelansky, Robert; Doody, Michael J; Narasimhan, Haritha; Boeger, Hinrich; Tripathi, Sarvind; et al (December 2022, Nature Communications)

   The chromatin architecture in promoters is thought to regulate gene expression, but it remains uncertain how most transcription factors (TFs) impact nucleosome position. The MuvB TF complex regulates cell-cycle dependent gene-expression and is critical for differentiation and proliferation during development and cancer. MuvB can both positively and negatively regulate expression, but the structure of MuvB and its biochemical function are poorly understood. Here we determine the overall architecture of MuvB assembly and the crystal structure of a subcomplex critical for MuvB function in gene repression. We find that the MuvB subunits LIN9 and LIN37 function as scaffolding proteins that arrange the other subunits LIN52, LIN54 and RBAP48 for TF, DNA, and histone binding, respectively. Biochemical and structural data demonstrate that MuvB binds nucleosomes through an interface that is distinct from LIN54-DNA consensus site recognition and that MuvB increases nucleosome occupancy in a reconstituted promoter. We find in arrested cells that MuvB primarily associates with a tightly positioned +1 nucleosome near the transcription start site (TSS) of MuvB-regulated genes. These results support a model that MuvB binds and stabilizes nucleosomes just downstream of the TSS on its target promoters to repress gene expression. 

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5. Covalently Immobilizing Interferon-γ Drives Filopodia Production through Specific Receptor–Ligand Interactions Independently of Canonical Downstream Signaling

   https://doi.org/10.1021/acs.bioconjchem.0c00105  

   Christie, Shaun M.; Ham, Trevor R.; Gilmore, Grant T.; Toth, Paul D.; Leipzig, Nic D.; Smith, Adam W. (May 2020, Bioconjugate Chemistry)