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1. Chromatin architectural proteins regulate flowering time by precluding gene looping

   https://doi.org/10.1126/sciadv.abg3097  

   Zhao, Bo ; Xi, Yanpeng ; Kim, Junghyun ; Sung, Sibum ( June 2021 , Science Advances)

   Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana , the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis , which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC . A genome-widemore »study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.« less
2. IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains

   https://doi.org/10.1073/pnas.2010003118  

   Kamei, Masayuki ; Ameri, Abigail J. ; Ferraro, Aileen R. ; Bar-Peled, Yael ; Zhao, Fangzhou ; Ethridge, Christina L. ; Lail, Kathleen ; Amirebrahimi, Mojgan ; Lipzen, Anna ; Ng, Vivian ; et al ( January 2021 , Proceedings of the National Academy of Sciences)

   Polycomb Group (PcG) proteins are part of an epigenetic cell memory system that plays essential roles in multicellular development, stem cell biology, X chromosome inactivation, and cancer. In animals, plants, and many fungi, Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to assemble transcriptionally repressed facultative heterochromatin. PRC2 is structurally and functionally conserved in the model fungusNeurospora crassa, and recent work in this organism has generated insights into PRC2 control and function. To identify components of the facultative heterochromatin pathway, we performed a targeted screen ofNeurosporadeletion strains lacking individual ATP-dependent chromatin remodeling enzymes. We foundmore »theNeurosporahomolog of IMITATION SWITCH (ISW) is critical for normal transcriptional repression, nucleosome organization, and establishment of typical histone methylation patterns in facultative heterochromatin domains. We also found that stable interaction between PRC2 and chromatin depends on ISW. A functional ISW ATPase domain is required for gene repression and normal H3K27 methylation. ISW homologs interact with accessory proteins to form multiple complexes with distinct functions. Using proteomics and molecular approaches, we identified three distinctNeurosporaISW-containing complexes. A triple mutant lacking three ISW accessory factors and disrupting multiple ISW complexes led to widespread up-regulation of PRC2 target genes and altered H3K27 methylation patterns, similar to an ISW-deficient strain. Taken together, our data show that ISW is a key component of the facultative heterochromatin pathway inNeurospora, and that distinct ISW complexes perform an apparently overlapping role to regulate chromatin structure and gene repression at PRC2 target domains.

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3. The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development

   https://doi.org/10.1093/nar/gkaa082  

   Zraly, Claudia B ; Zakkar, Abdul ; Perez, John Hertenstein ; Ng, Jeffrey ; White, Kevin P ; Slattery, Matthew ; Dingwall, Andrew K ( February 2020 , Nucleic Acids Research)

   Abstract The MLR COMPASS complex monomethylates H3K4 that serves to epigenetically mark transcriptional enhancers to drive proper gene expression during animal development. Chromatin enrichment analyses of the Drosophila MLR complex reveals dynamic association with promoters and enhancers in embryos with late stage enrichments biased toward both active and poised enhancers. RNAi depletion of the Cmi (also known as Lpt) subunit that contains the chromatin binding PHD finger domains attenuates enhancer functions, but unexpectedly results in inappropriate enhancer activation during stages when hormone responsive enhancers are poised, revealing critical epigenetic roles involved in both the activation and repression of enhancers dependingmore »on developmental context. Cmi is necessary for robust H3K4 monomethylation and H3K27 acetylation that mark active enhancers, but not for the chromatin binding of Trr, the MLR methyltransferase. Our data reveal two likely major regulatory modes of MLR function, contributions to enhancer commissioning in early embryogenesis and bookmarking enhancers to enable rapid transcriptional re-activation at subsequent developmental stages.« less
4. PCNA-mediated stabilization of E3 ligase RFWD3 at the replication fork is essential for DNA replication

   https://doi.org/10.1073/pnas.1814521115  

   Lin, Yo-Chuen ; Wang, Yating ; Hsu, Rosaline ; Giri, Sumanprava ; Wopat, Susan ; Arif, Mariam K. ; Chakraborty, Arindam ; Prasanth, Kannanganattu V. ; Prasanth, Supriya G. ( December 2018 , Proceedings of the National Academy of Sciences)

   RING finger and WD repeat domain-containing protein 3 (RFWD3) is an E3 ligase known to facilitate homologous recombination by removing replication protein A (RPA) and RAD51 from DNA damage sites. Further, RPA-mediated recruitment of RFWD3 to stalled replication forks is essential for interstrand cross-link repair. Here, we report that in unperturbed human cells, RFWD3 localizes at replication forks and associates with proliferating cell nuclear antigen (PCNA) via its PCNA-interacting protein (PIP) motif. PCNA association is critical for the stability of RFWD3 and for DNA replication. Cells lacking RFWD3 show slower fork progression, a prolonged S phase, and an increase inmore »the loading of several replication-fork components on the chromatin. These findings all point to increased frequency of stalled forks in the absence of RFWD3. The S-phase defect is rescued by WT RFWD3, but not by the PIP mutant, suggesting that the interaction of RFWD3 with PCNA is critical for DNA replication. Finally, we observe reduced ubiquitination of RPA in cells lacking RFWD3. We conclude that the stabilization of RFWD3 by PCNA at the replication fork enables the polyubiquitination of RPA and its subsequent degradation for proper DNA replication.

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5. The iron-dependent repressor YtgR is a tryptophan-dependent attenuator of the trpRBA operon in Chlamydia trachomatis

   https://doi.org/10.1038/s41467-020-20181-5  

   Pokorzynski, Nick D. ; Hatch, Nathan D. ; Ouellette, Scot P. ; Carabeo, Rey A. ( December 2020 , Nature Communications)

   Thetrpoperon ofChlamydia trachomatisis organized differently from other model bacteria. It containstrpR, an intergenic region (IGR), and the biosynthetictrpBandtrpAopen-reading frames. TrpR is a tryptophan-dependent repressor that regulates the major promoter (P_trpR), while the IGR harbors an alternative promoter (P_trpBA) and an operator sequence for the iron-dependent repressor YtgR to regulatetrpBAexpression. Here, we report that YtgR repression at P_trpBAis also dependent on tryptophan by regulating YtgR levels through a rare triple-tryptophan motif (WWW) in the YtgCR precursor. Inhibiting translation during tryptophan limitation at the WWW motif subsequently promotes Rho-independent transcription termination ofytgR, thereby de-repressing P_trpBA. Thus, YtgR represents an alternative strategymore »to attenuatetrpBAexpression, expanding the repertoire fortrpoperon attenuation beyond TrpL- and TRAP-mediated mechanisms described in other bacteria. Furthermore, repurposing the iron-dependent repressor YtgR underscores the fundamental importance of maintaining tryptophan-dependent attenuation of thetrpRBAoperon.

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