Relevant bibliographies by topics / Cbx chromodomains

Academic literature on the topic 'Cbx chromodomains'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Cbx chromodomains"

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Kaustov, Lilia, Hui Ouyang, Maria Amaya, Alexander Lemak, Nataliya Nady, Shili Duan, Gregory A. Wasney, et al. "Recognition and Specificity Determinants of the Human Cbx Chromodomains." Journal of Biological Chemistry 286, no. 1 (November 3, 2010): 521–29. http://dx.doi.org/10.1074/jbc.m110.191411.

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Denton, Kyle E., Sijie Wang, Michael C. Gignac, Natalia Milosevich, Fraser Hof, Emily C. Dykhuizen, and Casey J. Krusemark. "Robustness of In Vitro Selection Assays of DNA-Encoded Peptidomimetic Ligands to CBX7 and CBX8." SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, no. 5 (January 8, 2018): 417–28. http://dx.doi.org/10.1177/2472555217750871.

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The identification of protein ligands from a DNA-encoded library is commonly conducted by an affinity selection assay. These assays are often not validated for robustness, raising questions about selections that fail to identify ligands and the utility of enrichment values for ranking ligand potencies. Here, we report a method for optimizing and utilizing affinity selection assays to identify potent and selective peptidic ligands to the highly related chromodomains of CBX proteins. To optimize affinity selection parameters, statistical analyses (Z′ factors) were used to define the ability of selection assay conditions to identify and differentiate ligands of varying affinity. A DNA-encoded positional scanning library of peptidomimetics was constructed around a trimethyllysine-containing parent peptide, and parallel selections against the chromodomains from CBX8 and CBX7 were conducted over three protein concentrations. Relative potencies of off-DNA hit molecules were determined through a fluorescence polarization assay and were consistent with enrichments observed by DNA sequencing of the affinity selection assays. In addition, novel peptide-based ligands were discovered with increased potency and selectivity to the chromodomain of CBX8. The results indicate low DNA tag bias and show that affinity-based in vitro selection assays are sufficiently robust for both ligand discovery and determination of quantitative structure–activity relationships.
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Bernstein, Emily, Elizabeth M. Duncan, Osamu Masui, Jesus Gil, Edith Heard, and C. David Allis. "Mouse Polycomb Proteins Bind Differentially to Methylated Histone H3 and RNA and Are Enriched in Facultative Heterochromatin." Molecular and Cellular Biology 26, no. 7 (April 1, 2006): 2560–69. http://dx.doi.org/10.1128/mcb.26.7.2560-2569.2006.

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ABSTRACT The chromodomain (CD) of the Drosophila Polycomb protein exhibits preferential binding affinity for histone H3 when trimethylated at lysine 27. Here we have investigated the five mouse Polycomb homologs known as Cbx2, Cbx4, Cbx6, Cbx7, and Cbx8. Despite a high degree of conservation, the Cbx chromodomains display significant differences in binding preferences. Not all CDs bind preferentially to K27me3; rather, some display affinity towards both histone H3 trimethylated at K9 and H3K27me3, and one CD prefers K9me3. Cbx7, in particular, displays strong affinity for both H3K9me3 and H3K27me3 and is developmentally regulated in its association with chromatin. Cbx7 associates with facultative heterochromatin and, more specifically, is enriched on the inactive X chromosome. Finally, we find that, in vitro, the chromodomain of Cbx7 can bind RNA and that, in vivo, the interaction of Cbx7 with chromatin, and the inactive X chromosome in particular, depends partly on its association with RNA. We propose that the capacity of this mouse Polycomb homolog to associate with the inactive X chromosome, or any other region of chromatin, depends not only on its chromodomain but also on the combination of histone modifications and RNA molecules present at its target sites.
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Stuckey, Jacob I., Catherine Simpson, Jacqueline L. Norris-Drouin, Stephanie H. Cholensky, Junghyun Lee, Ryan Pasca, Nancy Cheng, et al. "Structure–Activity Relationships and Kinetic Studies of Peptidic Antagonists of CBX Chromodomains." Journal of Medicinal Chemistry 59, no. 19 (September 19, 2016): 8913–23. http://dx.doi.org/10.1021/acs.jmedchem.6b00801.

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Tie, Feng, Rakhee Banerjee, Chen Fu, Carl A. Stratton, Ming Fang, and Peter J. Harte. "Polycomb inhibits histone acetylation by CBP by binding directly to its catalytic domain." Proceedings of the National Academy of Sciences 113, no. 6 (January 22, 2016): E744—E753. http://dx.doi.org/10.1073/pnas.1515465113.

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Drosophila Polycomb (PC), a subunit of Polycomb repressive complex 1 (PRC1), is well known for its role in maintaining repression of the homeotic genes and many others and for its binding to trimethylated histone H3 on Lys 27 (H3K27me3) via its chromodomain. Here, we identify a novel activity of PC: inhibition of the histone acetylation activity of CREB-binding protein (CBP). We show that PC and its mammalian CBX orthologs interact directly with the histone acetyltransferase (HAT) domain of CBP, binding to the previously identified autoregulatory loop, whose autoacetylation greatly enhances HAT activity. We identify a conserved PC motif adjacent to the chromodomain required for CBP binding and show that PC binding inhibits acetylation of histone H3. CBP autoacetylation impairs PC binding in vitro, and PC is preferentially associated with unacetylated CBP in vivo. PC knockdown elevates the acetylated H3K27 (H3K27ac) level globally and at promoter regions of some genes that are bound by both PC and CBP. Conversely, PC overexpression decreases the H3K27ac level in vivo and also suppresses CBP-dependent Polycomb phenotypes caused by overexpression of Trithorax, an antagonist of Polycomb silencing. We find that PC is physically associated with the initiating form of RNA polymerase II (Pol II) and that many promoters co-occupied by PC and CBP are associated with paused Pol II, suggesting that PC may play a role in Pol II pausing. These results suggest that PC/PRC1 inhibition of CBP HAT activity plays a role in regulating transcription of both repressed and active PC-regulated genes.
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Ren, Xiaojun, Claudius Vincenz, and Tom K. Kerppola. "Changes in the Distributions and Dynamics of Polycomb Repressive Complexes during Embryonic Stem Cell Differentiation." Molecular and Cellular Biology 28, no. 9 (March 3, 2008): 2884–95. http://dx.doi.org/10.1128/mcb.00949-07.

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ABSTRACT Polycomb group (PcG) transcription regulatory proteins maintain cell identity by sustained repression of numerous genes. The differentiation of embryonic stem (ES) cells induces a genome-wide shift in PcG target gene expression. We investigated the effects of differentiation and protein interactions on CBX family PcG protein localization and dynamics by using fluorescence imaging. In mouse ES cells, different CBX proteins exhibited distinct distributions and mobilities. Most CBX proteins were enriched in foci known as Polycomb bodies. Focus formation did not affect CBX protein mobilities, and the foci dispersed during ES cell differentiation. The mobilities of CBX proteins increased upon the induction of differentiation and decreased as differentiation progressed. The deletion of the chromobox, which mediates interactions with RING1B, prevented the immobilization of CBX proteins. In contrast, the deletion of the chromodomain, which can bind trimethylated lysine 27 of histone H3, had little effect on CBX protein dynamics. The distributions and mobilities of most CBX proteins corresponded to those of CBX-RING1B complexes detected by using bimolecular fluorescence complementation analysis. Epigenetic reprogramming during ES cell differentiation is therefore associated with global changes in the subnuclear distributions and dynamics of CBX protein complexes.
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Chioccarelli, Teresa, Francesco Manfrevola, Veronica Porreca, Silvia Fasano, Lucia Altucci, Riccardo Pierantoni, and Gilda Cobellis. "The Cannabinoid Receptor CB1 Stabilizes Sperm Chromatin Condensation Status During Epididymal Transit by Promoting Disulphide Bond Formation." International Journal of Molecular Sciences 21, no. 9 (April 28, 2020): 3117. http://dx.doi.org/10.3390/ijms21093117.

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The cannabinoid receptor CB1 regulates differentiation of spermatids. We recently characterized spermatozoa from caput epididymis of CB1-knock-out mice and identified a considerable number of sperm cells with chromatin abnormality such as elevated histone content and poorly condensed chromatin. In this paper, we extended our findings and studied the role of CB1 in the epididymal phase of chromatin condensation of spermatozoa by analysis of spermatozoa from caput and cauda epididymis of wild-type and CB1-knock-out mouse in both a homozygous or heterozygous condition. Furthermore, we studied the impact of CB1-gene deletion on histone displacement mechanism by taking into account the hyperacetylation of histone H4 and players of displacement such as Chromodomain Y Like protein (CDYL) and Bromodomain testis-specific protein (BRDT). Our results show that CB1, via local and/or endocrine cell-to-cell signaling, modulates chromatin remodeling mechanisms that orchestrate a nuclear condensation extent of mature spermatozoa. We show that CB1-gene deletion affects the epididymal phase of chromatin condensation by interfering with inter-/intra-protamine disulphide bridges formation, and deranges the efficiency of histone removal by reducing the hyper-acetylation of histone H4. This effect is independent by gene expression of Cdyl and Brdt mRNA. Our results reveal a novel and important role for CB1 in sperm chromatin condensation mechanisms.
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Fan, Huitao, Yiran Guo, Yi-Hsuan Tsai, Aaron J. Storey, Arum Kim, Weida Gong, Ricky D. Edmondson, et al. "A conserved BAH module within mammalian BAHD1 connects H3K27me3 to Polycomb gene silencing." Nucleic Acids Research 49, no. 8 (April 6, 2021): 4441–55. http://dx.doi.org/10.1093/nar/gkab210.

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Abstract Trimethylation of histone H3 lysine 27 (H3K27me3) is important for gene silencing and imprinting, (epi)genome organization and organismal development. In a prevalent model, the functional readout of H3K27me3 in mammalian cells is achieved through the H3K27me3-recognizing chromodomain harbored within the chromobox (CBX) component of canonical Polycomb repressive complex 1 (cPRC1), which induces chromatin compaction and gene repression. Here, we report that binding of H3K27me3 by a Bromo Adjacent Homology (BAH) domain harbored within BAH domain-containing protein 1 (BAHD1) is required for overall BAHD1 targeting to chromatin and for optimal repression of the H3K27me3-demarcated genes in mammalian cells. Disruption of direct interaction between BAHD1BAH and H3K27me3 by point mutagenesis leads to chromatin remodeling, notably, increased histone acetylation, at its Polycomb gene targets. Mice carrying an H3K27me3-interaction-defective mutation of Bahd1BAH causes marked embryonic lethality, showing a requirement of this pathway for normal development. Altogether, this work demonstrates an H3K27me3-initiated signaling cascade that operates through a conserved BAH ‘reader’ module within BAHD1 in mammals.
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Veggiani, G., R. Villaseñor, G. D. Martyn, J. Q. Tang, W. M. Krone, J. Gu, C. Chen, et al. "High-affinity chromodomains engineered for improved detection of histone methylation and enhanced CRISPR-based gene repression." Nature Communications 13, no. 1 (November 15, 2022). http://dx.doi.org/10.1038/s41467-022-34269-7.

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AbstractHistone methylation is an important post-translational modification that plays a crucial role in regulating cellular functions, and its dysregulation is implicated in cancer and developmental defects. Therefore, systematic characterization of histone methylation is necessary to elucidate complex biological processes, identify biomarkers, and ultimately, enable drug discovery. Studying histone methylation relies on the use of antibodies, but these suffer from lot-to-lot variation, are costly, and cannot be used in live cells. Chromatin-modification reader domains are potential affinity reagents for methylated histones, but their application is limited by their modest affinities. We used phage display to identify key residues that greatly enhance the affinities of Cbx chromodomains for methylated histone marks and develop a general strategy for enhancing the affinity of chromodomains of the human Cbx protein family. Our strategy allows us to develop powerful probes for genome-wide binding analysis and live-cell imaging. Furthermore, we use optimized chromodomains to develop extremely potent CRISPR-based repressors for tailored gene silencing. Our results highlight the power of engineered chromodomains for analyzing protein interaction networks involving chromatin and represent a modular platform for efficient gene silencing.
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Dissertations / Theses on the topic "Cbx chromodomains"

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(5929607), Katelyn E. Connelly. "UNDERSTANDING THE CONTRIBUTIONS OF THE POLYCOMB CBX PARALOGS IN BINDING AND ONCOGENSIS." Thesis, 2019.

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The transcriptional repressor Polycomb Repressive Complex 1 (PRC1) is critical for stem cell maintenance and proper differentiation and as such is involved in the development and progression of cancer. Canonical PRC1, composed of PCGF, PHC, RING and CBX, binds histone H3 lysine 27 trimethylation (H3K27me3) allowing for ubiquitination, chromatin compaction and subsequently transcriptional silencing. In mammals, each subunit has multiple paralogs creating functional and compositional diversity. The greatest diversity is contributed by the CBX targeting subunit with five mutually exclusive paralogs (CBX2/4/6/7/8). The CBX paralogs contain an N-terminal chromodomain for methyllysine binding. There has been interest in the CBX paralogs due to their misregulation in various cancers and the “druggability” of the chromodomain histone interaction. However, the unique biochemical and transcriptional functions of the paralogs are unclear. Expression changes during lineage specification and the context-dependent misregulation of CBX paralogs in cancers suggest the paralogs have paralog-specific functions. However, little has been done to define differences in paralog-mediated chromatin binding and regulation. This work utilizes a variety of approaches to tease apart the biological and biochemical functions of the CBX paralogs in chromatin binding and oncogenesis. In this dissertation, we identify a combinatorial therapeutic strategy using a CBX chromodomain inhibitor to enhance chemotherapeutic response. Further, this work demonstrates a role for CBX8 and its chromodomain in glioblastoma oncogenesis suggesting it may serve as a therapeutic target. Finally, we identify a binding mechanism for the CBX8 chromodomain in which DNA and H3K27me3 binding contribute to full chromatin association.
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Simhadri, Chakravarthi. "Design, synthesis, and evaluation of polycomb reader protein Cbx7 antagonists." Thesis, 2017. https://dspace.library.uvic.ca//handle/1828/8637.

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Writer, eraser, and reader proteins are three classes of proteins/enzymes that add, remove, and recognize post-translational modifications (PTMs) on histone tails, respectively. The orchestrated action of these protein classes controls dynamic state of chromatin and influences gene expression. Dysregulation of these proteins are often associated with disease conditions. All three classes are targeted with small molecule inhibitors for various disease conditions. This is a promising area of research to develop therapeutics for various clinical conditions. I worked on a methyllysine reader protein Cbx7, which belong to polycomb group of proteins. Cbx7 is a chromodomain containing protein and it uses its chromodomain to recognize methyllysine partners such as H3K27me3. Aberrant expression of Cbx7 is observed in several cancers including prostate, breast, colon, thyroid, etc. Hence targeting Cbx7 with potent and selective inhibitors would be beneficial for therapeutic intervention for Cbx7 associated diseases. Here I report my work on design, synthesis, and evaluation of Cbx7 inhibitors. In my work, we identified several potent and selective inhibitors for Cbx7 and we published first-in-class antagonists for Cbx7. Few of these inhibitors were tested on cancer stem cell models. Further, I propose future work for targeting Cbx7 and other chromodomain containing proteins.
Graduate
2018-09-04
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