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Sepideh Khorasanizadeh - One of the best experts on this subject based on the ideXlab platform.
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Epigenetic virtues of Chromodomains.
Critical Reviews in Biochemistry and Molecular Biology, 2011Co-Authors: Bartlomiej J. Blus, Kimberly Wiggins, Sepideh KhorasanizadehAbstract:The chromatin organization modifier domain (Chromodomain) was first identified as a motif associated with chromatin silencing in Drosophila. There is growing evidence that Chromodomains are evolutionary conserved across different eukaryotic species to control diverse aspects of epigenetic regulation. Although originally reported as histone H3 methyllysine readers, the Chromodomain functions have now expanded to recognition of other histone and non-histone partners as well as interaction with nucleic acids. Chromodomain binding to a diverse group of targets is mediated by a conserved substructure called the chromobox homology region. This motif can be used to predict methyllysine binding and distinguish Chromodomains from related Tudor “Royal” family members. In this review, we discuss and classify various Chromodomains according to their context, structure and the mechanism of target recognition.
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Specificity of the Chromodomain Y Chromosome Family of Chromodomains for Lysine-methylated ARK(S/T) Motifs
Journal of Biological Chemistry, 2008Co-Authors: Wolfgang Fischle, Henriette Franz, S. A. Jacobs, C. D. Allis, Sepideh KhorasanizadehAbstract:Previous studies have shown two homologous Chromodomain modules in the HP1 and Polycomb proteins exhibit discriminatory binding to related methyllysine residues (embedded in ARKS motifs) of the histone H3 tail. Methylated ARK(S/T) motifs have recently been identified in other chromatin factors (e.g. linker histone H1.4 and lysine methyltransferase G9a). These are thought to function as peripheral docking sites for the HP1 Chromodomain. In vertebrates, HP1-like Chromodomains are also present in the Chromodomain Y chromosome (CDY) family of proteins adjacent to a putative catalytic motif. The human genome encodes three CDY family proteins, CDY, CDYL, and CDYL2. These have putative functions ranging from establishment of histone H4 acetylation during spermiogenesis to regulation of transcription co-repressor complexes. To delineate the biochemical functions of the CDY family Chromodomains, we analyzed their specificity of methyllysine recognition. We detected substantial differences among these factors. The CDY Chromodomain exhibits discriminatory binding to lysine-methylated ARK(S/T) motifs, whereas the CDYL2 Chromodomain binds with comparable strength to multiple ARK(S/T) motifs. Interestingly, subtle amino acid changes in the CDYL Chromodomain prohibit such binding interactions in vitro and in vivo. However, point mutations can rescue binding. In support of the in vitro binding properties of the Chromodomains, the full-length CDY family proteins exhibit substantial variability in chromatin localization. Our studies underscore the significance of subtle sequence differences in a conserved signaling module for diverse epigenetic regulatory pathways.
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recognition of trimethyllysine by a Chromodomain is not driven by the hydrophobic effect
Proceedings of the National Academy of Sciences of the United States of America, 2007Co-Authors: Robert M Hughes, Sepideh Khorasanizadeh, Kimberly Wiggins, Marcey L WatersAbstract:Posttranslational modifications of histone proteins regulate gene expression via complex protein-protein and protein-DNA interactions with chromatin. One such modification, the methylation of lysine, has been shown to induce binding to Chromodomains in an aromatic cage [Nielsen PR, et al. (2002) Nature 416:103-107]. The binding generally is attributed to the presence of cation-π interactions between the methylated lysine and the aromatic pocket. However, whether the cationic component of the interaction is necessary for binding in the aromatic cage has not been addressed. In this article, the interaction of trimethyllysine with tryptophan is compared with that of its neutral analog, tert-butylnorleucine (2-amino-7,7-dimethyloctanoic acid), within the context of a β-hairpin peptide model system. These two side chains have near-identical size, shape, and polarizabilities but differ in their charges. Comparison of the two peptides reveals that the neutral side chain has no preference for interacting with tryptophan, unlike trimethyllysine, which interacts strongly in a defined geometry. In vitro binding studies of the histone 3A peptide containing trimethyllysine or tert-butylnorleucine to HP1 Chromodomain indicate that the cationic moiety is critical for binding in the aromatic cage. This difference in binding affinities demonstrates the necessity of the cation-π interaction to binding with the Chromodomain and its role in providing specificity. This article presents an excellent example of synergy between model systems and in vitro studies that allows for the investigation of the key forces that control biomolecular recognition.
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Molecular Implications of Evolutionary Differences in CHD Double Chromodomains
Journal of Molecular Biology, 2007Co-Authors: John F. Flanagan, Bartlomiej J. Blus, Daesung Kim, Katrina L. Clines, Fraydoon Rastinejad, Sepideh KhorasanizadehAbstract:Double Chromodomains occur in CHD proteins, which are ATP-dependent chromatin remodeling factors implicated in RNA polymerase II transcription regulation. Biochemical studies suggest important differences in the histone H3 tail binding of different CHD Chromodomains. In human and Drosophila, CHD1 double Chromodomains bind lysine 4-methylated histone H3 tail, which is a hallmark of transcriptionally active chromatin in all eukaryotes. Here, we present the crystal structure of the yeast CHD1 double Chromodomains, and pinpoint their differences with that of the human CHD1 double Chromodomains. The most conserved residues in these double Chromodomains are the two chromoboxes that orient adjacently. Only a subset of CHD chromoboxes can form an aromatic cage for methyllysine binding, and methyllysine binding requires correctly oriented inserts. These factors preclude yeast CHD1 double Chromodomains from interacting with the histone H3 tail. Despite great sequence similarity between the human CHD1 and CHD2 Chromodomains, variation within an insert likely prevents CHD2 double Chromodomains from binding lysine 4-methylated histone H3 tail as efficiently as in CHD1. By using the available structural and biochemical data we highlight the evolutionary specialization of CHD double Chromodomains, and provide insights about their targeting capacities.
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The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation
Nature Structural and Molecular Biology, 2007Co-Authors: Xiaoyu Zhang, Sepideh Khorasanizadeh, Bartlomiej J. Blus, Sophie Germann, Valerie Gaudin, Steven E. JacobsenAbstract:Polycomb proteins are required for maintenance of silent chromatin states via histone H3 Lys27 trimethylation ( H3K27me3) in animals, but homologs are not found in plant genomes. Using a DamID- chip method, we found that the Arabidopsis thaliana Chromodomain- containing protein LHP1 colocalizes with H3K27me3 genome- wide. The LHP1 Chromodomain also binds H3K27me3 with high affinity, suggesting that LHP1 has functions similar to those of Polycomb.
Robert P. Perry - One of the best experts on this subject based on the ideXlab platform.
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CHD1 interacts with SSRP1 and depends on both its Chromodomain and its ATPase/helicase-like domain for proper association with chromatin.
Chromosoma, 1999Co-Authors: Dawn E. Kelley, David G. Stokes, Robert P. PerryAbstract:CHD1, an Mr∼200,000 protein that contains a Chromodomain (C), an ATPase/helicase-like domain (H) and a DNA-binding domain (D), was previously shown to be associated with decompacted interphase chromatin in mammalian cells and with transcriptionally active puffs and interbands in Drosophila polytene chromosomes. We now show by transient transfection experiments with genes expressing wild-type and mutant forms of CHD1 that both the C and H domains are essential for its proper association with chromatin. We also present evidence for an in vivo interaction between CHD1 and a novel HMG box-containing protein, SSRP1, which involves an amino-terminal segment of CHD1 that does not include the Chromodomain. Immunocytochemical analyses indicated that CHD1 and SSRP1 colocalize in both mammalian nuclei and Drosophila polytene chromosomes.
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chd1 interacts with ssrp1 and depends on both its Chromodomain and its atpase helicase like domain for proper association with chromatin
Chromosoma, 1999Co-Authors: Dawn E. Kelley, David G. Stokes, Robert P. PerryAbstract:CHD1, an Mr∼200,000 protein that contains a Chromodomain (C), an ATPase/helicase-like domain (H) and a DNA-binding domain (D), was previously shown to be associated with decompacted interphase chromatin in mammalian cells and with transcriptionally active puffs and interbands in Drosophila polytene chromosomes. We now show by transient transfection experiments with genes expressing wild-type and mutant forms of CHD1 that both the C and H domains are essential for its proper association with chromatin. We also present evidence for an in vivo interaction between CHD1 and a novel HMG box-containing protein, SSRP1, which involves an amino-terminal segment of CHD1 that does not include the Chromodomain. Immunocytochemical analyses indicated that CHD1 and SSRP1 colocalize in both mammalian nuclei and Drosophila polytene chromosomes.
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A mammalian DNA-binding protein that contains a Chromodomain and an SNF2/SWI2-like helicase domain.
Proceedings of the National Academy of Sciences of the United States of America, 1993Co-Authors: Véronique Delmas, David G. Stokes, Robert P. PerryAbstract:Abstract Two overlapping cDNAs that encode a 197-kDa sequence-selective DNA-binding protein were isolated from libraries derived from mouse lymphoid cell mRNA. In addition to a DNA-binding domain, the protein contains both a Chromodomain, which occurs in proteins that are implicated in chromatin compaction, and an SNF2/SWI2-like helicase domain, which occurs in proteins that are believed to activate transcription by counteracting the repressive effects of chromatin structure. A Southern blot analysis indicated that this protein, which we have named CHD-1, for Chromodomain-helicase-DNA-binding protein, is present in most, if not all, mammalian species. A Northern blot analysis revealed multiple CHD mRNA components that differed both qualitatively and quantitatively among various cell types. The various mRNAs, which are probably produced by alternative RNA processing, could conceivably encode tissue-specific and developmental stage-specific isoforms of the protein. Based on its interesting combination of features, we suspect that CHD-1 plays an important role in gene regulation.
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a mammalian dna binding protein that contains a Chromodomain and an snf2 swi2 like helicase domain
Proceedings of the National Academy of Sciences of the United States of America, 1993Co-Authors: Véronique Delmas, David G. Stokes, Robert P. PerryAbstract:Abstract Two overlapping cDNAs that encode a 197-kDa sequence-selective DNA-binding protein were isolated from libraries derived from mouse lymphoid cell mRNA. In addition to a DNA-binding domain, the protein contains both a Chromodomain, which occurs in proteins that are implicated in chromatin compaction, and an SNF2/SWI2-like helicase domain, which occurs in proteins that are believed to activate transcription by counteracting the repressive effects of chromatin structure. A Southern blot analysis indicated that this protein, which we have named CHD-1, for Chromodomain-helicase-DNA-binding protein, is present in most, if not all, mammalian species. A Northern blot analysis revealed multiple CHD mRNA components that differed both qualitatively and quantitatively among various cell types. The various mRNAs, which are probably produced by alternative RNA processing, could conceivably encode tissue-specific and developmental stage-specific isoforms of the protein. Based on its interesting combination of features, we suspect that CHD-1 plays an important role in gene regulation.
Yanli Liu - One of the best experts on this subject based on the ideXlab platform.
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A cellular chemical probe targeting the Chromodomains of Polycomb repressive complex 1
Nature Chemical Biology, 2016Co-Authors: Jacob I Stuckey, Wolfram Tempel, Bradley M. Dickson, Jacqueline L. Norris, Nancy Cheng, Yanli Liu, Stephanie H Cholensky, Su Qin, Katherine G Huber, Cari SagumAbstract:We report the design and characterization of UNC3866, a potent antagonist of the methyllysine (Kme) reading function of the Polycomb CBX and CDY families of Chromodomains. Polycomb CBX proteins regulate gene expression by targeting Polycomb repressive complex 1 (PRC1) to sites of H3K27me3 via their Chromodomains. UNC3866 binds the Chromodomains of CBX4 and CBX7 most potently, with a K _d of ∼100 nM for each, and is 6- to 18-fold selective as compared to seven other CBX and CDY Chromodomains while being highly selective over >250 other protein targets. X-ray crystallography revealed that UNC3866's interactions with the CBX Chromodomains closely mimic those of the methylated H3 tail. UNC4195, a biotinylated derivative of UNC3866, was used to demonstrate that UNC3866 engages intact PRC1 and that EED incorporation into PRC1 is isoform dependent in PC3 prostate cancer cells. Finally, UNC3866 inhibits PC3 cell proliferation, consistent with the known ability of CBX7 overexpression to confer a growth advantage, whereas UNC4219, a methylated negative control compound, has negligible effects. Chromodomains in chromatin-associated proteins act as ‘readers’ of methylated lysines within histones. Structural and computational design led to the identification of UNC3866, a potent, cell-active peptide-based inhibitor of the methyllysine reading functions of CBX and CDY Chromodomains.
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A cellular chemical probe targeting the Chromodomains of Polycomb repressive complex 1
Nature chemical biology, 2016Co-Authors: Jacob I Stuckey, Wolfram Tempel, Bradley M. Dickson, Jacqueline L. Norris, Nancy Cheng, Yanli Liu, Stephanie H Cholensky, Su Qin, Katherine G Huber, Cari SagumAbstract:We report the design and characterization of UNC3866, a potent antagonist of the methyllysine (Kme) reading function of the Polycomb CBX and CDY families of Chromodomains. Polycomb CBX proteins regulate gene expression by targeting Polycomb repressive complex 1 (PRC1) to sites of H3K27me3 via their Chromodomains. UNC3866 binds the Chromodomains of CBX4 and CBX7 most potently, with a K(d) of ∼100 nM for each, and is 6- to 18-fold selective as compared to seven other CBX and CDY Chromodomains while being highly selective over >250 other protein targets. X-ray crystallography revealed that UNC3866's interactions with the CBX Chromodomains closely mimic those of the methylated H3 tail. UNC4195, a biotinylated derivative of UNC3866, was used to demonstrate that UNC3866 engages intact PRC1 and that EED incorporation into PRC1 is isoform dependent in PC3 prostate cancer cells. Finally, UNC3866 inhibits PC3 cell proliferation, consistent with the known ability of CBX7 overexpression to confer a growth advantage, whereas UNC4219, a methylated negative control compound, has negligible effects.
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Crystal Structure of the Human SUV39H1 Chromodomain and Its Recognition of Histone H3K9me2/3.
PloS one, 2012Co-Authors: Tao Wang, Yanli Liu, Kai Fan, Xing Sun, Hui Ouyang, Xuecheng Zhang, Jiahai ZhangAbstract:SUV39H1, the first identified histone lysine methyltransferase in human, is involved in chromatin modification and gene regulation. SUV39H1 contains a Chromodomain in its N-terminus, which potentially plays a role in methyl-lysine recognition and SUV39H1 targeting. In this study, the structure of the Chromodomain of human SUV39H1 was determined by X-ray crystallography. The SUV39H1 Chromodomain displays a generally conserved structure fold compared with other solved Chromodomains. However, different from other Chromodomains, the SUV39H1 Chromodomain possesses a much longer helix at its C-terminus. Furthermore, the SUV39H1 Chromodomain was shown to recognize histone H3K9me2/3 specifically.
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crystal structure of the human suv39h1 Chromodomain and its recognition of histone h3k9me2 3
PLOS ONE, 2012Co-Authors: Tao Wang, Yanli Liu, Kai Fan, Xing Sun, Hui Ouyang, Xuecheng Zhang, Jiahai Zhang, F Mackenzie, Jinrong MinAbstract:SUV39H1, the first identified histone lysine methyltransferase in human, is involved in chromatin modification and gene regulation. SUV39H1 contains a Chromodomain in its N-terminus, which potentially plays a role in methyl-lysine recognition and SUV39H1 targeting. In this study, the structure of the Chromodomain of human SUV39H1 was determined by X-ray crystallography. The SUV39H1 Chromodomain displays a generally conserved structure fold compared with other solved Chromodomains. However, different from other Chromodomains, the SUV39H1 Chromodomain possesses a much longer helix at its C-terminus. Furthermore, the SUV39H1 Chromodomain was shown to recognize histone H3K9me2/3 specifically.
Yoshifumi Nishimura - One of the best experts on this subject based on the ideXlab platform.
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novel structural and functional mode of a knot essential for rna binding activity of the esa1 presumed Chromodomain
Journal of Molecular Biology, 2008Co-Authors: Hideaki Shimojo, Masahiko Okuda, Masami Horikoshi, Norihiko Sano, Yoshihito Moriwaki, Yoshifumi NishimuraAbstract:Chromodomains are methylated histone binding modules that have been widely studied. Interestingly, some Chromodomains are reported to bind to RNA and/or DNA, although the molecular basis of their RNA/DNA interactions has not been solved. Here we propose a novel binding mode for Chromodomain-RNA interactions. Essential Sas-related acetyltransferase 1 (Esa1) contains a presumed Chromodomain in addition to a histone acetyltransferase domain. We initially determined the solution structure of the Esa1 presumed Chromodomain and showed it to consist of a well-folded structure containing a five-stranded beta-barrel similar to the tudor domain rather than the canonical Chromodomain. Furthermore, the domain showed no RNA/DNA binding ability. Because the N-terminus of the protein forms a helical turn, we prepared an N-terminally extended construct, which we surprisingly found to bind to poly(U) and to be critical for in vivo function. This extended protein contains an additional beta-sheet that acts as a knot for the tudor domain and binds to oligo(U) and oligo(C) with greater affinity compared with other oligo-RNAs and DNAs examined thus far. The knot does not cause a global change in the core structure but induces a well-defined loop in the tudor domain itself, which is responsible for RNA binding. We made 47 point mutants in an esa1 mutant gene in yeast in which amino acids of the Esa1 knotted tudor domain were substituted to alanine residues and their functional abilities were examined. Interestingly, the knotted tudor domain mutations that were lethal to the yeast lost poly(U) binding ability. Amino acids that are related to RNA interaction sites, as revealed by both NMR and affinity binding experiments, are found to be important in vivo. These findings are the first demonstration of how the novel structure of the knotted tudor domain impacts on RNA binding and how this influences in vivo function.
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Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed Chromodomain.
Journal of molecular biology, 2008Co-Authors: Hideaki Shimojo, Masahiko Okuda, Masami Horikoshi, Norihiko Sano, Yoshihito Moriwaki, Yoshifumi NishimuraAbstract:Abstract Chromodomains are methylated histone binding modules that have been widely studied. Interestingly, some Chromodomains are reported to bind to RNA and/or DNA, although the molecular basis of their RNA/DNA interactions has not been solved. Here we propose a novel binding mode for Chromodomain–RNA interactions. Essential Sas-related acetyltransferase 1 (Esa1) contains a presumed Chromodomain in addition to a histone acetyltransferase domain. We initially determined the solution structure of the Esa1 presumed Chromodomain and showed it to consist of a well-folded structure containing a five-stranded β-barrel similar to the tudor domain rather than the canonical Chromodomain. Furthermore, the domain showed no RNA/DNA binding ability. Because the N-terminus of the protein forms a helical turn, we prepared an N-terminally extended construct, which we surprisingly found to bind to poly(U) and to be critical for in vivo function. This extended protein contains an additional β-sheet that acts as a knot for the tudor domain and binds to oligo(U) and oligo(C) with greater affinity compared with other oligo-RNAs and DNAs examined thus far. The knot does not cause a global change in the core structure but induces a well-defined loop in the tudor domain itself, which is responsible for RNA binding. We made 47 point mutants in an esa1 mutant gene in yeast in which amino acids of the Esa1 knotted tudor domain were substituted to alanine residues and their functional abilities were examined. Interestingly, the knotted tudor domain mutations that were lethal to the yeast lost poly(U) binding ability. Amino acids that are related to RNA interaction sites, as revealed by both NMR and affinity binding experiments, are found to be important in vivo. These findings are the first demonstration of how the novel structure of the knotted tudor domain impacts on RNA binding and how this influences in vivo function.
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Structural Polymorphism of Chromodomains in Chd1
Journal of molecular biology, 2006Co-Authors: Masahiko Okuda, Masami Horikoshi, Yoshifumi NishimuraAbstract:Abstract Chromodomain from heterochromatin protein 1 and polycomb protein is known to be a lysine-methylated histone H3 tail-binding module. Chromo-helicase/ATPase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodeling factor, containing two tandem Chromodomains. In human CHD1, both Chromodomains are essential for specific binding to a K4 methylated histone H3 (H3 MeK4) peptide and are found to bind cooperatively in the crystal structure. For the budding yeast homologue, Chd1, the second but not the first Chromodomain was once reported to bind to an H3 MeK4 peptide. Here, we reveal that neither the second Chromodomain nor a region containing tandem Chromodomains from yeast Chd1 bind to any lysine-methylated or arginine-methylated histone peptides that we examined. In addition, we examined the structures of the Chromodomains from Chd1 by NMR. Although the tertiary structure of the region containing tandem Chromodomains could not be obtained, the secondary structure deduced from NMR is well conserved in the tertiary structures of the corresponding first and second Chromodomains determined individually by NMR. Both Chromodomains of Chd1 demonstrate a structure similar to that of the corresponding part of CHD1, consisting of a three-stranded β-sheet followed by a C-terminal α-helix. However, an additional helix between the first and second β-strands, which is found in both of the first Chromodomains of Chd1 and CHD1, is positioned in an entirely different manner in Chd1 and CHD1. In human CHD1 this helix forms the peptide-binding site. The amino acid sequences of the Chromodomains could be well aligned on the basis of these structures. The alignment showed that yeast Chd1 lacks several key functional residues, which are responsible for specific binding to a methylated lysine residue in other Chromodomains. Chd1 is likely to have no binding affinity for any H3 MeK peptide, as found in other Chromodomain proteins.
Yongfeng Shang - One of the best experts on this subject based on the ideXlab platform.
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Chromodomain protein cdyl is required for transmission restoration of repressive histone marks
Journal of Molecular Cell Biology, 2017Co-Authors: Yongqing Liu, Shumeng Liu, Shuai Yuan, Yu Zhang, Xiaohan Yang, Guojia Xie, Zhe Chen, Luyang Sun, Yongfeng ShangAbstract:Faithful transmission or restoration of epigenetic information such as repressive histone modifications through generations is critical for the maintenance of cell identity. We report here that Chromodomain Y-like protein (CDYL), a Chromodomain-containing transcription corepressor, is physically associated with chromatin assembly factor 1 (CAF-1) and the replicative helicase MCM complex. We showed that CDYL bridges CAF-1 and MCM, facilitating histone transfer and deposition during DNA replication. We demonstrated that CDYL recruits histone-modifying enzymes G9a, SETDB1, and EZH2 to replication forks, leading to the addition of H3K9me2/3 and H3K27me2/3 on newly deposited histone H3. Significantly, depletion of CDYL impedes early S phase progression and sensitizes cells to DNA damage. Our data indicate that CDYL plays an important role in the transmission/restoration of repressive histone marks, thereby preserving the epigenetic landscape for the maintenance of cell identity.