The Experts below are selected from a list of 3267 Experts worldwide ranked by ideXlab platform
Ming-ming Zhou - One of the best experts on this subject based on the ideXlab platform.
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structural insights into acetylated histone h4 recognition by the bromodomain PHD Finger module of human transcriptional coactivator cbp
Structure, 2014Co-Authors: Alexander N Plotnikov, Shuai Yang, Thomas Jiachi Zhou, Elena Rusinova, Antonio Frasca, Ming-ming ZhouAbstract:Bromodomain functions as the acetyl-lysine binding domains to regulate gene transcription in chromatin. Bromodomains are rapidly emerging as new epigenetic drug targets for human diseases. However, owing to their transient nature and modest affinity, histone-binding selectivity of bromodomains has remained mostly elusive. Here, we report high-resolution crystal structures of the bromodomain-PHD tandem module of human transcriptional coactivator CBP bound to lysine-acetylated histone H4 peptides. The structures reveal that the PHD Finger serves a structural role in the tandem module and that the bromodomain prefers lysine-acetylated motifs comprising a hydrophobic or aromatic residue at -2 and a lysine or arginine at -3 or -4 position from the acetylated lysine. Our study further provides structural insights into distinct modes of singly and diacetylated histone H4 recognition by the bromodomains of CBP and BRD4 that function differently as a transcriptional coactivator and chromatin organizer, respectively, explaining their distinct roles in control of gene expression in chromatin.
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the PHD Finger a versatile epigenome reader
Trends in Biochemical Sciences, 2011Co-Authors: Roberto Sanchez, Ming-ming ZhouAbstract:PHD (plant homeodomain) zinc Fingers are structurally conserved modules found in proteins that modify chromatin as well as mediate molecular interactions in gene transcription. The original discovery of their role in gene transcription is attributed to the recognition of lysine-methylated histone H3. Recent studies show that PHD Fingers have a sophisticated histone sequence reading capacity that is modulated by the interplay between different histone modifications. These studies underscore the functional versatility of PHD Fingers as epigenome readers that control gene expression through molecular recruitment of multiprotein complexes of chromatin regulators and transcription factors. Moreover, they reinforce the concept that evolutionary changes in amino acids surrounding ligand binding sites on a conserved structural fold impart great functional diversity upon this family of proteins.
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mechanism and regulation of acetylated histone binding by the tandem PHD Finger of dpf3b
Nature, 2010Co-Authors: Lei Zeng, Qiang Zhang, Alexander N Plotnikov, Martin J Walsh, Ming-ming ZhouAbstract:Histone lysine acetylation or methylation helps to regulate chromatin functions during gene transcription. Histone acetylation marks are typically recognized by proteins containing bromodomains, but recently, an alternative mechanism of acetyl-lysine binding was recognized in the tandem plant homeodomain (PHD) Finger of human DPF3b, a protein that functions in gene activation. The three-dimensional solution structures of DPF3b bound to a lysine 14-acetylated histone H3 peptide have now been determined, offering mechanistic insight into the way the protein recognizes acetylation marks. The lysine residues of histone proteins can be acetylated or methylated, with important effects on gene expression. Until recently the protein modules that bind acetyl-lysine have been limited to bromodomains. However, the tandem plant homeodomain (PHD) Finger of human DPF3b — which is involved in gene activation — has also been reported to bind to acetylated histones. Here, three-dimensional solution structures of DPF3b offer mechanistic insight into how this protein recognizes acetylation marks. Histone lysine acetylation and methylation have an important role during gene transcription in a chromatin context1,2. Knowledge concerning the types of protein modules that can interact with acetyl-lysine has so far been limited to bromodomains1. Recently, a tandem plant homeodomain (PHD) Finger3 (PHD1–PHD2, or PHD12) of human DPF3b, which functions in association with the BAF chromatin remodelling complex to initiate gene transcription during heart and muscle development, was reported to bind histones H3 and H4 in an acetylation-sensitive manner4, making it the first alternative to bromodomains for acetyl-lysine binding5. Here we report the structural mechanism of acetylated histone binding by the double PHD Fingers of DPF3b. Our three-dimensional solution structures and biochemical analysis of DPF3b highlight the molecular basis of the integrated tandem PHD Finger, which acts as one functional unit in the sequence-specific recognition of lysine-14-acetylated histone H3 (H3K14ac). Whereas the interaction with H3 is promoted by acetylation at lysine 14, it is inhibited by methylation at lysine 4, and these opposing influences are important during transcriptional activation of the mouse DPF3b target genes Pitx2 and Jmjd1c. Binding of this tandem protein module to chromatin can thus be regulated by different histone modifications during the initiation of gene transcription.
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Structure and Site-Specific Recognition of Histone H3 by the PHD Finger of Human Autoimmune Regulator
Structure (London England : 1993), 2009Co-Authors: Suvobrata Chakravarty, Lei Zeng, Ming-ming ZhouAbstract:Human autoimmune regulator (AIRE) functions to control thymic expression of tissue-specific antigens via sequence-specific histone H3 recognition by its plant homeodomain (PHD) Finger. Mutations in the AIRE PHD Finger have been linked to autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). Here we report the three-dimensional solution structure of the first PHD Finger of human AIRE bound to a histone H3 peptide. The structure reveals a detailed network of interactions between the protein and the amino-terminal residues of histone H3, and particularly key electrostatic interactions of a conserved aspartic acid 297 in AIRE with the unmodified lysine 4 of histone H3 (H3K4). NMR binding study with H3 peptides carrying known posttranslational modifications flanking H3K4 confirms that transcriptional regulation by AIRE through its interactions with histone H3 is confined to the first N-terminal eight residues in H3. Our study offers a molecular explanation for the APECED mutations and helps define a subclass of the PHD Finger family proteins that recognize histone H3 in a sequence-specific manner.
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structural insights into human kap1 PHD Finger bromodomain and its role in gene silencing
Nature Structural & Molecular Biology, 2008Co-Authors: Lei Zeng, Kyoko L Yap, Alexey V Ivanov, Xueqi Wang, Shiraz Mujtaba, Olga Plotnikova, Frank J Rauscher, Ming-ming ZhouAbstract:The tandem PHD Finger–bromodomain, found in many chromatin-associated proteins, has an important role in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). Here we report the three-dimensional solution structure of the tandem PHD Finger–bromodomain of KAP1. The structure reveals a distinct scaffold unifying the two protein modules, in which the first helix, αZ, of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD Finger on the other. A comprehensive mutation-based structure-function analysis correlating transcriptional repression, ubiquitin-conjugating enzyme 9 (UBC9) binding and SUMOylation shows that the PHD Finger and the bromodomain of KAP1 cooperate as one functional unit to facilitate lysine SUMOylation, which is required for KAP1 co-repressor activity in gene silencing. These results demonstrate a previously unknown unified function for the tandem PHD Finger–bromodomain as an intramolecular small ubiquitin-like modifier (SUMO) E3 ligase for transcriptional silencing.
Yang Shi - One of the best experts on this subject based on the ideXlab platform.
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PHD Finger recognition of unmodified histone h3r2 links uhrf1 to regulation of euchromatic gene expression
Molecular Cell, 2011Co-Authors: Eerappa Rajakumara, Hao Chen, Zhentian Wang, Rui Guo, Fei Lan, Yan Lin, Yujiang Geno Shi, Dinshaw J Patel, Yang ShiAbstract:Histone methylation occurs on both lysine and arginine residues, and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD Finger (PHD(UHRF1)), an important regulator of DNA CpG methylation, as a histone H3 unmodified arginine 2 (H3R2) recognition modality. This conclusion is based on binding studies and cocrystal structures of PHD(UHRF1) bound to histone H3 peptides, where the guanidinium group of unmodified R2 forms an extensive intermolecular hydrogen bond network, with methylation of H3R2, but not H3K4 or H3K9, disrupting complex formation. We have identified direct target genes of UHRF1 from microarray and ChIP studies. Importantly, we show that UHRF1's ability to repress its direct target gene expression is dependent on PHD(UHRF1) binding to unmodified H3R2, thereby demonstrating the functional importance of this recognition event and supporting the potential for crosstalk between histone arginine methylation and UHRF1 function.
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recognition of unmethylated histone h3 lysine 4 links bhc80 to lsd1 mediated gene repression
Nature, 2007Co-Authors: Robe E Collins, Rossella De Cegli, Roma Alpatov, Joh R Horto, Xiaobing Shi, O Gozani, Xiaodong Cheng, Yang ShiAbstract:BHC80 is a component of the LSD1 co-repressor complex that demethylates histone H3 at lysine 4. The PHD domain of BHC80 interacts with the histone H3 tail only when lysine 4 is unmethylated, and BHC80 function is coupled to that of LSD1 in gene repression. Histone methylation is crucial for regulating chromatin structure, gene transcription and the epigenetic state of the cell. LSD1 is a lysine-specific histone demethylase that represses transcription by demethylating histone H3 on lysine 4 (ref. 1). The LSD1 complex contains a number of proteins, all of which have been assigned roles in events upstream of LSD1-mediated demethylation2,3,4 apart from BHC80 (also known as PHF21A), a plant homeodomain (PHD) Finger-containing protein. Here we report that, in contrast to the PHD Fingers of the bromodomain PHD Finger transcription factor (BPTF) and inhibitor of growth family 2 (ING2), which bind methylated H3K4 (H3K4me3)5,6, the PHD Finger of BHC80 binds unmethylated H3K4 (H3K4me0), and this interaction is specifically abrogated by methylation of H3K4. The crystal structure of the PHD Finger of BHC80 bound to an unmodified H3 peptide has revealed the structural basis of the recognition of H3K4me0. Knockdown of BHC80 by RNA inhibition results in the de-repression of LSD1 target genes, and this repression is restored by the reintroduction of wild-type BHC80 but not by a PHD-Finger mutant that cannot bind H3. Chromatin immunoprecipitation showed that BHC80 and LSD1 depend reciprocally on one another to associate with chromatin. These findings couple the function of BHC80 to that of LSD1, and indicate that unmodified H3K4 is part of the ‘histone code’7. They further raise the possibility that the generation and recognition of the unmodified state on histone tails in general might be just as crucial as post-translational modifications of histone for chromatin and transcriptional regulation.
Giovanna Musco - One of the best experts on this subject based on the ideXlab platform.
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sp140 is a multi sumo 1 target and its PHD Finger promotes sumoylation of the adjacent bromodomain
Biochimica et Biophysica Acta, 2019Co-Authors: Chiara Zucchelli, Simone Tamburri, Giacomo Quilici, Angela Bachi, Giuseppe Filosa, Michela Ghitti, Giovanna MuscoAbstract:Abstract Background Human Sp140 protein is a leukocyte-specific member of the speckled protein (Sp) family (Sp100, Sp110, Sp140, Sp140L), a class of multi-domain nuclear proteins involved in intrinsic immunity and transcriptional regulation. Sp140 regulates macrophage transcriptional program and is implicated in several haematologic malignancies. Little is known about Sp140 structural domains and its post-translational modifications. Methods We used mass spectrometry and biochemical experiments to investigate endogenous Sp140 SUMOylation in Burkitt's Lymphoma cells and Sp140 SUMOylation sites in HEK293T cells, FLAG-Sp140 transfected and His6-SUMO-1T95K infected. NMR spectroscopy and in vitro SUMOylation reactions were applied to investigate the role of Sp140 PHD Finger in the SUMOylation of the adjacent BRD. Results Endogenous Sp140 is a SUMO-1 target, whereby FLAG-Sp140 harbors at least 13 SUMOylation sites distributed along the protein sequence, including the BRD. NMR experiments prove direct binding of the SUMO E2 ligase Ubc9 and SUMO-1 to PHD-BRDSp140. In vitro SUMOylation reactions show that the PHDSp140 behaves as SUMO E3 ligase, assisting intramolecular SUMOylation of the adjacent BRD. Conclusions Sp140 is multi-SUMOylated and its PHD Finger works as versatile protein-protein interaction platform promoting intramolecular SUMOylation of the adjacent BRD. Thus, combinatorial association of Sp140 chromatin binding domains generates a multifaceted interaction scaffold, whose function goes beyond the canonical histone recognition. General significance The addition of Sp140 to the increasing lists of multi-SUMOylated proteins opens new perspectives for molecular studies on Sp140 transcriptional activity, where SUMOylation could represent a regulatory route and a docking surface for the recruitment and assembly of leukocyte-specific transcription regulators.
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structure of human sp140 PHD Finger an atypical fold interacting with pin1
FEBS Journal, 2014Co-Authors: Chiara Zucchelli, Part Peterson, Simone Tamburri, Giacomo Quilici, Eleonora Palagano, Andrea Berardi, Mario Saare, Angela Bachi, Giovanna MuscoAbstract:Sp140 is a nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. The presence of several chromatin related modules such as plant homeodomain (PHD), bromodomain and SAND domain suggests a role in chromatin-mediated regulation of gene expression; however, its real function is still elusive. Herein we present the solution structure of Sp140-PHD Finger and investigate its role as epigenetic reader in vitro. Sp140-PHD presents an atypical PHD Finger fold which does not bind to histone H3 tails but is recognized by peptidylprolyl isomerase Pin1. Pin1 specifically binds to a phosphopeptide corresponding to the L3 loop of Sp140-PHD and catalyzes cis–trans isomerization of a pThr-Pro bond. Moreover co-immunoprecipitation experiments demonstrate FLAG-Sp140 interaction with endogenous Pin1 in vivo. Overall these data include Sp140 in the list of the increasing number of Pin1 binders and expand the regulatory potential of PHD Fingers as versatile structural platforms for diversified interactions.
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the solution structure of the first PHD Finger of autoimmune regulator in complex with non modified histone h3 tail reveals the antagonistic role of h3r2 methylation
Nucleic Acids Research, 2009Co-Authors: Francesca Chignola, Part Peterson, Ana Rebane, Tonis Org, Massimiliano Gaetani, Luca Mollica, Chiara Zucchelli, Andrea Spitaleri, Valeria Mannella, Giovanna MuscoAbstract:Plant homeodomain (PHD) Fingers are often present in chromatin-binding proteins and have been shown to bind histone H3 N-terminal tails. Mutations in the autoimmune regulator (AIRE) protein, which harbours two PHD Fingers, cause a rare monogenic disease, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). AIRE activates the expression of tissue-specific antigens by directly binding through its first PHD Finger (AIRE-PHD1) to histone H3 tails non-methylated at K4 (H3K4me0). Here, we present the solution structure of AIRE-PHD1 in complex with H3K4me0 peptide and show that AIRE-PHD1 is a highly specialized non-modified histone H3 tail reader, as post-translational modifications of the first 10 histone H3 residues reduce binding affinity. In particular, H3R2 dimethylation abrogates AIRE-PHD1 binding in vitro and reduces the in vivo activation of AIRE target genes in HEK293 cells. The observed antagonism by R2 methylation on AIRE-PHD1 binding is unique among the H3K4me0 histone readers and represents the first case of epigenetic negative cross-talk between non-methylated H3K4 and methylated H3R2. Collectively, our results point to a very specific histone code responsible for non-modified H3 tail recognition by AIRE-PHD1 and describe at atomic level one crucial step in the molecular mechanism responsible for antigen expression in the thymus.
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PHD Finger of autoimmune regulator: An epigenetic link between the histone modifications and tissue-specific antigen expression in thymus
Epigenetics, 2008Co-Authors: Giovanna Musco, Part PetersonAbstract:Methylation of lysine residues on histone H3 tails regulates transcription. A recent addition to the list of known methylated histone binding modules is the plant homeodomain (PHD) Finger, which is usually found in nuclear proteins with chromatin-related functions. Autoimmune regulator (AIRE) protein contains two PHD Fingers and mutations in AIRE gene cause the monogenic disease autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). AIRE is expressed in thymic medullary epithelial cells where it promotes the expression of tissue-specific antigens. However the mechanism by which AIRE controls gene expression is currently unknown and the function of its domains, in particular of its PHD Fingers is still elusive and controversial. In this review we discuss recent works on AIRE PHD Finger(s) providing a new link between the status of histone modifications and the regulation of tissue-specific antigen expression in thymus.
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the autoimmune regulator PHD Finger binds to non methylated histone h3k4 to activate gene expression
EMBO Reports, 2008Co-Authors: Tonis Org, Ana Rebane, Francesca Chignola, Csaba Hetenyi, Massimiliano Gaetani, Ingrid Liiv, Uko Maran, Luca Mollica, Matthew J Bottomley, Giovanna MuscoAbstract:Mutations in the gene autoimmune regulator (AIRE) cause autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. AIRE is expressed in thymic medullary epithelial cells, where it promotes the expression of tissue-restricted antigens. By the combined use of biochemical and biophysical methods, we show that AIRE selectively interacts with histone H3 through its first plant homeodomain (PHD) Finger (AIRE–PHD1) and preferentially binds to non-methylated H3K4 (H3K4me0). Accordingly, in vivo AIRE binds to and activates promoters containing low levels of H3K4me3 in human embryonic kidney 293 cells. We conclude that AIRE–PHD1 is an important member of a newly identified class of PHD Fingers that specifically recognize H3K4me0, thus providing a new link between the status of histone modifications and the regulation of tissue-restricted antigen expression in thymus.
Dinshaw J Patel - One of the best experts on this subject based on the ideXlab platform.
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PHD Finger recognition of unmodified histone h3r2 links uhrf1 to regulation of euchromatic gene expression
Molecular Cell, 2011Co-Authors: Eerappa Rajakumara, Hao Chen, Zhentian Wang, Rui Guo, Fei Lan, Yan Lin, Yujiang Geno Shi, Dinshaw J Patel, Yang ShiAbstract:Histone methylation occurs on both lysine and arginine residues, and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD Finger (PHD(UHRF1)), an important regulator of DNA CpG methylation, as a histone H3 unmodified arginine 2 (H3R2) recognition modality. This conclusion is based on binding studies and cocrystal structures of PHD(UHRF1) bound to histone H3 peptides, where the guanidinium group of unmodified R2 forms an extensive intermolecular hydrogen bond network, with methylation of H3R2, but not H3K4 or H3K9, disrupting complex formation. We have identified direct target genes of UHRF1 from microarray and ChIP studies. Importantly, we show that UHRF1's ability to repress its direct target gene expression is dependent on PHD(UHRF1) binding to unmodified H3R2, thereby demonstrating the functional importance of this recognition event and supporting the potential for crosstalk between histone arginine methylation and UHRF1 function.
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haematopoietic malignancies caused by dysregulation of a chromatin binding PHD Finger
Nature, 2009Co-Authors: Gang Greg Wang, Dinshaw J Patel, Jikui Song, Zhanxin Wang, Holger L Dormann, Fabio Casadio, Junli Luo, David C AllisAbstract:Histone H3 lysine 4 methylation (H3K4me) has been proposed as a critical component in regulating gene expression, epigenetic states, and cellular identities1. The biological meaning of H3K4me is interpreted by conserved modules including plant homeodomain (PHD) Fingers that recognize varied H3K4me states. The dysregulation of PHD Fingers has been implicated in several human diseases, including cancers and immune or neurological disorders. Here we report that fusing an H3K4-trimethylation (H3K4me3)-binding PHD Finger, such as the carboxy-terminal PHD Finger of PHF23 or JARID1A (also known as KDM5A or RBBP2), to a common fusion partner nucleoporin-98 (NUP98) as identified in human leukaemias, generated potent oncoproteins that arrested haematopoietic differentiation and induced acute myeloid leukaemia in murine models. In these processes, a PHD Finger that specifically recognizes H3K4me3/2 marks was essential for leukaemogenesis. Mutations in PHD Fingers that abrogated H3K4me3 binding also abolished leukaemic transformation. NUP98-PHD fusion prevented the differentiation-associated removal of H3K4me3 at many loci encoding lineage-specific transcription factors (Hox(s), Gata3, Meis1, Eya1 and Pbx1), and enforced their active gene transcription in murine haematopoietic stem/progenitor cells. Mechanistically, NUP98-PHD fusions act as 'chromatin boundary factors', dominating over polycomb-mediated gene silencing to 'lock' developmentally critical loci into an active chromatin state (H3K4me3 with induced histone acetylation), a state that defined leukaemia stem cells. Collectively, our studies represent, to our knowledge, the first report that deregulation of the PHD Finger, an 'effector' of specific histone modification, perturbs the epigenetic dynamics on developmentally critical loci, catastrophizes cellular fate decision-making, and even causes oncogenesis during mammalian development.
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structural basis for lower lysine methylation state specific readout by mbt repeats of l3mbtl1 and an engineered PHD Finger
Molecular Cell, 2007Co-Authors: Wolfgang Fischle, Elizabeth M Duncan, David C Allis, Wooikoon Wang, Lena Liang, Satoko Murakamiishibe, Dinshaw J PatelAbstract:Human L3MBTL1, which contains three malignant brain tumor (MBT) repeats, binds monomethylated and dimethylated lysines, but not trimethylated lysines, in several histone sequence contexts. In crystal structures of L3MBTL1 complexes, the monomethyl- and dimethyllysines insert into a narrow and deep cavity of aromatic residue-lined pocket 2, while a proline ring inserts into shallower pocket 1. We have also engineered a single Y to E substitution within the aromatic cage of the BPTF PHD Finger, resulting in a reversal of binding preference from trimethyl- to dimethyllysine in an H3K4 sequence context. In both the "cavity insertion" (L3MBTL1) and "surface groove" (PHD Finger) modes of methyllysine recognition, a carboxylate group both hydrogen bonds and ion pairs to the methylammonium proton. Our structural and binding studies of these two modules provide insights into the molecular principles governing the decoding of lysine methylation states, thereby highlighting a methylation state-specific layer of histone mark readout impacting on epigenetic regulation.
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yng1 PHD Finger binding to h3 trimethylated at k4 promotes nua3 hat activity at k14 of h3 and transcription at a subset of targeted orfs
Molecular Cell, 2006Co-Authors: Sean D Taverna, Serge Ilin, Richard S Rogers, Jason C Tanny, Heather Lavender, Lindsey A Baker, John Boyle, Lauren P Blair, Brian T Chait, Dinshaw J PatelAbstract:Posttranslational histone modifications participate in modulating the structure and function of chromatin. Promoters of transcribed genes are enriched with K4 trimethylation and hyperacetylation on the N-terminal tail of histone H3. Recently, PHD Finger proteins, like Yng1 in the NuA3 HAT complex, were shown to interact with H3K4me3, indicating a biochemical link between K4 methylation and hyperacetylation. By using a combination of mass spectrometry, biochemistry, and NMR, we detail the Yng1 PHD-H3K4me3 interaction and the importance of NuA3-dependent acetylation at K14. Furthermore, genome-wide ChIP-Chip analysis demonstrates colocalization of Yng1 and H3K4me3 in vivo. Disrupting the K4me3 binding of Yng1 altered K14ac and transcription at certain genes, thereby demonstrating direct in vivo evidence of sequential trimethyl binding, acetyltransferase activity, and gene regulation by NuA3. Our data support a general mechanism of transcriptional control through which histone acetylation upstream of gene activation is promoted partially through availability of H3K4me3, “read” by binding modules in select subunits.
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molecular basis for site specific read out of histone h3k4me3 by the bptf PHD Finger of nurf
Nature, 2006Co-Authors: Serge Ilin, W Wang, Elizabeth M Duncan, Joanna Wysocka, David C Allis, Dinshaw J PatelAbstract:Mono-, di- and trimethylated states of particular histone lysine residues are selectively found in different regions of chromatin, thereby implying specialized biological functions for these marks ranging from heterochromatin formation to X-chromosome inactivation and transcriptional regulation. A major challenge in chromatin biology has centred on efforts to define the connection between specific methylation states and distinct biological read-outs impacting on function. For example, histone H3 trimethylated at lysine 4 (H3K4me3) is associated with transcription start sites of active genes, but the molecular 'effectors' involved in specific recognition of H3K4me3 tails remain poorly understood. Here we demonstrate the molecular basis for specific recognition of H3(1-15)K4me3 (residues 1-15 of histone H3 trimethylated at K4) by a plant homeodomain (PHD) Finger of human BPTF (bromodomain and PHD domain transcription factor), the largest subunit of the ATP-dependent chromatin-remodelling complex, NURF (nucleosome remodelling factor). We report on crystallographic and NMR structures of the bromodomain-proximal PHD Finger of BPTF in free and H3(1-15)K4me3-bound states. H3(1-15)K4me3 interacts through anti-parallel beta-sheet formation on the surface of the PHD Finger, with the long side chains of arginine 2 (R2) and K4me3 fitting snugly in adjacent pre-formed surface pockets, and bracketing an invariant tryptophan. The observed stapling role by non-adjacent R2 and K4me3 provides a molecular explanation for H3K4me3 site specificity. Binding studies establish that the BPTF PHD Finger exhibits a modest preference for K4me3- over K4me2-containing H3 peptides, and discriminates against monomethylated and unmodified counterparts. Furthermore, we identified key specificity-determining residues from binding studies of H3(1-15)K4me3 with PHD Finger point mutants. Our findings call attention to the PHD Finger as a previously uncharacterized chromatin-binding module found in a large number of chromatin-associated proteins.
Yunyu Shi - One of the best experts on this subject based on the ideXlab platform.
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solution structure of an atypical PHD Finger in brpf2 and its interaction with dna
Journal of Structural Biology, 2012Co-Authors: Lei Liu, Jiahai Zhang, Su Qin, Yunyu ShiAbstract:Plant homeodomain (PHD) Finger is found to be a versatile reader that functions in recruiting transcription factors and chromatin modification complexes. Bromodomain- and PHD Finger-containing (BRPF) proteins are identified as scaffold component in a couple of histone acetyltransferase (HATs) complexes but the biological function of PHD Fingers, composing the motif called PZPM (PHD/Zn-knuckle/PHD Motif), in BRPF proteins is far from being well understood. Here we report the three-dimensional solution structure of the second PHD Finger of PZPM in human BRPF2. According to the structure, BRPF2 PHD2 possesses a two-strand β sheet which is different from any other PHD Fingers. Functionally, this PHD Finger can potentially bind DNA non-specifically with an evolutionarily conserved and positively charged surface. We provide the structural and interaction information of this atypical PHD Finger and categorize this BRPF2 PHD2 into a new subset of PHD Finger. Moreover our work also shed light on the functional aspect of the PZPM.
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combinatorial readout of unmodified h3r2 and acetylated h3k14 by the tandem PHD Finger of moz reveals a regulatory mechanism for hoxa9 transcription
Genes & Development, 2012Co-Authors: Yu Qiu, Lei Liu, Chen Zhao, Chuanchun Han, Jiahai Zhang, Yan Wang, Yide Mei, Yunyu ShiAbstract:Histone acetylation is a hallmark for gene transcription. As a histone acetyltransferase, MOZ (monocytic leukemia zinc Finger protein) is important for HOX gene expression as well as embryo and postnatal development. In vivo, MOZ forms a tetrameric complex with other subunits, including several chromatin-binding modules with regulatory functions. Here we report the solution structure of the tandem PHD (plant homeodomain) Finger (PHD12) of human MOZ in a free state and the 1.47 Acrystal structure in complex with H3K14ac peptide, which reveals the structural basis for the recognition of unmodified R2 and acetylated K14 on histone H3. Moreover, the results of chromatin immunoprecipitation (ChIP) and RT-PCR assays indicate that PHD12 facilitates the localization of MOZ onto the promoter locus of the HOXA9 gene, thereby promoting the H3 acetylation around the promoter region and further up-regulating the HOXA9 mRNA level. Taken together, our findings suggest that the combinatorial readout of the H3R2/K14ac by PHD12 might represent an important epigenetic regulatory mechanism that governs transcription and also provide a clue of cross-talk between the MOZ complex and histone H3 modifications. (Keywords: histone acetyltransferase; MOZ; PHD Finger; H3R2me0; H3K14ac; HOXA9) Supplemental material is available for this article.
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recognition of unmodified histone h3 by the first PHD Finger of bromodomain PHD Finger protein 2 provides insights into the regulation of histone acetyltransferases monocytic leukemic zinc Finger protein moz and moz related factor morf
Journal of Biological Chemistry, 2011Co-Authors: Su Qin, Lei Liu, Jiahai Zhang, Lei Jin, Yunyu ShiAbstract:MOZ (monocytic leukemic zinc-Finger protein) and MORF (MOZ-related factor) are histone acetyltransferases important for HOX gene expression as well as embryo and postnatal development. They form complexes with other regulatory subunits through the scaffold proteins BRPF1/2/3 (bromodomain-PHD (plant homeodomain) Finger proteins 1, 2, or 3). BRPF proteins have multiple domains, including two PHD Fingers, for potential interactions with histones. Here we show that the first PHD Finger of BRPF2 specifically recognizes the N-terminal tail of unmodified histone H3 (unH3) and report the solution structures of this PHD Finger both free and in complex with the unH3 peptide. Structural analysis revealed that the unH3 peptide forms a third antiparallel β-strand that pairs with the PHD1 two-stranded antiparallel β-sheet. The binding specificity was determined primarily through the recognition of arginine 2 and lysine 4 of the unH3 by conserved aspartic acids of PHD1 and of threonine 6 of the unH3 by a conserved asparagine. Isothermal titration calorimetry and NMR assays showed that post-translational modifications such as H3R2me2as, H3T3ph, H3K4me, H3K4ac, and H3T6ph antagonized the interaction between histone H3 and PHD1. Furthermore, histone binding by PHD1 was important for BRPF2 to localize to the HOXA9 locus in vivo. PHD1 is highly conserved in yeast NuA3 and other histone acetyltransferase complexes, so the results reported here also shed light on the function and regulation of these complexes.