scholarly journals Evolutionary Adaptation of the Fly Pygo PHD Finger toward Recognizing Histone H3 Tail Methylated at Arginine 2

Structure ◽  
2013 ◽  
Vol 21 (12) ◽  
pp. 2208-2220 ◽  
Author(s):  
Thomas C.R. Miller ◽  
Juliusz Mieszczanek ◽  
María José Sánchez-Barrena ◽  
Trevor J. Rutherford ◽  
Marc Fiedler ◽  
...  
Keyword(s):  
Histone H3 ◽  
Evolutionary Adaptation ◽  
Phd Finger

scholarly journals HBO1 HAT Complexes Target Chromatin throughout Gene Coding Regions via Multiple PHD Finger Interactions with Histone H3 Tail

2009 ◽  
Vol 33 (2) ◽  
pp. 257-265 ◽  
Author(s):  
Nehmé Saksouk ◽  
Nikita Avvakumov ◽  
Karen S. Champagne ◽  
Tiffany Hung ◽  
Yannick Doyon ◽  
...  
Keyword(s):  
Histone H3 ◽  
Phd Finger ◽  
Coding Regions ◽  
Gene Coding

scholarly journals Histone H3 N-terminal mimicry drives a novel network of methyl-effector interactions

2021 ◽  
Author(s):  
Jianji Chen ◽  
John Horton ◽  
Cari Sagum ◽  
Jujun Zhou ◽  
Xiaodong Cheng ◽  
...  
Keyword(s):  
Histone H3 ◽  
Transcriptional Repressor ◽  
Protein Domain ◽  
Nurd Complex ◽  
Phd Finger ◽  
Effector Domains ◽  
Methionine Residue ◽  
Repressor Complex

The reader ability of PHD fingers is largely limited to the recognition of the histone H3 N-terminal tail. Distinct subsets of PHDs bind either H3K4me3 (a transcriptional activator mark) or H3K4me0 (a transcriptional repressor state). Structural studies have identified common features among the different H3K4me3 effector PHDs, including 1) removal of the initiator methionine residue of H3 to prevent steric interference, 2) a groove where arginine-2 binds, and 3) an aromatic cage that engages methylated lysine-4. We hypothesize that  PHDs  have the ability to engage with non-histone ligands, as long as they adhere to these three rules. A search of the human proteome revealed an enrichment of chromatin-binding proteins that met these criteria, which we termed H3 N-terminal mimicry proteins (H3TMs). Seven H3TMs were selected, and used to screen a protein domain microarray for potential effector domains, and they all had the ability to bind H3K4me3-interacting effector domains. Furthermore, the binding affinity between the VRK1 peptide and the PHD domain of PHF2 is ~3-fold stronger than that of PHF2 and H3K4me3 interaction. The crystal structure of PHF2 PHD finger bound with VRK1 K4me3 peptide provides a molecular basis for stronger binding of VRK1 peptide. In addition, a number of the H3TMs peptides, in their unmethylated form, interact with NuRD transcriptional repressor complex. Our findings provide in vitro evidence that methylation of H3TMs can promote interactions with PHD and Tudor domain-containing proteins and potentially block interactions with the NuRD complex. We propose that these interactions can occur in vivo as well.

scholarly journals 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

2009 ◽  
Vol 37 (9) ◽  
pp. 2951-2961 ◽  
Author(s):  
Francesca Chignola ◽  
Massimiliano Gaetani ◽  
Ana Rebane ◽  
Tõnis Org ◽  
Luca Mollica ◽  
...  
Keyword(s):  
Solution Structure ◽  
Histone H3 ◽  
Phd Finger ◽  
Autoimmune Regulator

scholarly journals Structural basis for site-specific reading of unmodified R2 of histone H3 tail by UHRF1 PHD finger

Cell Research ◽  
2011 ◽  
Vol 21 (9) ◽  
pp. 1379-1382 ◽  
Author(s):  
Chengkun Wang ◽  
Jie Shen ◽  
Zhongzheng Yang ◽  
Ping Chen ◽  
Bin Zhao ◽  
...  
Keyword(s):  
Histone H3 ◽  
Structural Basis ◽  
Site Specific ◽  
Phd Finger ◽  
Specific Reading

scholarly journals The Yng1p Plant Homeodomain Finger Is a Methyl-Histone Binding Module That Recognizes Lysine 4-Methylated Histone H3

2006 ◽  
Vol 26 (21) ◽  
pp. 7871-7879 ◽  
Author(s):  
David G. E. Martin ◽  
Kristin Baetz ◽  
Xiaobing Shi ◽  
Kay L. Walter ◽  
Vicki E. MacDonald ◽  
...  
Keyword(s):  
Histone H3 ◽  
General Role ◽  
Histone Binding ◽  
Phd Finger ◽  
Amino Terminal ◽  
Plant Homeodomain Finger ◽  
Plant Homeodomain ◽  
Insight Into

ABSTRACT The ING (inhibitor of growth) protein family includes a group of homologous nuclear proteins that share a highly conserved plant homeodomain (PHD) finger domain at their carboxyl termini. Members of this family are found in multiprotein complexes that posttranslationally modify histones, suggesting that these proteins serve a general role in permitting various enzymatic activities to interact with nucleosomes. There are three members of the ING family in Saccharomyces cerevisiae: Yng1p, Yng2p, and Pho23p. Yng1p is a component of the NuA3 histone acetyltransferase complex and is required for the interaction of NuA3 with chromatin. To gain insight into the function of the ING proteins, we made use of a genetic strategy to identify genes required for the binding of Yng1p to histones. Using the toxicity of YNG1 overexpression as a tool, we showed that Yng1p interacts with the amino-terminal tail of histone H3 and that this interaction can be disrupted by loss of lysine 4 methylation within this tail. Additionally, we mapped the region of Yng1p required for overexpression of toxicity to the PHD finger, showed that this region capable of binding lysine 4-methylated histone H3 in vitro, and demonstrated that mutations of the PHD finger that abolish binding in vitro are no longer toxic in vivo. These results identify a novel function for the Yng1p PHD finger in promoting stabilization of the NuA3 complex at chromatin through recognition of histone H3 lysine 4 methylation.

scholarly journals The double PHD finger domain of MOZ/MYST3 induces  -helical structure of the histone H3 tail to facilitate acetylation and methylation sampling and modification

2013 ◽  
Vol 42 (2) ◽  
pp. 822-835 ◽  
Author(s):  
I. Dreveny ◽  
S. E. Deeves ◽  
J. Fulton ◽  
B. Yue ◽  
M. Messmer ◽  
...  
Keyword(s):  
Histone H3 ◽  
Helical Structure ◽  
Phd Finger

scholarly journals Deficient histone H3 propionylation by BRPF1-KAT6 complexes in neurodevelopmental disorders and cancer

2020 ◽  
Vol 6 (4) ◽  
pp. eaax0021 ◽  
Author(s):  
Kezhi Yan ◽  
Justine Rousseau ◽  
Keren Machol ◽  
Laura A. Cross ◽  
Katherine E. Agre ◽  
...  
Keyword(s):  
Developmental Disorders ◽  
Immunofluorescence Microscopy ◽  
Histone H3 ◽  
Mouse Embryos ◽  
Active Chromatin ◽  
Phd Finger ◽  
Lysine Acetyltransferase ◽  
Shed Light

Lysine acetyltransferase 6A (KAT6A) and its paralog KAT6B form stoichiometric complexes with bromodomain- and PHD finger-containing protein 1 (BRPF1) for acetylation of histone H3 at lysine 23 (H3K23). We report that these complexes also catalyze H3K23 propionylation in vitro and in vivo. Immunofluorescence microscopy and ATAC-See revealed the association of this modification with active chromatin. Brpf1 deletion obliterates the acylation in mouse embryos and fibroblasts. Moreover, we identify BRPF1 variants in 12 previously unidentified cases of syndromic intellectual disability and demonstrate that these cases and known BRPF1 variants impair H3K23 propionylation. Cardiac anomalies are present in a subset of the cases. H3K23 acylation is also impaired by cancer-derived somatic BRPF1 mutations. Valproate, vorinostat, propionate and butyrate promote H3K23 acylation. These results reveal the dual functionality of BRPF1-KAT6 complexes, shed light on mechanisms underlying related developmental disorders and various cancers, and suggest mutation-based therapy for medical conditions with deficient histone acylation.

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