Role of the CBP catalytic core in intramolecular SUMOylation and control of histone H3 acetylation

The histone acetyl transferases CREB-binding protein (CBP) and its paralog p300 play a critical role in numerous cellular processes. Dysregulation of their catalytic activity is associated with several human diseases. Previous work has elucidated the regulatory mechanisms of p300 acetyltransferase activity, but it is not known whether CBP activity is controlled similarly. Here, we present the crystal structure of the CBP catalytic core encompassing the bromodomain (BRD), CH2 (comprising PHD and RING), HAT, and ZZ domains at 2.4-Å resolution. The BRD, PHD, and HAT domains form an integral structural unit to which the RING and ZZ domains are flexibly attached. The structure of the apo-CBP HAT domain is similar to that of acyl-CoA–bound p300 HAT complexes and shows that the acetyl-CoA binding site is stably formed in the absence of cofactor. The BRD, PHD, and ZZ domains interact with small ubiquitin-like modifier 1 (SUMO-1) and Ubc9, and function as an intramolecular E3 ligase for SUMOylation of the cell cycle regulatory domain 1 (CRD1) of CBP, which is located adjacent to the BRD. In vitro HAT assays suggest that the RING domain, the autoregulatory loop (AL) within the HAT domain, and the ZZ domain do not directly influence catalytic activity, whereas the BRD is essential for histone H3 acetylation in nucleosomal substrates. Several lysine residues in the intrinsically disordered AL are autoacetylated by the HAT domain. Upon autoacetylation, acetyl-K1596 (Ac-K1596) binds intramolecularly to the BRD, competing with histones for binding to the BRD and acting as a negative regulator that inhibits histone H3 acetylation.

Download Full-text

The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation

Eukaryotic Cell ◽

10.1128/ec.00291-12 ◽

2013 ◽

Vol 12 (5) ◽

pp. 654-664 ◽

Cited By ~ 11

Author(s):

Ernest Radovani ◽

Matthew Cadorin ◽

Tahireh Shams ◽

Suzan El-Rass ◽

Abdel R. Karsou ◽

...

Keyword(s):

Histone Acetyltransferase ◽

Histone H3 ◽

Chromatin Assembly ◽

Carboxyl Terminus ◽

Histone Chaperones ◽

Content Type ◽

Histone H3 Acetylation ◽

H3 Acetylation

ABSTRACT Rtt109 is a fungal histone acetyltransferase (HAT) that catalyzes histone H3 acetylation functionally associated with chromatin assembly. Rtt109-mediated H3 acetylation involves two histone chaperones, Asf1 and Vps75. In vivo , Rtt109 requires both chaperones for histone H3 lysine 9 acetylation (H3K9ac) but only Asf1 for full H3K56ac. In vitro , Rtt109-Vps75 catalyzes both H3K9ac and H3K56ac, whereas Rtt109-Asf1 catalyzes only H3K56ac. In this study, we extend the in vitro chaperone-associated substrate specificity of Rtt109 by showing that it acetylates vertebrate linker histone in the presence of Vps75 but not Asf1. In addition, we demonstrate that in Saccharomyces cerevisiae a short basic sequence at the carboxyl terminus of Rtt109 (Rtt109C) is required for H3K9ac in vivo . Furthermore, through in vitro and in vivo studies, we demonstrate that Rtt109C is required for optimal H3K56ac by the HAT in the presence of full-length Asf1. When Rtt109C is absent, Vps75 becomes important for H3K56ac by Rtt109 in vivo . In addition, we show that lysine 290 (K290) in Rtt109 is required in vivo for Vps75 to enhance the activity of the HAT. This is the first in vivo evidence for a role for Vps75 in H3K56ac. Taken together, our results contribute to a better understanding of chaperone control of Rtt109-mediated H3 acetylation.

Download Full-text

Drosophila Ada2b Is Required for Viability and Normal Histone H3 Acetylation

Molecular and Cellular Biology ◽

10.1128/mcb.24.18.8080-8089.2004 ◽

2004 ◽

Vol 24 (18) ◽

pp. 8080-8089 ◽

Cited By ~ 37

Author(s):

Dai Qi ◽

Jan Larsson ◽

Mattias Mannervik

Keyword(s):

Gene Expression ◽

Transcriptional Activation ◽

Protein Complexes ◽

P53 Protein ◽

Polytene Chromosomes ◽

Histone H3 ◽

Saga Complex ◽

Histone H3 Acetylation ◽

H3 Acetylation

ABSTRACT Regulation of chromatin through histone acetylation is an important step in gene expression. The Gcn5 histone acetyltransferase is part of protein complexes, e.g., the SAGA complex, that interact with transcriptional activators, targeting the enzyme to specific promoters and assisting in recruitment of the basal RNA polymerase transcription machinery. The Ada2 protein directly binds to Gcn5 and stimulates its catalytic activity. Drosophila contains two Ada2 proteins, Drosophila Ada2a (dAda2a) and dAda2b. We have generated flies that lack dAda2b, which is part of a Drosophila SAGA-like complex. dAda2b is required for viability in Drosophila, and its deletion causes a reduction in histone H3 acetylation. A global hypoacetylation of chromatin was detected on polytene chromosomes in dAda2b mutants. This indicates that the dGcn5-dAda2b complex could have functions in addition to assisting in transcriptional activation through gene-specific acetylation. Although the Drosophila p53 protein was previously shown to interact with the SAGA-like complex in vitro, we find that p53 induction of reaper gene expression occurs normally in dAda2b mutants. Moreover, dAda2b mutant animals show excessive p53-dependent apoptosis in response to gamma radiation. Based on this result, we speculate that dAda2b may be necessary for efficient DNA repair or generation of a DNA damage signal. This could be an evolutionarily conserved function, since a yeast ada2 mutant is also sensitive to a genotoxic agent.

Download Full-text

H4R3 methylation facilitates β-globin transcription by regulating histone acetyltransferase binding and H3 acetylation

Blood ◽

10.1182/blood-2009-07-236059 ◽

2010 ◽

Vol 115 (10) ◽

pp. 2028-2037 ◽

Cited By ~ 55

Author(s):

Xingguo Li ◽

Xin Hu ◽

Bhavita Patel ◽

Zhuo Zhou ◽

Shermi Liang ◽

...

Keyword(s):

Histone Acetylation ◽

Chromatin Structure ◽

Globin Gene ◽

Histone H3 ◽

Arginine Methylation ◽

Globin Genes ◽

Erythroid Progenitor ◽

Histone H3 Acetylation ◽

H3 Acetylation

Abstract Histone modifications play an important role in the process of transcription. However, in contrast to lysine methylation, the role of arginine methylation in chromatin structure and transcription has been underexplored. The globin genes are regulated by a highly organized chromatin structure that juxtaposes the locus control region (LCR) with downstream globin genes. We report here that the targeted recruitment of asymmetric dimethyl H4R3 catalyzed by PRMT1 (protein arginine methyltransferase 1) facilitates histone H3 acetylation on Lys9/Lys14. Dimethyl H4R3 provides a binding surface for P300/CBP-associated factor (PCAF) and directly enhances histone H3 acetylation in vitro. We show that these active modifications are essential for efficient interactions between the LCR and the βmaj-promoter as well as transcription of the β-globin gene. Furthermore, knockdown (KD) of PRMT1 by RNA interference in erythroid progenitor cells prevents histone acetylation, enhancer and promoter interaction, and recruitment of transcription complexes to the active β-globin promoter. Reintroducing rat PRMT1 into the PRMT1 KD MEL cells rescues PRMT1 binding, β-globin transcription, and erythroid differentiation. Taken together, our data suggest that PRMT1-mediated dimethyl H4R3 facilitates histone acetylation and enhancer/promoter communications, which lead to the efficient recruitment of transcription preinitiation complexes to active promoters.

Download Full-text

Multivalency enables unidirectional switch-like competition between intrinsically disordered proteins

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2117338119 ◽

2022 ◽

Vol 119 (3) ◽

pp. e2117338119

Author(s):

Rebecca B. Berlow ◽

H. Jane Dyson ◽

Peter E. Wright

Keyword(s):

Transcriptional Control ◽

Intrinsically Disordered Proteins ◽

Binding Protein ◽

Critical Role ◽

Molecular Switch ◽

Negative Regulator ◽

Disordered Proteins ◽

Creb Binding Protein ◽

Binding Motifs ◽

Intrinsically Disordered

Intrinsically disordered proteins must compete for binding to common regulatory targets to carry out their biological functions. Previously, we showed that the activation domains of two disordered proteins, the transcription factor HIF-1α and its negative regulator CITED2, function as a unidirectional, allosteric molecular switch to control transcription of critical adaptive genes under conditions of oxygen deprivation. These proteins achieve transcriptional control by competing for binding to the TAZ1 domain of the transcriptional coactivators CREB-binding protein (CBP) and p300 (CREB: cyclic-AMP response element binding protein). To characterize the mechanistic details behind this molecular switch, we used solution NMR spectroscopy and complementary biophysical methods to determine the contributions of individual binding motifs in CITED2 to the overall competition process. An N-terminal region of the CITED2 activation domain, which forms a helix when bound to TAZ1, plays a critical role in initiating competition with HIF-1α by enabling formation of a ternary complex in a process that is highly dependent on the dynamics and disorder of the competing partners. Two other conserved binding motifs in CITED2, the LPEL motif and an aromatic/hydrophobic motif that we term ϕC, function synergistically to enhance binding of CITED2 and inhibit rebinding of HIF-1α. The apparent unidirectionality of competition between HIF-1α and CITED2 is lost when one or more of these binding regions is altered by truncation or mutation of the CITED2 peptide. Our findings illustrate the complexity of molecular interactions involving disordered proteins containing multivalent interaction motifs and provide insight into the unique mechanisms by which disordered proteins compete for occupancy of common molecular targets within the cell.

Download Full-text

Histone H3 acetylation of StAR and decrease in DAX-1 is involved in the luteinization of bovine granulosa cells during in vitro culture

Molecular and Cellular Biochemistry ◽

10.1007/s11010-009-0072-y ◽

2009 ◽

Vol 328 (1-2) ◽

pp. 41-47 ◽

Cited By ~ 12

Author(s):

Takashi Shimizu ◽

Natsuko Sudo ◽

Hiromichi Yamashita ◽

Chiaki Murayama ◽

Hitoshi Miyazaki ◽

...

Keyword(s):

In Vitro Culture ◽

Granulosa Cells ◽

Histone H3 ◽

Histone H3 Acetylation ◽

H3 Acetylation

Download Full-text

Cross-talk between Histone Modifications in Response to Histone Deacetylase Inhibitors

Journal of Biological Chemistry ◽

10.1074/jbc.m606773200 ◽

2006 ◽

Vol 282 (7) ◽

pp. 4408-4416 ◽

Cited By ~ 134

Author(s):

Karl P. Nightingale ◽

Susanne Gendreizig ◽

Darren A. White ◽

Charlotte Bradbury ◽

Florian Hollfelder ◽

...

Keyword(s):

Histone Deacetylase ◽

Histone Modifications ◽

Histone Deacetylase Inhibitors ◽

Gene Activation ◽

Histone H3 ◽

H3k4 Methylation ◽

Histone H3 Acetylation ◽

H3 Acetylation

Histones are subject to a wide variety of post-translational modifications that play a central role in gene activation and silencing. We have used histone modification-specific antibodies to demonstrate that two histone modifications involved in gene activation, histone H3 acetylation and H3 lysine 4 methylation, are functionally linked. This interaction, in which the extent of histone H3 acetylation determines both the abundance and the “degree” of H3K4 methylation, plays a major role in the epigenetic response to histone deacetylase inhibitors. A combination of in vivo knockdown experiments and in vitro methyltransferase assays shows that the abundance of H3K4 methylation is regulated by the activities of two opposing enzyme activities, the methyltransferase MLL4, which is stimulated by acetylated substrates, and a novel and as yet unidentified H3K4me3 demethylase.

Download Full-text

Arabidopsis SUMO E3 Ligase SIZ1 Interacts with HDA6 and Negatively Regulates HDA6 Function during Flowering

Cells ◽

10.3390/cells10113001 ◽

2021 ◽

Vol 10 (11) ◽

pp. 3001

Author(s):

Sujuan Gao ◽

Xueqin Zeng ◽

Jianhao Wang ◽

Yingchao Xu ◽

Chunwei Yu ◽

...

Keyword(s):

Target Genes ◽

Environmental Changes ◽

Histone H3 ◽

E3 Ligase ◽

Histone Deacetylase 6 ◽

Histone H3 Acetylation ◽

Sumo E3 Ligase ◽

H3 Acetylation

The changes in histone acetylation mediated by histone deacetylases (HDAC) play a crucial role in plant development and response to environmental changes. Mammalian HDACs are regulated by post-translational modifications (PTM), such as phosphorylation, acetylation, ubiquitination and small ubiquitin-like modifier (SUMO) modification (SUMOylation), which affect enzymatic activity and transcriptional repression. Whether PTMs of plant HDACs alter their functions are largely unknown. In this study, we demonstrated that the Arabidopsis SUMO E3 ligase SAP AND MIZ1 DOMAIN-CONTAINING LIGASE1 (SIZ1) interacts with HISTONE DEACETYLASE 6 (HDA6) both in vitro and in vivo. Biochemical analyses indicated that HDA6 is not modified by SUMO1. Overexpression of HDA6 in siz1-3 background results in a decreased level of histone H3 acetylation, indicating that the activity of HDA6 is increased in siz1-3 plants. Chromatin immunoprecipitation (ChIP) assays showed that SIZ1 represses HDA6 binding to its target genes FLOWERING LOCUS C (FLC) and MADS AFFECTING FLOWERING 4 (MAF4), resulting in the upregulation of FLC and MAF4 by increasing the level of histone H3 acetylation. Together, these findings indicate that the Arabidopsis SUMO E3 ligase SIZ1 interacts with HDA6 and negatively regulates HDA6 function.

Download Full-text

Inhibition of class I HDACs preserves hair follicle inductivity in postnatal dermal cells

Scientific Reports ◽

10.1038/s41598-021-03508-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Minji Park ◽

Sunhyae Jang ◽

Jin Ho Chung ◽

Ohsang Kwon ◽

Seong Jin Jo

Keyword(s):

Histone H3 ◽

Wnt Signaling Pathway ◽

Hair Follicles ◽

Class I ◽

Histone H3 Acetylation ◽

Dermal Cells ◽

Class I Hdacs ◽

H3 Acetylation

AbstractInduction of new hair follicles (HFs) may be an ultimate treatment goal for alopecia; however, functional cells with HF inductivity must be expanded in bulk for clinical use. In vitro culture conditions are completely different from the in vivo microenvironment. Although fetal and postnatal dermal cells (DCs) have the potential to induce HFs, they rapidly lose this HF inductivity during culture, accompanied by a drastic change in gene expression. This suggests that epigenetic regulation may be involved. Of the various histone deacetylases (HDACs), Class I HDACs are noteworthy because they are ubiquitously expressed and have the strongest deacetylase activity. This study revealed that DCs from postnatal mice rapidly lose HF inductivity and that this reduction is accompanied by a significant decrease in histone H3 acetylation. However, MS-275, an inhibitor of class I HDACs, preserves HF inductivity in DCs during culture, increasing alkaline phosphatase activity and upregulating HF inductive genes such as BMP4, HEY1, and WIF1. In addition, the inhibition of class I HDACs activates the Wnt signaling pathway, the most well-described molecular pathway in HF development, via increased histone H3 acetylation within the promoter region of the Wnt transcription factor LEF1. Our results suggest that class I HDACs could be a potential target for the neogenesis of HFs.

Download Full-text