scholarly journals Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Wallace H. Liu ◽  
Jie Zheng ◽  
Jessica L. Feldman ◽  
Mark A. Klein ◽  
Vyacheslav I. Kuznetsov ◽  
...  
Keyword(s):  
Histone Deacetylases ◽  
Nucleosome Core ◽  
Intrinsically Disordered ◽  
Nucleosome Core Particles ◽  
Nucleosomal Dna ◽  
C Terminus ◽  
Intrinsic Capacity ◽  
Multivalent Interactions ◽  
H3 Acetylation ◽  
Nucleosome Binding

Abstract The protein deacetylase SIRT6 maintains cellular homeostasis through multiple pathways that include the deacetylation of histone H3 and repression of transcription. Prior work suggests that SIRT6 is associated with chromatin and can substantially reduce global levels of H3 acetylation, but how SIRT6 is able to accomplish this feat is unknown. Here, we describe an exquisitely tight interaction between SIRT6 and nucleosome core particles, in which a 2:1 enzyme:nucleosome complex assembles via asymmetric binding with distinct affinities. While both SIRT6 molecules associate with the acidic patch on the nucleosome, we find that the intrinsically disordered SIRT6 C-terminus promotes binding at the higher affinity site through recognition of nucleosomal DNA. Together, multivalent interactions couple productive binding to efficient deacetylation of histones on endogenous chromatin. Unique among histone deacetylases, SIRT6 possesses the intrinsic capacity to tightly interact with nucleosomes for efficient activity.

Dri1 mediates heterochromatin assembly via RNAi and histone deacetylation

Genetics ◽  
2021 ◽  
Author(s):  
Hyoju Ban ◽  
Wenqi Sun ◽  
Yu-hang Chen ◽  
Yong Chen ◽  
Fei Li
Keyword(s):  
Histone Deacetylases ◽  
Genome Stability ◽  
Rna Binding ◽  
Histone Deacetylation ◽  
Rnai Pathway ◽  
Chromatin Domain ◽  
Heterochromatin Protein 1 ◽  
Intrinsically Disordered ◽  
C Terminus ◽  
Heterochromatin Assembly

Abstract Heterochromatin, a transcriptionally silenced chromatin domain, is important for genome stability and gene expression. Histone 3 lysine 9 methylation (H3K9me) and histone hypoacetylation are conserved epigenetic hallmarks of heterochromatin. In fission yeast, RNA interference (RNAi) plays a key role in H3K9 methylation and heterochromatin silencing. However, how RNAi machinery and histone deacetylases (HDACs) are coordinated to ensure proper heterochromatin assembly is still unclear. Previously, we showed that Dpb4, a conserved DNA polymerase epsilon subunit, plays a key role in the recruitment of HDACs to heterochromatin during S phase. Here, we identified a novel RNA-binding protein Dri1 that interacts with Dpb4. GFP-tagged Dri1 forms distinct foci mostly in the nucleus, showing a high degree of colocalization with Swi6/Heterochromatin Protein 1. Deletion of dri1+ leads to defects in silencing, H3K9me, and heterochromatic siRNA generation. We also showed that Dri1 physically associates with heterochromatic transcripts, and is required for the recruitment of the RNA-induced transcriptional silencing (RITS) complex via interacting with the complex. Furthermore, loss of Dri1 decreases the association of the Sir2 HDAC with heterochromatin. We further demonstrated that the C-terminus of Dri1 that includes an intrinsically disordered (IDR) region and three zinc fingers is crucial for its role in silencing. Together, our evidences suggest that Dri1 facilitates heterochromatin assembly via the RNAi pathway and HDAC.

scholarly journals Defining p53 pioneering capabilities with competitive nucleosome binding assays

2018 ◽  
Author(s):  
Xinyang Yu ◽  
Michael J. Buck
Keyword(s):  
Binding Site ◽  
Specific Binding ◽  
Regulatory Sequences ◽  
Binding Assays ◽  
Nucleosome Core ◽  
Nucleosomal Dna ◽  
Free Region ◽  
A Cell ◽  
Nucleosome Binding

AbstractAccurate gene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. The ability to target a transcription factor binding site (TFBS) within a nucleosome has been the defining characteristic for a special class of TFs known as pioneer factors. Recent studies suggest p53 functions as a pioneer factor that can target its TFBS within nucleosomes, but it remains unclear how p53 binds to nucleosomal DNA. To comprehensively examine p53 nucleosome binding we competitively bound p53 to multiple in vitro formed nucleosomes containing a high or low-affinity p53 TFBS located at differing translational and rotational positions within the nucleosome. Stable p53-nucleosome complexes were isolated and quantified using next generation sequencing. Our results demonstrate p53 binding is limited to nucleosome edges with significant binding inhibition occurring within 50-bp of the nucleosome dyad. Binding site affinity only affects p53 binding for TFBS located outside the nucleosome core at the same nucleosomal positions. Furthermore, p53 has strong non-specific nucleosome binding facilitating its interaction with chromatin. Our in vitro findings were confirmed by examining p53 induced binding in a cell line model, showing induced binding at nucleosome edges flanked by a nucleosome free region. Overall, our results suggest that the pioneering capabilities of p53 are driven by non-specific nucleosome binding with specific binding at nucleosome edges.

scholarly journals Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory

2015 ◽  
Vol 17 (34) ◽  
pp. 21866-21879 ◽  
Author(s):  
Patrick Norman ◽  
Joseph Parello ◽  
Prasad L. Polavarapu ◽  
Mathieu Linares
Keyword(s):  
Circular Dichroism ◽  
Density Functional ◽  
Time Dependent ◽  
Functional Theory ◽  
Electronic Circular Dichroism ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
Nucleosomal Dna ◽  
Circular Dichroïsm ◽  
Dependent Density

It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles.

scholarly journals Histone dynamics mediate DNA unwrapping and sliding in nucleosomes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Grigoriy A. Armeev ◽  
Anastasiia S. Kniazeva ◽  
Galina A. Komarova ◽  
Mikhail P. Kirpichnikov ◽  
Alexey K. Shaytan
Keyword(s):  
Building Blocks ◽  
Dna Dynamics ◽  
Conformational Variability ◽  
Nucleosome Core ◽  
Nucleosome Dynamics ◽  
Nucleosome Core Particles ◽  
Nucleosomal Dna ◽  
Dna Base ◽  
Dna Unwrapping ◽  
Dynamics Simulations

AbstractNucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly wrap ∼147 DNA base pairs around an octamer of histone proteins. How nucleosome structural dynamics affect genome functioning is not completely clear. Here we report all-atom molecular dynamics simulations of nucleosome core particles at a timescale of 15 microseconds. At this timescale, functional modes of nucleosome dynamics such as spontaneous nucleosomal DNA breathing, unwrapping, twisting, and sliding were observed. We identified atomistic mechanisms of these processes by analyzing the accompanying structural rearrangements of the histone octamer and histone-DNA contacts. Octamer dynamics and plasticity were found to enable DNA unwrapping and sliding. Through multi-scale modeling, we showed that nucleosomal DNA dynamics contribute to significant conformational variability of the chromatin fiber at the supranucleosomal level. Our study further supports mechanistic coupling between fine details of histone dynamics and chromatin functioning, provides a framework for understanding the effects of various chromatin modifications.

scholarly journals The effect of linker DNA on the structure and interaction of nucleosome core particles

Soft Matter ◽  
2018 ◽  
Vol 14 (45) ◽  
pp. 9096-9106 ◽  
Author(s):  
Yen-Chih Huang ◽  
Chun-Jen Su ◽  
Nikolay Korolev ◽  
Nikolay V. Berezhnoy ◽  
Sai Wang ◽  
...  
Keyword(s):  
Small Angle ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
X Ray ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
X Ray Scattering ◽  
Nucleosomal Dna ◽  
The Impact

Small angle X-ray scattering reveals linker DNA-induced partial unwrapping of nucleosomal DNA on the nucleosome core particle (NCP) and the impact on NCP interaction demonstrating the crucial role of linker DNA.

scholarly journals Cryo-EM structure of the human MLL1 core complex bound to the nucleosome

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Sang Ho Park ◽  
Alex Ayoub ◽  
Young-Tae Lee ◽  
Jing Xu ◽  
Hanseong Kim ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Histone H4 ◽  
Core Complex ◽  
Regulate Gene Expression ◽  
Histone Methyltransferases ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
Nucleosomal Dna ◽  
Histone H3k4 ◽  
Methylation Activity

AbstractMixed lineage leukemia (MLL) family histone methyltransferases are enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive structural and biochemical studies, the molecular mechanisms whereby the MLL complexes recognize histone H3K4 within nucleosome core particles (NCPs) remain unclear. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the NCP-bound human MLL1 core complex. We show that the MLL1 core complex anchors to the NCP via the conserved RbBP5 and ASH2L, which interact extensively with nucleosomal DNA and the surface close to the N-terminal tail of histone H4. Concurrent interactions of RbBP5 and ASH2L with the NCP uniquely align the catalytic MLL1SET domain at the nucleosome dyad, thereby facilitating symmetrical access to both H3K4 substrates within the NCP. Our study sheds light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity.

scholarly journals Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies

2021 ◽  
Vol 7 (2) ◽  
pp. eabd4413
Author(s):  
Jung-Hoon Lee ◽  
Daniel Bollschweiler ◽  
Tillman Schäfer ◽  
Robert Huber
Keyword(s):  
Transcriptional Repression ◽  
Histone Deacetylases ◽  
Active Sites ◽  
Chromatin Modification ◽  
Structural Basis ◽  
Amino Terminal ◽  
Cryo Electron Microscopy ◽  
Multiple Contacts ◽  
Lysine Residues ◽  
Nucleosome Binding

The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive. Our cryo–electron microscopy structures of the yeast class II HDAC ensembles show that the HDAC protomer comprises a triangle-shaped assembly of stoichiometry Hda12-Hda2-Hda3, in which the active sites of the Hda1 dimer are freely accessible. We also observe a tetramer of protomers, where the nucleosome binding modules are inaccessible. Structural analysis of the nucleosome-bound complexes indicates how positioning of Hda1 adjacent to histone H2B affords HDAC catalysis. Moreover, it reveals how an intricate network of multiple contacts between a dimer of protomers and the nucleosome creates a platform for expansion of the HDAC activities. Our study provides comprehensive insight into the structural plasticity of the HDAC complex and its functional mechanism of chromatin modification.

scholarly journals Phosphorylation within Intrinsic Disordered Region Discriminates Histone Variant macroH2A1 Splicing Isoforms—macroH2A1.1 and macroH2A1.2

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 659
Author(s):  
Sebastiano Giallongo ◽  
Oriana Lo Re ◽  
Gabriela Lochmanová ◽  
Luca Parca ◽  
Francesco Petrizzelli ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Regulatory Element ◽  
Histone Variants ◽  
Histone H2a ◽  
Human Hepatoma Cells ◽  
Nucleosome Core ◽  
Intrinsically Disordered ◽  
Splicing Isoforms ◽  
The Impact

Background: Gene expression in eukaryotic cells can be governed by histone variants, which replace replication-coupled histones, conferring unique chromatin properties. MacroH2A1 is a histone H2A variant containing a domain highly similar to H2A and a large non-histone (macro) domain. MacroH2A1, in turn, is present in two alternatively exon-spliced isoforms: macroH2A1.1 and macroH2A1.2, which regulate cell plasticity and proliferation in a remarkably distinct manner. The N-terminal and the C-terminal tails of H2A histones stem from the nucleosome core structure and can be target sites for several post-translational modifications (PTMs). MacroH2A1.1 and macroH2A1.2 isoforms differ only in a few amino acids and their ability to bind NAD-derived metabolites, a property allegedly conferring their different functions in vivo. Some of the modifications on the macroH2A1 variant have been identified, such as phosphorylation (T129, S138) and methylation (K18, K123, K239). However, no study to our knowledge has analyzed extensively, and in parallel, the PTM pattern of macroH2A1.1 and macroH2A1.2 in the same experimental setting, which could facilitate the understanding of their distinct biological functions in health and disease. Methods: We used a mass spectrometry-based approach to identify the sites for phosphorylation, acetylation, and methylation in green fluorescent protein (GFP)-tagged macroH2A1.1 and macroH2A1.2 expressed in human hepatoma cells. The impact of selected PTMs on macroH2A1.1 and macroH2A1.2 structure and function are demonstrated using computational analyses. Results: We identified K7 as a new acetylation site in both macroH2A1 isoforms. Quantitative comparison of histone marks between the two isoforms revealed significant differences in the levels of phosphorylated T129 and S170. Our computational analysis provided evidence that the phosphorylation status in the intrinsically disordered linker region in macroH2A1 isoforms might represent a key regulatory element contributing to their distinct biological responses. Conclusions: Taken together, our results report different PTMs on the two macroH2A1 splicing isoforms as responsible for their distinct features and distribution in the cell.

scholarly journals Disorder in a two-domain neuronal Ca2+-binding protein regulates domain stability and dynamics using ligand mimicry

2020 ◽  
Author(s):  
Lasse Staby ◽  
Katherine R. Kemplen ◽  
Amelie Stein ◽  
Michael Ploug ◽  
Jane Clarke ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Life Time ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Order And Disorder ◽  
C Terminus ◽  
Close Relationship ◽  
Stability Dynamics ◽  
And Function

Abstract Understanding the interplay between sequence, structure and function of proteins has been complicated in recent years by the discovery of intrinsically disordered proteins (IDPs), which perform biological functions in the absence of a well-defined three-dimensional fold. Disordered protein sequences account for roughly 30% of the human proteome and in many proteins, disordered and ordered domains coexist. However, few studies have assessed how either feature affects the properties of the other. In this study, we examine the role of a disordered tail in the overall properties of the two-domain, calcium-sensing protein neuronal calcium sensor 1 (NCS-1). We show that loss of just six of the 190 residues at the flexible C-terminus is sufficient to severely affect stability, dynamics, and folding behavior of both ordered domains. We identify specific hydrophobic contacts mediated by the disordered tail that may be responsible for stabilizing the distal N-terminal domain. Moreover, sequence analyses indicate the presence of an LSL-motif in the tail that acts as a mimic of native ligands critical to the observed order–disorder communication. Removing the disordered tail leads to a shorter life-time of the ligand-bound complex likely originating from the observed destabilization. This close relationship between order and disorder may have important implications for how investigations into mixed systems are designed and opens up a novel avenue of drug targeting exploiting this type of behavior.

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