Nucleosome allostery in pioneer transcription factor binding

While recent experiments revealed that some pioneer transcription factors (TFs) can bind to their target DNA sequences inside a nucleosome, the binding dynamics of their target recognitions are poorly understood. Here we used the latest coarse-grained models and molecular dynamics simulations to study the nucleosome-binding procedure of the two pioneer TFs, Sox2 and Oct4. In the simulations for a strongly positioning nucleosome, Sox2 selected its target DNA sequence only when the target was exposed. Otherwise, Sox2 entropically bound to the dyad region nonspecifically. In contrast, Oct4 plastically bound on the nucleosome mainly in two ways. First, the two POU domains of Oct4 separately bound to the two parallel gyres of the nucleosomal DNA, supporting the previous experimental results of the partial motif recognition. Second, the POUSdomain of Oct4 favored binding on the acidic patch of histones. Then, simulating the TFs binding to a genomic nucleosome, theLIN28Bnucleosome, we found that the recognition of a pseudo motif by Sox2 induced the local DNA bending and shifted the population of the rotational position of the nucleosomal DNA. The redistributed DNA phase, in turn, changed the accessibility of a distant TF binding site, which consequently affected the binding probability of a second Sox2 or Oct4. These results revealed a nucleosomal DNA-mediated allosteric mechanism, through which one TF binding event can change the global conformation, and effectively regulate the binding of another TF at distant sites. Our simulations provide insights into the binding mechanism of single and multiple TFs on the nucleosome.

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Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data

10.1101/288795 ◽

2018 ◽

Author(s):

Cheng Tan ◽

Shoji Takada

Keyword(s):

Structure Data ◽

Dna Sequences ◽

Complex Structure ◽

Specific Protein ◽

Coarse Grained ◽

Binding Modes ◽

Binding Assays ◽

Dna Interactions ◽

Protein Dna Interactions ◽

Dynamics Simulations

ABSTRACTHow transcription factors (TFs) recognize their DNA sequences is often investigated complementarily by high-throughput protein binding assays and by structural biology experiments. The former quantifies the specificity of TF binding sites for numerous DNA sequences, often represented as the position-weight-matrix (PWM). The latter provides mechanistic insights into the interactions via the protein-DNA complex structures. However, these two types of data are not readily integrated. Here, we propose and test a new modeling method that incorporates the PWM with complex structure data. Based on pre-tuned coarse-grained models for proteins and DNAs, we model the specific protein-DNA interactions, PWMcos, in terms of an orientation-dependent potential function, which enables us to perform molecular dynamics simulations at unprecedentedly large scales. We show that the PWMcos model reproduces subtle specificity in the protein-DNA recognition. During the target search in genomic sequences, TF moves on highly rugged landscapes and occasionally flips on DNA depending on the sequence. The TATA-binding protein exhibits two remarkably distinct binding modes, of which frequencies differ between TATA-containing and TATA-less promoters. The PWMcos is general and can be applied to any protein-DNA interactions given their PWMs and complex structure data are available.

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Linker DNA and histone contributions in nucleosome binding by p53

The Journal of Biochemistry ◽

10.1093/jb/mvaa081 ◽

2020 ◽

Vol 168 (6) ◽

pp. 669-675 ◽

Cited By ~ 1

Author(s):

Masahiro Nishimura ◽

Yasuhiro Arimura ◽

Kayo Nozawa ◽

Hitoshi Kurumizaka

Keyword(s):

Transcription Factors ◽

Amino Acid Region ◽

Cycle Arrest ◽

Nucleosomal Dna ◽

Tumour Suppressor Protein ◽

Specific Complex ◽

Pioneer Transcription Factor ◽

Binding Sequence ◽

Nucleosome Binding ◽

Acid Region

Abstract The tumour suppressor protein p53 regulates various genes involved in cell-cycle arrest, apoptosis and DNA repair in response to cellular stress, and apparently functions as a pioneer transcription factor. The pioneer transcription factors can bind nucleosomal DNA, where many transcription factors are largely restricted. However, the mechanisms by which p53 recognizes the nucleosomal DNA are poorly understood. In the present study, we found that p53 requires linker DNAs for the efficient formation of p53-nucleosome complexes. p53 forms an additional specific complex with the nucleosome, when the p53 binding sequence is located around the entry/exit region of the nucleosomal DNA. We also showed that p53 directly binds to the histone H3-H4 complex via its N-terminal 1–93 amino acid region. These results shed light on the mechanism of nucleosome recognition by p53.

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Structural basis of the regulation of normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2

10.1101/2020.12.05.413278 ◽

2020 ◽

Author(s):

Ko Sato ◽

Amarjeet Kumar ◽

Keisuke Hamada ◽

Chikako Okada ◽

Asako Oguni ◽

...

Keyword(s):

Histone H3 ◽

Point Mutations ◽

Polycomb Group ◽

Structural Basis ◽

Nucleosomal Dna ◽

Oncogenic Mutations ◽

Repressive Effect ◽

Binding Cleft ◽

Dynamics Simulations ◽

Nucleosome Binding

SummaryDimethylated histone H3 Lys36 (H3K36me2) regulates gene expression by antagonizing the repressive effect of polycomb-group proteins. Aberrant upregulation of H3K36me2, either by overexpression or point mutations of NSD2/MMSET, an H3K36 dimethyltransferase, is found in various cancers, including multiple myeloma. To understand the mechanism underlying its regulation, here we report the cryo-electron microscopy structure of the catalytic fragment of NSD2 bound to the nucleosome at 2.8 Å resolution. The nucleosomal DNA is partially unwrapped at superhelix location +5.5, facilitating the access of NSD2 to H3K36. NSD2 interacts with DNA and H2A along with H3. The autoinhibitory loop of NSD2 changes its conformation upon nucleosome binding to accommodate H3 in its substrate-binding cleft. Kinetic analysis revealed two oncogenic mutations, E1099K and T1150A, to aberrantly activate NSD2 by increasing its catalytic turnover but not the nucleosome affinity. Molecular dynamics simulations suggested that in both mutants, the autoinhibitory loop adopts an open state that can accommodate H3 more often than the wild type. We propose that E1099K and T1150A destabilize the interactions that keep the autoinhibitory loop closed, thereby enhancing the catalytic turnover. Our analyses would guide the development of specific inhibitors of NSD2 for the treatment of various cancers.

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Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2

Nature Communications ◽

10.1038/s41467-021-26913-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ko Sato ◽

Amarjeet Kumar ◽

Keisuke Hamada ◽

Chikako Okada ◽

Asako Oguni ◽

...

Keyword(s):

Histone H3 ◽

Structural Basis ◽

Wild Type ◽

Cryo Electron Microscopy ◽

Nucleosomal Dna ◽

Oncogenic Mutations ◽

Binding Cleft ◽

Dynamics Simulations ◽

Nucleosome Binding ◽

Nucleosomal Histone

AbstractDimethylated histone H3 Lys36 (H3K36me2) regulates gene expression, and aberrant H3K36me2 upregulation, resulting from either the overexpression or point mutation of the dimethyltransferase NSD2, is found in various cancers. Here we report the cryo-electron microscopy structure of NSD2 bound to the nucleosome. Nucleosomal DNA is partially unwrapped, facilitating NSD2 access to H3K36. NSD2 interacts with DNA and H2A along with H3. The NSD2 autoinhibitory loop changes its conformation upon nucleosome binding to accommodate H3 in its substrate-binding cleft. Kinetic analysis revealed that two oncogenic mutations, E1099K and T1150A, increase NSD2 catalytic turnover. Molecular dynamics simulations suggested that in both mutants, the autoinhibitory loop adopts an open state that can accommodate H3 more often than the wild-type. We propose that E1099K and T1150A destabilize the interactions that keep the autoinhibitory loop closed, thereby enhancing catalytic turnover. Our analyses guide the development of specific inhibitors of NSD2.

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Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails

10.1101/2020.10.30.360990 ◽

2020 ◽

Author(s):

Yunhui Peng ◽

Shuxiang Li ◽

Alexey Onufriev ◽

David Landsman ◽

Anna R. Panchenko

Keyword(s):

Solvent Accessibility ◽

Binding Modes ◽

Dna Interactions ◽

Histone Tail ◽

Histone Tails ◽

Post Translational Modifications ◽

Conformational Ensembles ◽

Nucleosomal Dna ◽

Dynamics Simulations ◽

Nucleosome Binding

AbstractDespite histone tails’ critical roles in epigenetic regulation, little is known about mechanisms of how histone tails modulate the nucleosomal DNA solvent accessibility and recognition of nucleosomes by other macromolecules. Here we generate extensive atomic level conformational ensembles of histone tails in the context of the full human nucleosome, totaling 26 microseconds of molecular dynamics simulations. We explore the histone tail binding with the nucleosomal and linker DNA and observe rapid conformational transitions between bound and unbound states allowing us to estimate kinetic and thermodynamic properties of the histone tail-DNA interactions. Different histone types exhibit distinct, although conformationally heterogeneous, binding modes and each histone type occludes specific DNA regions from the solvent. Using a comprehensive set of experimental data on nucleosome structural complexes, we find that majority of the studied nucleosome-binding proteins and histone tails target mutually exclusive regions on nucleosomal or linker DNA around the super-helical locations ±1, ±2, and ±7. This finding is explained within the generalized competitive binding and tail displacement models of partners recruitment to nucleosomes. Finally, we demonstrate the crosstalk between different histone post-translational modifications, where charge-altering modifications and mutations typically suppress tail-DNA interactions and enhance histone tail dynamics.

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DNA translocase repositions a nucleosome by the lane-switch mechanism

10.1101/2021.02.15.431322 ◽

2021 ◽

Author(s):

Fritz Nagae ◽

Giovanni B. Brandani ◽

Shoji Takada ◽

Tsuyoshi Terakawa

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Deep Sequencing ◽

Restriction Enzyme ◽

Enzyme Digestion ◽

Coarse Grained ◽

Restriction Enzyme Digestion ◽

Nucleosomal Dna ◽

Dynamics Simulations ◽

Histone Core

ABSTRACTTranslocases such as DNA/RNA polymerases, replicative helicases, and exonucleases are involved in eukaryotic DNA transcription, replication, and repair. Since eukaryotic genomic DNA wraps around histone core complexes and forms nucleosomes, translocases inevitably encounter nucleosomes. Previous studies have shown that a histone core complex repositions upstream (downstream) when SP6RNA or T7 RNA polymerase (bacterial exonuclease, RecBCD) partially unwraps nucleosomal DNA. However, the molecular mechanism of the downstream repositioning remains unclear. In this study, we identify the lane-shift mechanism for downstream nucleosome repositioning via coarse-grained molecular dynamics simulations, which we validated by restriction enzyme digestion assays and deep sequencing assays. In this mechanism, after a translocase unwraps nucleosomal DNA up to the site proximal to the dyad, the remaining wrapped DNA switches its binding region (lane) to that vacated by the unwrapping, and the downstream DNA rewraps, completing downstream repositioning. This mechanism may have crucial implications for transcription through nucleosomes, histone recycling, and nucleosome remodeling.SIGNIFICANCEEukaryotic chromosomes are composed of repeating subunits termed nucleosomes. Thus, proteins that translocate along the chromosome, DNA translocases, inevitably collide with nucleosomes. Previous studies revealed that a translocase repositions a nucleosome upstream or downstream upon their collision. Though the molecular mechanisms of the upstream repositioning have been extensively studied, that of downstream repositioning remains elusive. In this study, we performed coarse-grained molecular dynamics simulations, proposed the lane-shift mechanism for downstream repositioning, and validated this mechanism by restriction enzyme digestion assays and deep sequencing assays. This mechanism has broad implications for how translocases deal with nucleosomes for their functions.

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Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1910044117 ◽

2020 ◽

Vol 117 (13) ◽

pp. 7216-7224 ◽

Cited By ~ 5

Author(s):

Akshay Sridhar ◽

Stephen E. Farr ◽

Guillem Portella ◽

Tamar Schlick ◽

Modesto Orozco ◽

...

Keyword(s):

Large Scale ◽

Coarse Grained ◽

Multiscale Approach ◽

Protein Disorder ◽

Wide Range ◽

Chromatin Structural ◽

Degree Of Condensation ◽

Dynamics Simulations ◽

Nucleosome Binding

Protein flexibility and disorder is emerging as a crucial modulator of chromatin structure. Histone tail disorder enables transient binding of different molecules to the nucleosomes, thereby promoting heterogeneous and dynamic internucleosome interactions and making possible recruitment of a wide-range of regulatory and remodeling proteins. On the basis of extensive multiscale modeling we reveal the importance of linker histone H1 protein disorder for chromatin hierarchical looping. Our multiscale approach bridges microsecond-long bias-exchange metadynamics molecular dynamics simulations of atomistic 211-bp nucleosomes with coarse-grained Monte Carlo simulations of 100-nucleosome systems. We show that the long C-terminal domain (CTD) of H1—a ubiquitous nucleosome-binding protein—remains disordered when bound to the nucleosome. Notably, such CTD disorder leads to an asymmetric and dynamical nucleosome conformation that promotes chromatin structural flexibility and establishes long-range hierarchical loops. Furthermore, the degree of condensation and flexibility of H1 can be fine-tuned, explaining chromosomal differences of interphase versus metaphase states that correspond to partial and hyperphosphorylated H1, respectively. This important role of H1 protein disorder in large-scale chromatin organization has a wide range of biological implications.

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Parameterization of Divalent Cations for Coarse-Grained Simulations

10.26434/chemrxiv.11881716 ◽

2020 ◽

Author(s):

Florencia Klein ◽

Daniela Cáceres-Rojas ◽

Monica Carrasco ◽

Juan Carlos Tapia ◽

Julio Caballero ◽

...

Keyword(s):

Molecular Dynamics ◽

Metal Ions ◽

Molecular Dynamics Simulations ◽

Divalent Cations ◽

Computational Cost ◽

Data Bank ◽

Coarse Grained ◽

Interaction Parameters ◽

Dynamics Simulations ◽

Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

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