Controlling gene expression by DNA mechanics: emerging insights and challenges

Levens, David; Baranello, Laura; Kouzine, Fedor

doi:10.1007/s12551-016-0243-5

Cited by 11 publications

(11 citation statements)

References 81 publications

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“…Fishman, 1995; Kouzine et al, 2004). This is likely driven by structure formation releasing the negative supercoiling generated in the wake of translocating RNA polymerase (Liu & Wang, 1987;Levens et al, 2016). Similar topology-induced structure formation could also contribute to leading strand secondary structure formation behind the replicative helicase (reviewed in Kurth et al, 2013;Yu & Droge, 2014).…”

Section: Discussionmentioning

confidence: 99%

R‐loop formation during S phase is restricted by PrimPol‐mediated repriming

Šviković

Crisp

Tan-Wong³

et al. 2018

The EMBO Journal

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During DNA replication, conflicts with ongoing transcription are frequent and require careful management to avoid genetic instability. R‐loops, three‐stranded nucleic acid structures comprising a DNA:RNA hybrid and displaced single‐stranded DNA, are important drivers of damage arising from such conflicts. How R‐loops stall replication and the mechanisms that restrain their formation during S phase are incompletely understood. Here, we show in vivo how R‐loop formation drives a short purine‐rich repeat, (GAA)10, to become a replication impediment that engages the repriming activity of the primase‐polymerase PrimPol. Further, the absence of PrimPol leads to significantly increased R‐loop formation around this repeat during S phase. We extend this observation by showing that PrimPol suppresses R‐loop formation in genes harbouring secondary structure‐forming sequences, exemplified by G quadruplex and H‐DNA motifs, across the genome in both avian and human cells. Thus, R‐loops promote the creation of replication blocks at susceptible structure‐forming sequences, while PrimPol‐dependent repriming limits the extent of unscheduled R‐loop formation at these sequences, mitigating their impact on replication.

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Section: Discussionmentioning

confidence: 99%

R‐loop formation during S phase is restricted by PrimPol‐mediated repriming

Šviković

Crisp

Tan-Wong³

et al. 2018

The EMBO Journal

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“…For example, the pericentromere can act as a mechanical spring, governing chromosome separation and spindle length during mitosis (5). Thus, chromatin physics can help to address questions about chromatin ordering (6)(7)(8), how DNA is both stable and distortable (9,10), how glassy DNA dynamics gives rise to cell-to-cell variability (11), and even how the mechanical micro-environment tunes genetic expression (12,13). Chromatin states are altered by posttranslational modifications (PTMs) (14) and by histone variant deposition at the macromolecular scale (9).…”

Section: Introductionmentioning

confidence: 99%

Minimal Cylinder Analysis Reveals the Mechanical Properties of Oncogenic Nucleosomes

Pitman

Dalal

Papoian

2020

Biophysical Journal

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Histone variants regulate replication, transcription, DNA damage repair, and chromosome segregation. Though widely accepted as a paradigm, it has not been rigorously demonstrated that histone variants encode unique mechanical properties. Here, we present a new theoretical approach called Minimal Cylinder Analysis (MCA) to determine the Young's modulus of nucleosomes from all-atom Molecular Dynamics (MD) simulations. Recently, we validated this computational analysis against in vitro single-molecule nanoindentation of histone variant nucleosomes. In this report, we further extend MCA to study the biophysical properties of hybrid nucleosomes that are known to exist in human cancer cells and contain H3 histone variants CENP-A and H3.3. We investigate the mechanism by which the elasticity of these heterotypic 2 nucleosomes augments cryptic binding surfaces. Further, we derive biological predictions that might arise when such heterotypic nucleosomes take over large parts of the genome. Statement of SignificanceNucleosomes are the base unit of eukaryotic genome organization. Histone variants create unique local chromatin domains that fine-tune transcription, replication, DNA damage repair, and faithful chromosome segregation. It is becoming increasingly clear that the mechanical response of chromatin, through material properties such as elasticity, regulates genetic function.We developed a theoretical method, validated by in vitro nanoindentation studies, called Minimal Cylinder Analysis (MCA), to determine the Young's modulus of nucleosomes from Molecular Dynamics simulations. We then postulate specific biological predictions about oncogenic hybrid nucleosomes using MCA. In the future, this computational method can serve as a fast and high-throughput tool to discern how macromolecular systems respond to mechanical forces.

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“…This feature may be particularly important during transcription, when tetrasomes can arise from nucleosomes by loss or removal of H2A/H2B dimers, and when torque can be generated by elongating RNA polymerase II (68)(69)(70). Although most transcription-linked torsional stress is removed by topoisomerases (71,72), high-affinity tetrasomes may provide extra protection against complete histone ejection at crucial locations in the genome by their inherently stronger ability to absorb this stress.…”

Section: Discussionmentioning

confidence: 99%

DNA sequence is a major determinant of tetrasome dynamics

Ordu

Lusser

Dekker

2019

Preprint

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Eukaryotic genomes are hierarchically organized into protein-DNA assemblies for compaction into the nucleus. Nucleosomes, with the (H3-H4) 2 tetrasome as a likely intermediate, are highly dynamic in nature by way of several different mechanisms. We have recently shown that tetrasomes spontaneously change the direction of their DNA wrapping between left-and right-handed conformations, which may prevent torque build-up in chromatin during active transcription or replication. DNA sequence has been shown to strongly affect nucleosome positioning throughout chromatin. It is not known, however, whether DNA sequence also impacts the dynamic properties of tetrasomes. To address this question, we examined tetrasomes assembled on a highaffinity DNA sequence using freely orbiting magnetic tweezers. In this context, we also studied the effects of mono-and divalent salts on the flipping dynamics. We found that neither DNA sequence nor altered buffer conditions affect overall tetrasome structure. In contrast, tetrasomes bound to high-affinity DNA sequences showed significantly altered flipping kinetics, predominantly via a reduction in the lifetime of the canonical state of left-handed wrapping. Increased mono-and divalent salt concentrations counteracted this behaviour. Thus, our study indicates that high-affinity DNA sequences impact not only the positioning of the nucleosome, but that they also endow the subnucleosomal tetrasome with enhanced conformational plasticity. This may provide a means to prevent histone loss upon exposure to torsional stress, thereby contributing to the integrity of chromatin at high-affinity sites. STATEMENT OF SIGNIFICANCECanonical (H3-H4) 2 tetrasomes possess high conformational flexibility, as evidenced by their spontaneous flipping between states of left-and right-handed DNA wrapping. Here, we show that these conformational dynamics of tetrasomes cannot be described by a fixed set of rates over all conditions. Instead, an accurate description of their behavior must take into account details of their loading, in particular the underlying DNA sequence. In vivo, differences in tetrasome flexibility could be regulated by modifications of the histone core or the tetrasomal DNA, and as such constitute an intriguing, potentially adjustable mechanism for chromatin to accommodate the torsional stress generated by processes such as transcription and replication.Recent research has provided significant new insights into the structure and especially the dynamics of nucleosomes (10). For example, studies using single-molecule techniques have revealed the intrinsically dynamic nature of nucleosomes in the form of 'breathing', i.e. the transient un-and rewrapping of the

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Controlling gene expression by DNA mechanics: emerging insights and challenges

Cited by 11 publications

References 81 publications

R‐loop formation during S phase is restricted by PrimPol‐mediated repriming

R‐loop formation during S phase is restricted by PrimPol‐mediated repriming

Minimal Cylinder Analysis Reveals the Mechanical Properties of Oncogenic Nucleosomes

DNA sequence is a major determinant of tetrasome dynamics

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