scholarly journals A critical role for linker DNA in higher-order folding of chromatin fibers

2021 ◽  
Author(s):  
Thomas Brouwer ◽  
Chi Pham ◽  
Artur Kaczmarczyk ◽  
Willem-Jan de Voogd ◽  
Margherita Botto ◽  
...  
Keyword(s):  
Single Molecule ◽  
Base Pair ◽  
Critical Role ◽  
Periodic Variation ◽  
Higher Order ◽  
Rigid Base ◽  
Order Structure ◽  
Linker Length ◽  
Chromatin Fibers

Abstract Nucleosome-nucleosome interactions drive the folding of nucleosomal arrays into dense chromatin fibers. A better physical account of the folding of chromatin fibers is necessary to understand the role of chromatin in regulating DNA transactions. Here, we studied the unfolding pathway of regular chromatin fibers as a function of single base pair increments in linker length, using both rigid base-pair Monte Carlo simulations and single-molecule force spectroscopy. Both computational and experimental results reveal a periodic variation of the folding energies due to the limited flexibility of the linker DNA. We show that twist is more restrictive for nucleosome stacking than bend, and find the most stable stacking interactions for linker lengths of multiples of 10 bp. We analyzed nucleosomes stacking in both 1- and 2-start topologies and show that stacking preferences are determined by the length of the linker DNA. Moreover, we present evidence that the sequence of the linker DNA also modulates nucleosome stacking and that the effect of the deletion of the H4 tail depends on the linker length. Importantly, these results imply that nucleosome positioning in vivo not only affects the phasing of nucleosomes relative to DNA but also directs the higher-order structure of chromatin.

Quantum dot probes for observation of single molecule DNA and a synthetic polyelectrolyte higher-order structure

Soft Matter ◽  
2010 ◽  
Vol 6 (12) ◽  
pp. 2834 ◽  
Author(s):  
Ning Chen ◽  
Anatoly A. Zinchenko ◽  
Yuka Yamazaki ◽  
Yuko Yoshikawa ◽  
Shizuaki Murata ◽  
...  
Keyword(s):  
Quantum Dot ◽  
Single Molecule ◽  
Higher Order ◽  
Order Structure

scholarly journals Natural chromatin is heterogeneous and self-associates in vitro

2018 ◽  
Vol 29 (13) ◽  
pp. 1652-1663 ◽  
Author(s):  
Shujun Cai ◽  
Yajiao Song ◽  
Chen Chen ◽  
Jian Shi ◽  
Lu Gan
Keyword(s):  
Divalent Cations ◽  
Large Mass ◽  
Higher Order ◽  
Linker Histone ◽  
Order Structure ◽  
Face To Face ◽  
Chromatin Packing ◽  
Electron Cryotomography

The 30-nm fiber is commonly formed by oligonucleosome arrays in vitro but rarely found inside cells. To determine how chromatin higher-order structure is controlled, we used electron cryotomography (cryo-ET) to study the undigested natural chromatin released from two single-celled organisms in which 30-nm fibers have not been observed in vivo: picoplankton and yeast. In the presence of divalent cations, most of the chromatin from both organisms is condensed into a large mass in vitro. Rare irregular 30-nm fibers, some of which include face-to-face nucleosome interactions, do form at the periphery of this mass. In the absence of divalent cations, picoplankton chromatin decondenses into open zigzags. By contrast, yeast chromatin mostly remains condensed, with very few open motifs. Yeast chromatin packing is largely unchanged in the absence of linker histone and mildly decondensed when histones are more acetylated. Natural chromatin is therefore generally nonpermissive of regular motifs, even at the level of oligonucleosomes.

Aged and post-mitotic cells share a very stable higher-order structure in the cell nucleus in vivo

2010 ◽  
Vol 11 (6) ◽  
pp. 703-716 ◽  
Author(s):  
Janeth Alva-Medina ◽  
Myrna A. R. Dent ◽  
Armando Aranda-Anzaldo
Keyword(s):  
Cell Nucleus ◽  
Higher Order ◽  
Order Structure ◽  
Mitotic Cells

scholarly journals Nucleosome packing in interphase chromatin.

1979 ◽  
Vol 81 (2) ◽  
pp. 453-457 ◽  
Author(s):  
J B Rattner ◽  
B A Hamkalo
Keyword(s):  
Electron Microscope ◽  
Chromatin Condensation ◽  
Higher Order ◽  
Chromatin Fiber ◽  
Interphase Chromatin ◽  
Metaphase Chromosomes ◽  
Microscope Analysis ◽  
Electron Microscope Analysis ◽  
Chromatin Fibers

Higher-order chromatin fibers (200--300 A in diameter) are reproducibly released from nuclei after lysis in the absence of formalin and/or detergent. Electron microscope analysis of these fibers shows that they are composed of a continuous array of closely apposed nucleosomes which display several distinct packing patterns. Analysis of the organization of nucleosomes within these arrays and their distribution along long stretches of chromatin suggest that the basic 100-A chromatin fiber is not packed into discrete superbeads and is not folded into a uniform solenoid within the native 250-A fiber. Furthermore, because similar higher-order fibers have been visualized in metaphase chromosomes, the existence of this fiber class appears to be independent of the degree of in vivo chromatin condensation.

scholarly journals Folding and Persistence Time of Intramolecular G-Quadruplexes Transiently Embedded in a DNA duplex

2021 ◽  
Author(s):  
Phong Lan Thao Tran ◽  
Martin Rieu ◽  
Samar Hodeib ◽  
Alexandra Joubert ◽  
Jimmy Ouellet ◽  
...  
Keyword(s):  
Single Molecule ◽  
Critical Role ◽  
Genetic Regulation ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Folding Rate ◽  
Persistence Time ◽  
G4 Dna

ABSTRACTG-quadruplex (G4) DNA structures have emerged as important regulatory elements during DNA replication, transcription or repair. While many in-vitro studies have focused on the kinetics of G4 formation within DNA single-strands, G4 are found in-vivo in double-stranded DNA regions, where their formation is challenged by pairing between the two complementary strands. Since the energy of hybridization of Watson-Crick structures dominates the energy of G4 folding, this competition should play a critical role on the persistence of G4 in vivo. To address this issue, we designed a single molecule assay allowing measuring G4 folding and persistence while the structure is periodically challenged by the complementary strand. We quantified both the folding rate and the persistence time of biologically relevant G4 structures and showed that the dynamics of G4 formation depends strongly on the genomic location. G4 are found much more stable in promoter regions and replication origins than in telomeric regions. In addition, we characterized how G4 dynamics was affected by G4 ligands and showed that both folding rate and persistence increased. Our assay opens new perspectives for the measurement of G4 dynamics, which is critical to understand their role in genetic regulation.

Transitions between in situ and isolated chromatin

1993 ◽  
Vol 105 (2) ◽  
pp. 551-561 ◽  
Author(s):  
P.J. Giannasca ◽  
R.A. Horowitz ◽  
C.L. Woodcock
Keyword(s):  
Higher Order ◽  
Chromatin Fiber ◽  
Sperm Chromatin ◽  
Order Structure ◽  
Native State ◽  
Chromatin Fibers

We show that the mechanism by which chromatin displaying higher-order structure is usually isolated from nuclei involves a transition to an extended nucleosomal arrangement. After being released from nuclei, chromatin must refold in order to produce the typical chromatin fibers observed in solution. For starfish sperm chromatin with a long nucleosome repeat (222 bp), isolated fibers are significantly wider than those in the nucleus, indicating that the refolding process does not regenerate the native higher-order structure. We also propose that for typical eukaryotic nuclei, the concept that the native state of the (inactive) bulk of the genome is a chromatin fiber with defined architecture be reconsidered.

The higher order structure of chicken erythrocyte chromosomes in vivo

Nature ◽  
1980 ◽  
Vol 288 (5791) ◽  
pp. 620-622 ◽  
Author(s):  
J. P. Langmore ◽  
C. Schutt
Keyword(s):  
Higher Order ◽  
Order Structure ◽  
Chicken Erythrocyte

scholarly journals Highly disordered histone H1−DNA model complexes and their condensates

2018 ◽  
Vol 115 (47) ◽  
pp. 11964-11969 ◽  
Author(s):  
Abigail L. Turner ◽  
Matthew Watson ◽  
Oscar G. Wilkins ◽  
Laura Cato ◽  
Andrew Travers ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Chromatin Condensation ◽  
Bound State ◽  
Histone H1 ◽  
Higher Order ◽  
Disordered Proteins ◽  
Order Structure ◽  
Dependent Manner ◽  
Model Complexes

Disordered proteins play an essential role in a wide variety of biological processes, and are often posttranslationally modified. One such protein is histone H1; its highly disordered C-terminal tail (CH1) condenses internucleosomal linker DNA in chromatin in a way that is still poorly understood. Moreover, CH1 is phosphorylated in a cell cycle-dependent manner that correlates with changes in the chromatin condensation level. Here we present a model system that recapitulates key aspects of the in vivo process, and also allows a detailed structural and biophysical analysis of the stages before and after condensation. CH1 remains disordered in the DNA-bound state, despite its nanomolar affinity. Phase-separated droplets (coacervates) form, containing higher-order assemblies of CH1/DNA complexes. Phosphorylation at three serine residues, spaced along the length of the tail, has little effect on the local properties of the condensate. However, it dramatically alters higher-order structure in the coacervate and reduces partitioning to the coacervate phase. These observations show that disordered proteins can bind tightly to DNA without a disorder-to-order transition. Importantly, they also provide mechanistic insights into how higher-order structures can be exquisitely sensitive to perturbation by posttranslational modifications, thus broadening the repertoire of mechanisms that might regulate chromatin and other macromolecular assemblies.

Forces and torques in the nucleus: chromatin under mechanical constraintsThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 307-322 ◽  
Author(s):  
Christophe Lavelle
Keyword(s):  
Single Molecule ◽  
Ad Hoc ◽  
Peer Review Process ◽  
Critical Role ◽  
Experimental Studies ◽  
Dynamic Changes ◽  
Physical Constraints ◽  
Mechanical Constraints ◽  
Selection Of

Genomic DNA in eukaryotic cells is organized in discrete chromosome territories, each consisting of a single huge hierarchically supercoiled nucleosomal fiber. Through dynamic changes in structure, resulting from chemical modifications and mechanical constraints imposed by numerous factors in vivo, chromatin plays a critical role in the regulation of DNA metabolism processes, including replication and transcription. Indeed, DNA-translocating enzymes, such as polymerases, produce physical constraints that chromatin has to overcome. Recent techniques, in particular single-molecule micromanipulation, have allowed precise quantization of forces and torques at work in the nucleus and have greatly improved our understanding of chromatin behavior under physiological mechanical constraints. These new biophysical approaches should enable us to build realistic mechanistic models and progressively specify the ad hoc and hazy “because of chromatin structure” argument often used to interpret experimental studies of biological function in the context of chromatin.

Sign in / Sign up

Export Citation Format

Share Document