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.

scholarly journals Chromatin fiber structural motifs as regulatory hubs of genome function?

2019 ◽  
Vol 63 (1) ◽  
pp. 123-132 ◽  
Author(s):  
Manuela Moraru ◽  
Thomas Schalch
Keyword(s):  
Recent Progress ◽  
Higher Order ◽  
Chromatin Fiber ◽  
Structural Level ◽  
Structural Motifs ◽  
Random Structures ◽  
Fractal Characteristics ◽  
Chromatin Fibers ◽  
Eukaryotic Genomes

Abstract Nucleosomes cover eukaryotic genomes like beads on a string and play a central role in regulating genome function. Isolated strings of nucleosomes have the potential to compact and form higher order chromatin structures, such as the well-characterized 30-nm fiber. However, despite tremendous advances in observing chromatin fibers in situ it has not been possible to confirm that regularly ordered fibers represent a prevalent structural level in the folding of chromosomes. Instead, it appears that folding at a larger scale than the nucleosome involves a variety of random structures with fractal characteristics. Nevertheless, recent progress provides evidence for the existence of structural motifs in chromatin fibers, potentially localized to strategic sites in the genome. Here we review the current understanding of chromatin fiber folding and the emerging roles that oligonucleosomal motifs play in the regulation of genome function.

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 Higher-order structure of the 30-nm chromatin fiber revealed by cryo-EM

IUBMB Life ◽  
2016 ◽  
Vol 68 (11) ◽  
pp. 873-878 ◽  
Author(s):  
Ping Zhu ◽  
Guohong Li
Keyword(s):  
Higher Order ◽  
Chromatin Fiber ◽  
Order Structure

scholarly journals Higher order structure in a short repeat length chromatin.

1984 ◽  
Vol 98 (4) ◽  
pp. 1320-1327 ◽  
Author(s):  
J Allan ◽  
D C Rau ◽  
N Harborne ◽  
H Gould
Keyword(s):  
Higher Order ◽  
Chromatin Fiber ◽  
Repeat Length ◽  
Order Structure ◽  
Dependent Manner ◽  
Chicken Erythrocyte ◽  
Base Pairs ◽  
Short Repeat ◽  
Cortical Neurone

Polynucleosomes from calf brain cortical neurone nuclei have an average repeat length of less than 168 base pairs. The ability of this material to adopt higher order structure has been assessed by various physical techniques. Although containing on average less DNA per nucleosome than is required to form a chromatosome, this short repeat length chromatin folded in an H1 dependent manner to a structure with properties similar to those observed for longer repeat length chromatins such as that of chicken erythrocyte (McGhee, J.D., D.C. Rau, E. Charney, and G. Felsenfeld, 1980, Cell, 22:87-96). These observations are discussed in the context of H1 location in the higher order chromatin fiber.

scholarly journals Structure of the bacterial cellulose ribbon and its assembly-guiding cytoskeleton by electron cryotomography

2020 ◽  
Author(s):  
William J. Nicolas ◽  
Debnath Ghosal ◽  
Elitza I. Tocheva ◽  
Elliot M. Meyerowitz ◽  
Grant J. Jensen
Keyword(s):  
Focused Ion Beam ◽  
Electron Tomography ◽  
Ion Beam ◽  
Bacterial Species ◽  
Higher Order ◽  
Crystalline Cellulose ◽  
Bacterial Biofilms ◽  
Order Structure ◽  
Native State ◽  
Electron Cryotomography

AbstractCellulose is a widespread component of bacterial biofilms, where its properties of exceptional water retention, high tensile strength and stiffness prevents dehydration and mechanical disruption of the biofilm. Bacteria in the Gluconacetobacter genus secrete crystalline cellulose, with a structure very similar to that found in plant cell walls. How this higher-order structure is produced is poorly understood. We used cryo-electron tomography and focused ion beam milling of native bacterial biofilms to image cellulose-synthesizing G. hansenii and G. xylinus bacteria in a frozen-hydrated, near-native state. We confirm previous results suggesting that cellulose crystallization occurs serially following its secretion along one side of the cell, leading to a cellulose ribbon that can reach several microns in length and combine with ribbons from other cells to form a robust biofilm matrix. We were able to take direct measurements in a near-native state of the cellulose sheets. Our results also reveal a novel cytoskeletal structure, that we name the cortical belt, adjacent to the inner membrane and underlying the sites where cellulose is seen emerging from the cell. We find that this structure is not present in other cellulose-synthesizing bacterial species, Agrobacterium tumefaciens and Escherichia coli 1094, which do not produce organized cellulose ribbons. We therefore propose that the cortical belt holds the cellulose synthase complexes in a line, to form higher-order cellulose structures such as sheets and ribbons.

Super-resolution Imaging of Individual Human Subchromosomal Regions in Situ Reveals Nanoscopic Building Blocks of Higher-Order Structure

ACS Nano ◽  
2018 ◽  
Vol 12 (5) ◽  
pp. 4909-4918 ◽  
Author(s):  
Ke Fang ◽  
Xuecheng Chen ◽  
Xiaowei Li ◽  
Yi Shen ◽  
Jielin Sun ◽  
...  
Keyword(s):  
Super Resolution ◽  
Building Blocks ◽  
Higher Order ◽  
Order Structure ◽  
Resolution Imaging ◽  
Individual Human

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.

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