Chromatin hierarchical branching visualized at the nanoscale by electron microscopy

Zhou, Zhongwu; Yan, Rui; Jiang, Wen; Irudayaraj, Joseph

doi:10.1039/d0na00359j

Cited by 7 publications

(3 citation statements)

References 49 publications

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“…[ 36 ] Additionally, the hierarchical branching of chromatin structure at the nanoscale has been visualized through uranyl acetate‐based staining. [ 37 ] DNA EM also provides the capability to visualize DNA topology in chromatin with differing nucleosome spacing, which results in distinct higher order structures with either active or repressed genes. [ 38 ] Figure 1E depicts a replication fork, including two daughter strands, a single parental strand, ssDNA gaps on the daughter strands, and ssDNA gap at the replication fork junction.…”

Section: Visualizing Genomic Dna Through Heavy Metal Stainingmentioning

confidence: 99%

Toward Visualizing Genomic DNA Using Electron Microscopy via DNA Metallization

et al. 2023

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Figure 5. DNA-templated silver nanowire. The top left image is the electrode pattern used for silver nanowire assembly. A) Thiolated oligonucleotides complementary to the sticky ends of λ DNA are attached to the electrodes. B) λ DNA bridge connects the two gold electrodes. C) Silver ions are loaded on the DNA bridge. D) A silver nanowire is assembled by chemical reduction. E) Metallic silver aggregates on the λ DNA. Reproduced with permission. [55]

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Section: Visualizing Genomic Dna Through Heavy Metal Stainingmentioning

confidence: 99%

Toward Visualizing Genomic DNA Using Electron Microscopy via DNA Metallization

et al. 2023

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“…Therefore, it is not surprising that different approaches have been developed to study 3D chromatin organization in physiological and pathological conditions ( Cremer et al, 2015 ; Hausmann et al, 2020 ). Among these, there is considerable interest in electron-microscopy-based techniques that allow not only the visualization of DNA–DNA contacts between genomic regions that can be distant from each other along the primary structure of the DNA strand, but also reveal information on the physical structure of the chromatin and how it is spatially organized in the nucleus ( Trzaskoma et al, 2020 ; Zhou et al, 2021 ; Yusuf et al, 2022 ). Indeed, thanks to the short wavelength of the accelerated electrons of the microscope beam (which is much shorter than that of the photons of the visible spectrum), the resolution limit of a conventional transmission electron microscope can go down to about 0.2 nm.…”

Section: Introductionmentioning

confidence: 99%

A chromEM-staining protocol optimized for cardiac tissue

Musolino

Pagiatakis

Pierin

et al. 2023

Front. Cell Dev. Biol.

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Three-dimensional (3D) chromatin organization has a key role in defining the transcription program of cells during development. Its alteration is the cause of gene expression changes responsible for several diseases. Thus, we need new tools to study this aspect of gene expression regulation. To this end, ChromEM was recently developed: this is an electron-microscopy staining technique that selectively marks nuclear DNA without altering its structure and, thus, allows better visualization of 3D chromatin conformation. However, despite increasingly frequent application of this staining technique on cells, it has not yet been applied to visualize chromatin ultrastructure in tissues. Here, we provide a protocol to carry out ChromEM on myocardial tissue harvested from the left ventricles of C57BL/6J mice and use this in combination with transmission electron microscopy (TEM) to measure some morphological parameters of peripheral heterochromatin in cardiomyocytes. This protocol could also be used, in combination with electron tomography, to study 3D chromatin organization in cardiomyocytes in different aspects of heart pathobiology (e.g., heart development, cardiac aging, and heart failure) as well as help to set-up ChromEM in other tissues.

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“…Besides characterization of the unique metabolic phenotype of malignantly transformed cells, the better understanding of their epigenetic alterations is another cornerstone of current cancer research, casting new light on targeted therapeutic interventions. Pioneering work carried out by Miescher, Flemming, Kossel and Heitz between 1869 and 1928 resulted in the cytological distinction between regions of euchromatin and heterochromatin [6,7]. The first definition of epigenetics originated from Conrad Hal Waddington, who established this term in 1942 to describe inherited changes in phenotype without changes in the sequence of the DNA [8,9].…”

Section: Introductionmentioning

confidence: 99%

MicroRNAs and Metabolism: Revisiting the Warburg Effect with Emphasis on Epigenetic Background and Clinical Applications

Gaál

2021

Biomolecules

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Since the well-known hallmarks of cancer were described by Hanahan and Weinberg, fundamental advances of molecular genomic technologies resulted in the discovery of novel puzzle pieces in the multistep pathogenesis of cancer. MicroRNAs are involved in the altered epigenetic pattern and metabolic phenotype of malignantly transformed cells. They contribute to the initiation, progression and metastasis-formation of cancers, also interacting with oncogenes, tumor-suppressor genes and epigenetic modifiers. Metabolic reprogramming of cancer cells results from the dysregulation of a complex network, in which microRNAs are located at central hubs. MicroRNAs regulate the expression of several metabolic enzymes, including tumor-specific isoforms. Therefore, they have a direct impact on the levels of metabolites, also influencing epigenetic pattern due to the metabolite cofactors of chromatin modifiers. Targets of microRNAs include numerous epigenetic enzymes, such as sirtuins, which are key regulators of cellular metabolic homeostasis. A better understanding of reversible epigenetic and metabolic alterations opened up new horizons in the personalized treatment of cancer. MicroRNA expression levels can be utilized in differential diagnosis, prognosis stratification and prediction of chemoresistance. The therapeutic modulation of microRNA levels is an area of particular interest that provides a promising tool for restoring altered metabolism of cancer cells.

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Chromatin hierarchical branching visualized at the nanoscale by electron microscopy

Abstract: Chromatin is spatially organized in a hierarchical manner initiating from single nucleosomes condensing into higher order chromatin structures conferring various mechanical properties and biochemical signals. These higher order chromatin structures...

Cited by 7 publications

References 49 publications

Toward Visualizing Genomic DNA Using Electron Microscopy via DNA Metallization

Toward Visualizing Genomic DNA Using Electron Microscopy via DNA Metallization

A chromEM-staining protocol optimized for cardiac tissue

MicroRNAs and Metabolism: Revisiting the Warburg Effect with Emphasis on Epigenetic Background and Clinical Applications

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