Characterizing chromatin packing scaling in whole nuclei using interferometric microscopy

Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division.

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Hierarchical dinucleotide distribution in genome along evolution and its effect on chromatin packing

Life Science Alliance ◽

10.26508/lsa.202101028 ◽

2021 ◽

Vol 4 (8) ◽

pp. e202101028

Author(s):

Zhicheng Cai ◽

Yueying He ◽

Sirui Liu ◽

Yue Xue ◽

Hui Quan ◽

...

Keyword(s):

Phylogenetic Tree ◽

Chromatin Structure ◽

Distribution Patterns ◽

Length Scales ◽

Multi Scale ◽

Topologically Associating Domain ◽

Domain Boundaries ◽

Chromatin Packing ◽

The Difference ◽

Genomic Length

Dinucleotide densities and their distribution patterns vary significantly among species. Previous studies revealed that CpG is susceptible to methylation, enriched at topologically associating domain boundaries and its distribution along the genome correlates with chromatin compartmentalization. However, the multi-scale organizations of CpG in the linear genome, their role in chromatin organization, and how they change along the evolution are only partially understood. By comparing the CpG distribution at different genomic length scales, we quantify the difference between the CpG distributions of different species and evaluate how the hierarchical uneven CpG distribution appears in evolution. The clustering of species based on the CpG distribution is consistent with the phylogenetic tree. Interestingly, we found the CpG distribution and chromatin structure to be correlated in many different length scales, especially for mammals and avians, consistent with the mosaic CpG distribution in the genomes of these species.

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Nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform bridges 4-D chromatin organization with molecular function

10.1101/2020.01.26.920363 ◽

2020 ◽

Author(s):

Yue Li ◽

Adam Eshein ◽

Ranya K.A. Virk ◽

Aya Eid ◽

Wenli Wu ◽

...

Keyword(s):

Chromatin Structure ◽

Electron Tomography ◽

Population Level ◽

Average Diameter ◽

Chromatin Organization ◽

Live Cells ◽

Molecular Function ◽

Label Free ◽

A Cell ◽

Chromatin Packing

AbstractIn eukaryotic cells, chromatin structure is linked to transcription processes through the regulation of genome organization. Extending across multiple length-scales - from the nucleosome to higher-order three-dimensional structures - chromatin is a dynamic system which evolves throughout the lifetime of a cell. However, no individual technique can fully elucidate the behavior of chromatin organization and its relation to molecular function at all length- and timescales at both a single-cell and a cell population level. Herein, we present a multi-technique nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform that bridges electron tomography and optical superresolution imaging of chromatin conformation and transcriptional processes, with resolution down to the level of individual nucleosomes, with high-throughput, label-free analysis of chromatin packing and its dynamics in live cells. Utilizing nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nm, sub-Mb genomic size, and an internal fractal structure. The chromatin packing behavior of these domains is directly influenced by active gene transcription. Furthermore, we demonstrated that the chromatin packing domain structure is correlated among progenitor cells and all their progeny, indicating that the organization of chromatin into fractal packing domains is heritable across cell division. Further studies employing the nano-ChIA platform have the potential to provide a more coherent picture of chromatin structure and its relation to molecular function.

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CASA derived human sperm abnormalities: correlation with chromatin packing and DNA fragmentation

Journal of Assisted Reproduction and Genetics ◽

10.1007/s10815-012-9885-9 ◽

2012 ◽

Vol 29 (12) ◽

pp. 1327-1334 ◽

Cited By ~ 18

Author(s):

T. Sivanarayana ◽

Ch. Ravi Krishna ◽

G. Jaya Prakash ◽

K. Murali Krishna ◽

K. Madan ◽

...

Keyword(s):

Dna Fragmentation ◽

Human Sperm ◽

Sperm Abnormalities ◽

Chromatin Packing

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Transgene-Induced Silencing of the Zoosporogenesis-Specific NIFC Gene Cluster of Phytophthora infestans Involves Chromatin Alterations

Eukaryotic Cell ◽

10.1128/ec.00311-06 ◽

2007 ◽

Vol 6 (7) ◽

pp. 1200-1209 ◽

Cited By ~ 48

Author(s):

Howard S. Judelson ◽

Shuji Tani

Keyword(s):

Phytophthora Infestans ◽

Gene Cluster ◽

Sequence Similarity ◽

Transcriptional Regulator ◽

Hairpin Rna ◽

High Sequence Similarity ◽

Genes Encoding ◽

Cognate Gene ◽

Chromatin Packing ◽

Nif Proteins

ABSTRACT Clustered within the genome of the oomycete phytopathogen Phytophthora infestans are four genes encoding spore-specific nuclear LIM interactor-interacting factors (NIF proteins, a type of transcriptional regulator) that are moderately conserved in DNA sequence. NIFC1, NIFC2, and NIFC3 are zoosporogenesis-induced and grouped within 4 kb, and 20 kb away resides a sporulation-induced form, NIFS. To test the function of the NIFC family, plasmids expressing full-length hairpin constructs of NIFC1 or NIFC2 were stably transformed into P. infestans. This triggered silencing of the cognate gene in about one-third of transformants, and all three NIFC genes were usually cosilenced. However, NIFS escaped silencing despite its high sequence similarity to the NIFC genes. Silencing of the three NIFC genes impaired zoospore cyst germination by 60% but did not affect other aspects of the life cycle. Silencing was transcriptional based on nuclear run-on assays and associated with tighter chromatin packing based on nuclease accessibility experiments. The chromatin alterations extended a few hundred nucleotides beyond the boundaries of the transcribed region of the NIFC cluster and were not associated with increased DNA methylation. A plasmid expressing a short hairpin RNA having sequence similarity only to NIFC1 silenced both that gene and an adjacent member of the gene cluster, likely due to the expansion of a heterochromatic domain from the targeted locus. These data help illuminate the mechanism of silencing in Phytophthora and suggest that caution should be used when interpreting silencing experiments involving closely spaced genes.

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Natural chromatin is heterogeneous and self-associates in vitro

Molecular Biology of the Cell ◽

10.1091/mbc.e17-07-0449 ◽

2018 ◽

Vol 29 (13) ◽

pp. 1652-1663 ◽

Cited By ~ 12

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.

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Fluorometric identification of chromatin-packing level beyond resolution of light microscopy

Cell and Tissue Biology ◽

10.1134/s1990519x11010093 ◽

2011 ◽

Vol 5 (1) ◽

pp. 98-102 ◽

Cited By ~ 2

Author(s):

L. I. Lebedeva ◽

T. D. Dubatolova ◽

L. V. Omelyanchuk

Keyword(s):

Light Microscopy ◽

Chromatin Packing

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Long-range looping of a locus control region drives tissue-specific chromatin packing within a multigene cluster

Nucleic Acids Research ◽

10.1093/nar/gkw090 ◽

2016 ◽

Vol 44 (10) ◽

pp. 4651-4664 ◽

Cited By ~ 7

Author(s):

Yu-Cheng Tsai ◽

Nancy E. Cooke ◽

Stephen A. Liebhaber

Keyword(s):

Long Range ◽

Control Region ◽

Locus Control Region ◽

Tissue Specific ◽

Chromatin Packing

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Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs that Enable Degradation

Molecules ◽

10.3390/molecules26185606 ◽

2021 ◽

Vol 26 (18) ◽

pp. 5606

Author(s):

Laura Márquez-Cantudo ◽

Ana Ramos ◽

Claire Coderch ◽

Beatriz de Pascual-Teresa

Keyword(s):

Cell Cycle ◽

Hdac Inhibitors ◽

Ubiquitin Proteasome System ◽

Protein Targets ◽

E3 Ligases ◽

Design And Synthesis ◽

Ubiquitin Proteasome ◽

Chromatin Packing ◽

The Many ◽

Cycle Regulation

Protein degradation by the Ubiquitin-Proteasome System is one of the main mechanisms of the regulation of cellular proteostasis, and the E3 ligases are the key effectors for the protein recognition and degradation. Many E3 ligases have key roles in cell cycle regulation, acting as checkpoints and checkpoint regulators. One of the many important proteins involved in the regulation of the cell cycle are the members of the Histone Deacetylase (HDAC) family. The importance of zinc dependent HDACs in the regulation of chromatin packing and, therefore, gene expression, has made them targets for the design and synthesis of HDAC inhibitors. However, achieving potency and selectivity has proven to be a challenge due to the homology between the zinc dependent HDACs. PROteolysis TArgeting Chimaera (PROTAC) design has been demonstrated to be a useful strategy to inhibit and selectively degrade protein targets. In this review, we attempt to summarize the E3 ligases that naturally ubiquitinate HDACs, analyze their structure, and list the known ligands that can bind to these E3 ligases and be used for PROTAC design, as well as the already described HDAC-targeted PROTACs.

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