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Spatio-temporal organization of the chromosome from base to cellular length scales.

作者信息

Royzenblat Sonya K, Freddolino Lydia

机构信息

Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.

Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA.

出版信息

EcoSal Plus. 2024 Dec 12;12(1):eesp00012022. doi: 10.1128/ecosalplus.esp-0001-2022. Epub 2024 Jun 12.


DOI:10.1128/ecosalplus.esp-0001-2022
PMID:38864557
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11636183/
Abstract

has been a vital model organism for studying chromosomal structure, thanks, in part, to its small and circular genome (4.6 million base pairs) and well-characterized biochemical pathways. Over the last several decades, we have made considerable progress in understanding the intricacies of the structure and subsequent function of the nucleoid. At the smallest scale, DNA, with no physical constraints, takes on a shape reminiscent of a randomly twisted cable, forming mostly random coils but partly affected by its stiffness. This ball-of-spaghetti-like shape forms a structure several times too large to fit into the cell. Once the physiological constraints of the cell are added, the DNA takes on overtwisted (negatively supercoiled) structures, which are shaped by an intricate interplay of many proteins carrying out essential biological processes. At shorter length scales (up to about 1 kb), nucleoid-associated proteins organize and condense the chromosome by inducing loops, bends, and forming bridges. Zooming out further and including cellular processes, topological domains are formed, which are flanked by supercoiling barriers. At the megabase-scale both large, highly self-interacting regions (macrodomains) and strong contacts between distant but co-regulated genes have been observed. At the largest scale, the nucleoid forms a helical ellipsoid. In this review, we will explore the history and recent advances that pave the way for a better understanding of chromosome organization and structure, discussing the cellular processes that drive changes in DNA shape, and what contributes to compaction and formation of dynamic structures, and in turn how bacterial chromatin affects key processes such as transcription and replication.

摘要

相似文献

[1]
Spatio-temporal organization of the chromosome from base to cellular length scales.

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[2]
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[3]
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[4]
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[5]
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[6]
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[8]
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[9]
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[10]
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本文引用的文献

[1]
Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes.

Nat Struct Mol Biol. 2024-3

[2]
IHF and Fis as Cell Cycle Regulators: Activation of the Replication Origin and the Regulatory Cycle of the DnaA Initiator.

Int J Mol Sci. 2023-7-18

[3]
Interplay between chromosomal architecture and termination of DNA replication in bacteria.

Front Microbiol. 2023-6-26

[4]
Three-dimensional chromosome re-modelling: The integral mechanism of transcription regulation in bacteria.

Mol Microbiol. 2023-7

[5]
DNA Segregation in Enterobacteria.

EcoSal Plus. 2023-12-12

[6]
Single-nucleotide resolution detection of Topo IV cleavage activity in the genome with Topo-Seq.

Front Microbiol. 2023-4-6

[7]
The bacterial nucleoid-associated proteins, HU and Dps, condense DNA into context-dependent biphasic or multiphasic complex coacervates.

J Biol Chem. 2023-5

[8]
MukBEF-dependent chromosomal organization in widened .

Front Microbiol. 2023-3-3

[9]
Interdependent progression of bidirectional sister replisomes in .

Elife. 2023-1-9

[10]
Heterotypic phase separation of Hfq is linked to its roles as an RNA chaperone.

Cell Rep. 2022-12-27

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