Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome length and individualization

Choppakatla, Pavan; Dekker, Bastiaan; Cutts, Erin E.; Vannini, Alessandro; Dekker, Job

doi:10.1101/2020.12.20.423657

Cited by 6 publications

(10 citation statements)

References 173 publications

(346 reference statements)

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“…For example, a recent study of mitotic chromosome condensation [ 167 ] explored the interaction between linker histone (regulator of short-range chromatin fiber behavior that binds individual nucleosomes) and condensins (large ring-like complexes with ATPase activity that can extrude loops of DNA) [ 168 ]. In vitro , linker histone inhibits condensin binding to nucleosome arrays, which has been proposed to play a role in tuning the compaction and topology of mitotic chromosomes [ 167 ]. Thus, it is important to consider both the distinctions and the connections in compaction at different length scales.…”

Section: Regulation Of Accessibility By the Chromatin Fiber And Nucle...mentioning

confidence: 99%

Chromatin accessibility: methods, mechanisms, and biological insights

Mansisidor

Risca

2022

Nucleus

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Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation – processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.

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Section: Regulation Of Accessibility By the Chromatin Fiber And Nucle...mentioning

confidence: 99%

Chromatin accessibility: methods, mechanisms, and biological insights

Mansisidor

Risca

2022

Nucleus

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“…At least, our theory provides insight into the mechanism of the assembly of the reconstituted chromosomes, which have been studied intensively in recent years. [12][13][14]29,32…”

Section: Discussionmentioning

confidence: 99%

Loop extrusion driven volume phase transition of entangled chromosomes

Yamamoto

Schiessel

2022

Preprint

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Mitotic chromosomes without nucleosomes have been reconstituted in recent experiments. When topo II is depleted from the reconstituted chromosomes, these chromosomes are entangled and form 'sparklers', where DNA is condensed in the core with linker histone H1.8 and condensin is localized at the periphery. To understand the mechanism of the assembly of sparklers, we here take into account the loop extrusion by condensin in an extension of the theory of entangled polymer gels. The loop extrusion stiffens an entangled DNA network because DNA segments in the elastically effective chains are translocated to loops, which are elastically ineffective. Our theory predicts that the loop extrusion by condensin drives the volume phase transition that collapses a swollen entangled DNA gel as the stiffening of the network destabilizes the swollen phase. This is an important element to understand the mechanism of the assembly of the reconstituted chromosomes.

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“…For simplicity, we here treat cases in which the loading rate of condensin molecules is relatively small and they do not form nested loops, see also Discussion. Condensin is not loaded to the DNA binding sites that are already bound by linker histones, 29 but can be loaded to unoccupied DNA binding sites with equal probability. In this paper, we treat cases in which the concentration of linker histones is relatively small, ϵ − µ > 0, and the binding between DNA and linker histones is stabilized by the interaction energy (the third term of eq.…”

Section: Loop Extrusion Dynamicsmentioning

confidence: 99%