The scales, mechanisms, and dynamics of the genome architecture

Lizana, Ludvig; Schwartz, Yuri B.

doi:10.1126/sciadv.adm8167

Cited by 2 publications

(1 citation statement)

References 153 publications

(193 reference statements)

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“…Insulator-binding proteins (IBPs) play pivotal role among the various forces and mechanisms that contribute to shaping and maintaining of genome topology [ 1 , 2 ]. In Drosophila , several IBPs enriched in topologically associated domain (TAD) borders have been identified [ 3 – 7 ].…”

Section: Introductionmentioning

confidence: 99%

Su(Hw) interacts with Combgap to establish long-range chromatin contacts

Vorobyeva,

Krasnov,

Erokhin

et al. 2024

Epigenetics & Chromatin

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Background Insulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in Drosophila has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) insulator-binding protein to genome topology remains unclear. Results In this study, we provide evidence for the existence of long-range interactions between chromatin bound Su(Hw) and Combgap, which was first characterised as Polycomb response elements binding protein. Loss of Su(Hw) binding to chromatin results in the disappearance of Su(Hw)-Combgap long-range interactions and in a decrease in spatial self-interactions among a subset of Su(Hw)-bound genome sites. Our findings suggest that Su(Hw)-Combgap long-range interactions are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators’ binding. Conclusions This study demonstrates that Su(Hw) insulator binding protein can form long-range interactions with Combgap, Polycomb response elements binding protein, and that these interactions are associated with active chromatin factors rather than with Polycomb dependent repression.

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Section: Introductionmentioning

confidence: 99%

Su(Hw) interacts with Combgap to establish long-range chromatin contacts

Vorobyeva,

Krasnov,

Erokhin

et al. 2024

Epigenetics & Chromatin

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Motorized chain models of the ideal chromosome

Cao,

Wolynes

2024

Proc. Natl. Acad. Sci. U.S.A.

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An array of motor proteins consumes chemical energy in setting up the architectures of chromosomes. Here, we explore how the structure of ideal polymer chains is influenced by two classes of motors. The first class which we call “swimming motors” acts to propel the chromatin fiber through three-dimensional space. They represent a caricature of motors such as RNA polymerases. Previously, they have often been described by adding a persistent flow onto Brownian diffusion of the chain. The second class of motors, which we call “grappling motors” caricatures the loop extrusion processes in which segments of chromatin fibers some distance apart are brought together. We analyze these models using a self-consistent variational phonon approximation to a many-body Master equation incorporating motor activities. We show that whether the swimming motors lead to contraction or expansion depends on the susceptibility of the motors, that is, how their activity depends on the forces they must exert. Grappling motors in contrast to swimming motors lead to long-ranged correlations that resemble those first suggested for fractal globules and that are consistent with the effective interactions inferred by energy landscape analyses of Hi-C data on the interphase chromosome.

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The scales, mechanisms, and dynamics of the genome architecture

Cited by 2 publications

References 153 publications

Su(Hw) interacts with Combgap to establish long-range chromatin contacts

Su(Hw) interacts with Combgap to establish long-range chromatin contacts

Motorized chain models of the ideal chromosome

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