High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope

Hetzer, Martin W.; Chen, F.; Huang, Jialiang

doi:10.1101/2021.05.10.443506

Cited by 2 publications

(2 citation statements)

References 55 publications

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“…NPCs are known to help in a genomic organization by helping tether both silenced genes to the lamina to maintain their silenced state and position active genes under NPCs to allow for RNA export. 86,97,98 We find that loss of stwl results in loss of lamin association of an early oogenesis gene rpS19b. Chavan et al show that Stwl also physically interacts with NPCs, promoting the anchoring of silenced genes to the nuclear periphery.…”

Section: Stonewall Coordinates Global Genome Reorganization and Npc F...mentioning

confidence: 74%

Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis

Kotb,

Ulukaya,

Chavan

et al. 2023

Preprint

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Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we find that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ-cell genes into a silenced state and activating a group of oocyte genes and Nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, crosstalk between genome architecture and NPCs is essential for successful cell fate transitions.

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Section: Stonewall Coordinates Global Genome Reorganization and Npc F...mentioning

confidence: 74%

Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis

Kotb,

Ulukaya,

Chavan

et al. 2023

Preprint

View full text Add to dashboard Cite

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“…Thus, Nups may both facilitate histone modifications and enhance the formation of phase-separated condensates such as those frequently associated with transcription. Indeed, tethering Nup153 to chromatin promotes the formation of phase separated foci that include RNAPII and Mediator 72 . We propose that Nups, together with Mediator, strengthen enhancer function to promote burst frequency.…”

Section: Discussionmentioning

confidence: 99%

Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

Ge,

Brickner,

Zehr

et al. 2024

Preprint

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Nuclear pore proteins (Nups) in yeast, flies and mammals physically interact with hundreds or thousands of chromosomal sites, which impacts transcriptional regulation. In budding yeast, transcription factors mediate interaction of Nups with enhancers of highly active genes. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC) without altering its DNA binding or activation domains. SILAC mass spectrometry revealed that this mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 both interacts with the same sites as Nups genome-wide and is required for Nup2 to interact with the yeast genome. In vivo, Crm1 undergoes extensive and stable interactions with the NPC. In vitro, Crm1 binds to Gcn4 and these proteins form a complex with the nuclear pore protein Nup2. Importantly, the interaction between Crm1 and Gcn4 does not require Ran-GTP, suggesting that it is not through the nuclear export sequence binding site. Finally, Crm1 stimulates DNA binding by Gcn4, supporting a model in which allosteric coupling between Crm1 binding and DNA binding permits docking of transcription factor-bound enhancers at the NPC.

show abstract

High-precision mapping of nuclear pore-chromatin interactions reveals new principles of genome organization at the nuclear envelope

Cited by 2 publications

References 55 publications

Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis

Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis

Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

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