An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains

Lerra, Luigi; Panatta, Martina; Bär, Dominik; Zanini, Isabella; Tan, Jennifer Yihong; Pisano, Agnese; Mungo, Chiara; Baroux, Célia; Panse, Vikram Govind; Marques, Ana C.; Santoro, Raffaella

doi:10.1016/j.molcel.2024.03.015

Cited by 1 publication

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“…ChIP analysis was performed as previously described 51 . Briefly, 1% formaldehyde was added to cultured cells to cross-link proteins to DNA.…”

Section: Methodsmentioning

confidence: 99%

Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq)

Walavalkar,

Gupta,

Kresoja-Rakic

et al. 2024

Preprint

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Gene position in the nuclear space plays an important role in gene regulation. This is exemplified by repressive chromatin domains frequently contacting nuclear lamina or nucleoli. The nucleolus undergoes structural changes in response to various cellular states, potentially impacting genome organization. However, how the 3D-genome organization responds to nucleolar states has remained underinvestigated due to the lack of methods able to identify nucleolar associated domains (NADs) in single cells and under nucleolar stress. To address this, we developed NoLMseq, a method combining laser-capture microdissection and DNA sequencing to map NADs in single cells. NoLMseq identified many unexplored features of chromosome organization around single nucleoli such as NAD heterogeneity among ESCs, culminating in two major populations with distinct chromatin states. The data also revealed that NADs prevalently contact nucleoli in a monoallelic manner and allelic nucleolar contact frequency sets gene expression and chromatin states. NoLMseq also revealed how chromosomes reorganise around nucleoli under nucleolar stress conditions, highlighting the importance of nucleolus integrity in genome organization and 3D-genome response to nucleolar stress. The results demonstrated that NoLMseq accurately measures chromosome contacts around single healthy and stressed nucleoli and it will be a critical tool to study NADs within biological populations and determine how the 3D-genome responds to nucleolar stress in healthy and disease states.

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“…ChIP analysis was performed as previously described 51 . Briefly, 1% formaldehyde was added to cultured cells to cross-link proteins to DNA.…”

Section: Methodsmentioning

confidence: 99%

Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq)

Walavalkar,

Gupta,

Kresoja-Rakic

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains

Cited by 1 publication

References 67 publications

Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq)

Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq)

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