Mapping and engineering RNA-driven architecture of the multiphase nucleolus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1257945 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33405174_1.fastq.gz | Fastqsanger.gz | |||
| SRR33405174_2.fastq.gz | Fastqsanger.gz | |||
| SRR33405175_1.fastq.gz | Fastqsanger.gz | |||
| SRR33405175_2.fastq.gz | Fastqsanger.gz | |||
| SRR33405176_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:Mapping and engineering RNA-driven architecture of the multiphase nucleolus
| PRJNA1257780 | ENA
Project description:Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a multiphase liquid-like structure where ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps to form the small and large ribosomal subunits (SSU and LSU). However, how rRNA processing is coupled to the layered nucleolar organization is poorly understood due to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here, we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. By generating synthetic nucleoli in cells through an engineered rDNA plasmid system, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.
2025-06-16 | GSE296080 | GEO
Project description:Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a multiphase liquid-like structure where ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps to form the small and large ribosomal subunits (SSU and LSU). However, how rRNA processing is coupled to the layered nucleolar organization is poorly understood due to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here, we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. Furthermore, by generating synthetic nucleoli in cells through an engineered rDNA plasmid system, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.
2025-06-17 | GSE296162 | GEO
Project description:Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a layered multiphase liquid-like structure and the site of ribosome biogenesis. In the nucleolus, ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps that ultimately result in formation of the ribosomal small subunit (SSU) and large subunit (LSU). However, how rRNA processing is coupled to the layered nucleolar organization is poorly understood due to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here, we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. Furthermore, by generating synthetic de novo nucleoli through an engineered rDNA plasmid system in cells, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.
| S-EPMC11463421 | biostudies-literature
Project description:Nucleolus plays a key role in organizing global nuclear structure and facilitating gene regulation, but the three dimensional information within the nucleolus associated chromatins are still unknown, so here we development the Nucleolus Hi-C (NHi-C) experimental technique, which combines the nucleolus isolation with Hi-C experiment, and study the interactions within and surrounding nucleolus in human cells with a high resolution. With NHi-C experiment, we report how the nucleolus-associated chromatin regions interact at genome scale, and how these interactions organize the repressive nucleus architecture.
2021-02-01 | GSE90003 | GEO
Project description:Nucleolus-associated DNA was isolated from cross-linked proliferating and senescent IMR90 human fibroblasts and hybridized against genomic (1) or non-nucleolar (2) DNA to map nucleolus-associated chromosomal domains.
2017-06-18 | GSE78043 | GEO
Project description:Multiphase Environmental Microorganisms in Landfills Raw sequence reads
| PRJNA1366923 | ENA
Project description:Nucleolus is a multiphase biomolecular assembly containing three distinct subcompartments. Evidence is just emerging that nucleolar proteins with characteristic electrochemical properties condense to generate a pH gradient, which serves as a key driving force for organizing the nucleolar sub-phases. Given the indispensable functionality of the nucleolus in most, if not all, cellular activities, it is vital for a cell to sense potential fluctuations in the nucleolar pH and subsequently maintain pH homeostasis. The mechanisms by which a cell achieves this task remain poorly decoded. Here, we show that splicing factor SRSF1 is shuttled from nuclear speckle (NS) to the nucleolus during times of stress, which interrogates the nucleolar pH. SRSF1 nucleolar localization is reliant on an acidic patch. Loss of SRSF1 impedes pH homeostasis in the dark nucleolar cap and subsequently obstructs the restoration of the nucleolar multiphase and function. The RS (arginine/serine rich) domain of SRSF1, due to its high isoelectric point (pI), directly alkalizes the nucleolar microenvironment. Interestingly, synthetic arginine-rich dipeptide derivatives of SRSF1 RS domain safeguard the nucleolus from pH and functional disturbance. Our findings uncover unprecedented mechanistic insights into nucleolar pH-sensing and regulation.
2026-04-16 | GSE319593 | GEO
Project description:EFFECT OF A MULTIPHASE DIETARY INTERVENTION IN METABOLIC PROFILE AND GUT MICROBIOTA COMPOSITION IN METABOLICALLY HEALTHY AND UNHEALTHY OBESE SUBJECTS
| PRJEB83574 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below. Gene positioning in nuclear space is central to regulation, with repressive chromatin domains often contacting the nuclear lamina or nucleoli. The nucleolus undergoes structural changes in different cellular states, potentially altering genome organization. Yet, how nucleolar states influence 3D-genome architecture remains underexplored, largely due to the lack of methods able to map nucleolar-associated domains (NADs) in single cells and stressed nucleoli. We developed NoLMseq, a technique combining laser-capture microdissection and DNA sequencing to map NADs in single cells. NoLMseq uncovered unexplored features of chromosome organization around nucleoli, including NAD heterogeneity in mouse embryonic stem cells, yielding two major populations with distinct chromatin and developmental states. NADs predominantly contact nucleoli monoallelically, with contact frequency correlating with gene expression and chromatin states. Under nucleolar stress, NoLMseq revealed extensive chromosome reorganization, highlighting the importance of nucleolus integrity in genome organization. Thus, NoLMseq provides a critical tool to study 3D-genome responses to nucleolar states in health and disease.
2025-10-05 | GSE269201 | GEO