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Phosphorylation-dependent Charge Blocks Regulate the Coarsening of Nuclear Speckle Networks

ABSTRACT: Phosphorylation-dependent Charge Blocks Regulate the Coarsening of Nuclear Speckle Networks

PROVIDER: PRJNA1208960 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31951848_1.fastq.gz	Fastqsanger.gz
	SRR31951848_2.fastq.gz	Fastqsanger.gz
	SRR31951849_1.fastq.gz	Fastqsanger.gz
	SRR31951849_2.fastq.gz	Fastqsanger.gz
	SRR31951850_1.fastq.gz	Fastqsanger.gz

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Phosphorylation-dependent Charge Blocks Regulate the Coarsening of Nuclear Speckle Networks

Project description:Nuclear speckles (NSs) are viscoelastic network fluids formed via phase separation coupled to percolation (PSCP). Intermolecular cross-links of SRRM2, a key scaffold of NSs lead to the emergence of system-spanning networks, although the physiochemical grammar governing SRRM2 PSCP remains poorly decoded. Here, we demonstrate that SRRM2 is extensively phosphorylated within the intrinsically disordered domain (IDR) that are prominently positively charged. Rather than attaching phosphate groups to specific sites, the purpose of phosphorylation is to create alternating charge blocks. Employing a suite of biophysical approach, we show that in contrast to the leading theories that charge blocks lower condensation threshold of biopolymers, this specific charge pattern does not markedly alter the percolation threshold of SRRM2 in cells. Instead, SRRM2 charge blocks intensify intra-network molecular interactions to modulate the material properties of mesoscopic SRRM2 condensates. We further identify casein kinase 2 (CK2) as the upstream enzyme to catalyze SRRM2 phosphorylation. Phosphorylation of SRRM2 IDR by CK2 facilitates NS relaxation under physiological condition, but can be employed to safeguard genome stability in times of DNA damage. Our findings reveal important regulatory mechanisms of charge blocks and functionality in modulating the material properties of biomolecular condensates in cells. We interpretate our observation in the theoretical framework of stickers-and-spacers model. In addition to the chemistry- or sequence-specific associative interaction, spacers (e.g. SRRM2 IDR) can also engage in charge pattern-specific molecular interactions, which are spatiotemporally regulated, to dictate the biophysical properties of percolated macromolecular assemblies.

2025-03-10 | GSE286350 | GEO

Functional partitioning of transcriptional regulators by patterned charge blocks

Project description:Components of the transcriptional machinery are dynamically compartmentalized by weak multivalent interactions, yet we know little about how specificity or selectivity of partitioning is achieved. Here we show that condensates composed of the intrinsically disordered region (IDR) of MED1 (MED1_IDR) selectively partition positive regulators of transcription(SPT6, CTR9, IWS1) with RNA Pol II while excluding negative regulators of transcription (NELF and HP1a).This selective compartmentalization by MED1_IDR is sufficient to activate transcription and is required for gene activation during a cell state transition. Surprisingly, the IDRs of partitioned proteins are sufficient to recapitulate selective compartmentalization. We find that IDR-mediated selective partitioning requires multivalent blocks of positive and negative charge on MED1_IDR and IDRs of partitioned proteins. The charge patterns required for partitioning are also required for gene activation. These findings demonstrate that proteins can be functionally compartmentalized by specific multivalent interactions driven by the charge patterning within disordered regions.

2023-01-03 | GSE210875 | GEO

Functional partitioning of transcriptional regulators by patterned charge blocks

Project description:Functional partitioning of transcriptional regulators by patterned charge blocks

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Phosphorylation controls mRNA retention via nuclear speckle cohesion - APEX2-seq

Project description:Nuclear speckles are membraneless organelles that associate with active transcription sites and participate in post-transcriptional mRNA processing. During mitosis, nuclear speckles dissolve following phosphorylation of their protein components. Here, we identify PP1 phosphatases as responsible for counteracting kinase-mediated dissolution. Their overexpression increases speckle cohesion and leads to retention of polyadenylated RNA within speckles and the nucleus. By performing APEX2 proximity labeling combined with RNA-sequencing, we characterized the association of specific RNAs with nuclear speckles depending on their cohesion state. We find that many transcripts are preferentially enriched within nuclear speckles compared to the nucleoplasm, particularly chromatin- and nucleus-associated transcripts. While total polyadenylated RNA retention increased with greater nuclear speckle cohesion, the ratios of most mRNA species to each other were constant, indicating non-selective, or proportional, retention. We then explored whether nuclear speckle cohesion changes in response to environmental perturbations associated with changes in kinase or phosphatase activity. We found that cellular responses to heat shock, oxidative stress, and hypoxia include changes to the cohesion of nuclear speckles and mRNA retention. Our results demonstrate that tuning the material properties of nuclear speckles provides a mechanism for the acute control of mRNA localization.

2024-11-10 | GSE240891 | GEO

Phosphorylation controls mRNA retention via nuclear speckle cohesion - APEX2-seq

Project description:Phosphorylation controls mRNA retention via nuclear speckle cohesion - APEX2-seq

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Phosphorylation controls mRNA retention via nuclear speckle cohesion - cellular fractionation data

2024-11-10 | GSE240883 | GEO

Phosphorylation controls mRNA retention via nuclear speckle cohesion during environmental perturbations

Project description:Phosphorylation controls mRNA retention via nuclear speckle cohesion during environmental perturbations

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Phosphorylation controls mRNA retention via nuclear speckle cohesion - cellular fractionation data

Project description:Phosphorylation controls mRNA retention via nuclear speckle cohesion - cellular fractionation data

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