Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multi-omics analysis using antibody-based in situ biotinylation technique reveals the mechanism of Cajal body formation

ABSTRACT: Membrane-less subcellular compartments such as cytoplasmic bodies, nuclear bodies, and paraspeckles play important roles in a variety of cellular functions. Although many of the techniques for identifying the components of cellular bodies were developed to address their function, no technique to comprehensively identify the components of these bodies in both static and dynamic states has been established. Here, we developed an antibody-based in situ biotinylation proximity-labeling technique and succeeded in identifying the components of both static and dynamic nuclear bodies, nucleolus and γH2AX foci, respectively. Using this technique, we comprehensively identified the components of Cajal bodies (CBs), including DNAs, RNAs, and proteins, and clarified their interactome in CBs. Furthermore, we captured the dynamic change of CBs by inhibiting transcription. Our analysis revealed that nascent snRNAs transcribed in CBs play a role in CB nucleation through assembling RNA binding proteins, including FTD-related proteins, RBMs and HNRNPs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE235853 | GEO | 2024/10/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Multi-omics analysis using antibody-based in situ biotinylation technique reveals the mechanism of Cajal body formation

Project description:Membrane-less subcellular compartments such as cytoplasmic bodies, nuclear bodies, and paraspeckles play important roles in a variety of cellular functions. Although many of the techniques for identifying the components of cellular bodies were developed to address their function, no technique to comprehensively identify the components of these bodies in both static and dynamic states has been established. Here, we developed an antibody-based in situ biotinylation proximity-labeling technique and succeeded in identifying the components of both static and dynamic nuclear bodies, nucleolus and γH2AX foci, respectively. Using this technique, we comprehensively identified the components of Cajal bodies (CBs), including DNAs, RNAs, and proteins, and clarified their interactome in CBs. Furthermore, we captured the dynamic change of CBs by inhibiting transcription. Our analysis revealed that nascent snRNAs transcribed in CBs play a role in CB nucleation through assembling RNA binding proteins, including frontotemporal dementia-related proteins, RBMs and HNRNPs.

2024-07-06 | PXD043574 | JPOST Repository

TDRD6 instructs correct assembly of mRNPs in the chromatoid body to potentiate UPF1 dependent mRNA decay.

2015-12-08 | GSE63948 | GEO

Identification of coilin interactors reveals coordinated control of Cajal body number and substructure

Project description:The cell nucleus contains distinct biomolecular condensates that form at specific genetic loci, organize chromosomes in 3D space, and regulate RNA processing. Among these, Cajal bodies (CBs) require key “scaffolding” proteins for their assembly, which is not fully understood. Here we employ proximity biotinylation, mass spectrometry, and functional screening to comprehensively identify and test functions of CB components. We document 144 protein interactors of coilin, of which 70 were newly detected, and establish 25 players needed for CB assembly and/or maintenance. Surprisingly, depletion of nine coilin interactors – mostly constituents of the 60S ribosome (RPLs) – increased CB number and caused subdomains defined by coilin and the Survival of Motor Neuron protein (SMN) to merge. These phenotypes were traceable to altered nuclear levels of dimethylarginine. Our data implicate RPL24 and other players in the regulation of CBs by modulating post-translational modifications. Moreover, the prevalence of transcription factors among the identified components highlights roles for gene activity in CB assembly and nuclear positioning.

2024-11-10 | PXD042406 | Pride

TDRD6 instructs correct assembly of mRNPs in the chromatoid body to potentiate UPF1 dependent mRNA decay.

Project description:RNA sequencing of heterozygote or Tudor domain contian protein 6 (TDRD6) knockout round spermatid cells. Chromatoid bodies (CBs) are germ cell-specific organelles of largely unknown function. CBs harbor various RNA species, RNA-associated proteins and proteins of the tudor domain family such as TDRD6. Proteome analysis of purified CBs revealed components of the nonsense-mediated mRNA decay machinery such as UPF1. TDRD6 is essential for UPF1 localization to CBs, for UPF1-UPF2 interaction, and for assembly of UPFs and other RNA binding proteins into super-complexes. In absence of TDRD6, the association of some mRNAs with UPF1 is impaired, and the long 3â UTR-stimulated but not the exon junction complex-stimulated pathway of NMD is distorted. Reduced association of mRNAs with UPF1 correlated with increased stability and presence in polysome fractions, i.e. enhanced translational activity. Thus, we define CBs as sites of UPF1-dependent mRNA degradation and provide evidence for the requirement for NMD in spermiogenesis. This function of CBs depends on TDRD6-promoted assembly of mRNA decay enzymes within mRNPs. RNA was extracted from quadruplicate samples and libraries generated for sequencing using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) at the Deep Sequencing Group SFB 655, Biotechnology Center of Technische UniversitÃ¤t Dresden. After enrichment and XP bead (Agencourt AMPure Kit; Beckman Coulter, Inc.) purification, quality control was done using Fragment AnalyzerTM (Advanced Analytical). The bar-coded libraries were equimolarly pooled and subjected to 76 bp single-end sequencing on Illumina HiSeq 2000, resulting in an average of 33 million reads per sample.

2015-12-08 | E-GEOD-63948 | biostudies-arrayexpress

Atypical modes of CTCF binding facilitate tissue-specific and neuronal activity-dependent gene expression states [SMC1_ChIP-seq]

Project description:The multivalent binding of CTCF to a variety of DNA sequences is thought to underlie its ability to mediate a large repertoire of cellular functions. CTCF is a 11 zinc-finger (ZF) protein that is anchored to a majority of its target sites via binding to a 20 base-pair core DNA sequence. Yet the diversity of CTCF binding sites (CBS) has not fully been characterized. Here we assessed CTCF occupancy in cultured mouse cortical neurons as a function of neuronal activity and observed that ~ 22 % of CBS lack the consensus CTCF motif. We report that sequence diversity at most of these atypical CBS is not random but involves degeneracy at specific nucleotide positions within the core CTCF position weight matrix (PWM) that likely affect the binding of ZFs 6 and 7. Surprisingly, degeneracy at the same nucleotides not only define most atypical CBS, but also CBS within most gene promoters, and CBS that are dynamically altered following neuronal stimulation, revealing how atypical CTCF binding could affect gene activity. Dynamic CBS across neural differentiation and neuronal stimulation are found both within and outside loop anchors and TADs, indicating that dynamic CBS could regulate gene activity independently of loop anchoring. Finally, we identified a second mode of atypical CTCF binding that defines most tissue-specific CBS. Unlike other atypical CBS, tissue-specific CBS largely bind sequences unrelated to the core CTCF motif and are enriched within the bodies of tissue-specific genes. Overall, these results indicate how CTCF binding at atypical CBS could allow it to dynamically regulate gene activity patterns during differentiation, development, and in response to environmental cues.

2023-08-30 | GSE235971 | GEO

Atypical modes of CTCF binding facilitate tissue-specific and neuronal activity-dependent gene expression states [CTCF_ChIP-seq]

2023-08-30 | GSE235970 | GEO

Global Analysis of Yeast mRNPs

Project description:Proteins regulate gene expression by controlling mRNA biogenesis, localization, translation and decay. Identifying the composition, diversity and function of mRNPs (mRNA protein complexes) is essential to understanding these processes. In a global survey of S. cerevisiae mRNA binding proteins we identified 120 proteins that cross-link to mRNA, including 66 new mRNA binding proteins. These include kinases, RNA modification enzymes, metabolic enzymes, and tRNA and rRNA metabolism factors. These proteins show dynamic subcellular localization during stress, including assembly into stress granules and P-bodies (Processing-bodies). CLIP (cross-linking and immunoprecipitation) analyses of the P-body components Pat1, Lsm1, Dhh1 and Sbp1 identified sites of interaction on specific mRNAs revealing positional binding preferences and co-assembly preferences. Taken together, this work defines the major yeast mRNP proteins, reveals widespread changes in their subcellular location during stress, and begins to define assembly rules for P-body mRNPs. CLIP-seq analysis of Dhh1, Lsm1, Pat1 and Sbp1

2013-04-18 | E-GEOD-46142 | biostudies-arrayexpress

Nuclear IQGAP1 promotes gastric cancer cell growth by altering the splicing of a cell-cycle regulon in co-operation with hnRNPM

Project description:Heterogeneous nuclear ribonucleoproteins (hnRNPs) play a decisive role in alternative splicing, regulating the cell proteome and contributing to human diseases. hnRNPs are nuclear proteins but it is still an open question where they localize in the nucleus and what determines their tethering to nuclear assemblies in response to signals. Here we report that IQGAP1, a cytosolic scaffold protein, localizes in the nucleus of gastric cancer cells acting as a tethering module for hnRNPM as well as other spliceosome components. The IQGAP1-hnRNPM interaction alters, among others, the alternative splicing of ANAPC10 and is required for the response of hnRNPM to heat-induced stress signals. Together, IQGAP1 and hnRNPM promote gastric cancer cell growth while their depletion leads to cell cycle arrest and halts tumour progression. We propose that IQGAP1 localizes in the nucleus and coordinates gastric tumour growth by recruiting, in response to stress-signals, spliceosome components that drive cell cycle progression.

2021-09-09 | GSE146283 | GEO

The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies

Project description:The non-polyadenylated mRNAs of replication-dependent histones (RDHs) and small nuclear RNAs (snRNAs) are synthesized by RNA polymerase II at histone locus bodies (HLBs) and Cajal bodies (CBs), respectively. We previously showed that MED26-containing Mediator regulates the 3'-end processing of non-polyadenylated transcripts by recruiting Little Elongation Complex (LEC) to the genes. HLBs frequently associate with CBs, in which 3'-end processing factors for RDH genes are enriched; however, this association’s role has not been elucidated. Here, we show that disruption of the Mediator docking site for LEC by mutating the MED26-binding site of EAF1, a subunit of LEC, interferes with CBs’ association with HLBs, resulting in decreased inter-chromosome interaction between RDH gene clusters and increased aberrant unprocessed RDH gene transcripts. Our findings suggest a model in which LEC recruitment by Mediator plays a role in CBs’ association with HLBs to facilitate the 3'-end processing of RDH genes by supplying 3'-end processing factors.

2022-04-26 | GSE164144 | GEO