Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Widespread specific intron-retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts

ABSTRACT: Many essential cellular processes require RNA to interact with protein(s) to form ribonucleic protein complexes (RNPs). For example, all cellular proteins are produced by the ribosome - a large and stable RNP, gene splicing requires a choreography of numerous small and large RNPs, even the replication of telomeric DNA requires an RNP. All these examples are stable RNPs that exhibit specific sedimentation rates (e.g., in a sucrose gradient) based on the composition of RNA and protein. In this study we aimed to identify RNAs components of RNPs on a transcriptome-wide scale. Using sucrose-gradient followed by sequencing we identified 1,057 RNA transcripts that are likely to be components of cellular RNPs. Our approach determined that RNP are not due to the cellular abundance nor length of the constituent RNA transcripts. The RNPs identified were predominantly nuclear, containing a specified retained intron and resistant to RNA degradation. Collectively our study reveals a widespread phenomena of a specific intron being retained in a stable nuclear RNP.

ORGANISM(S): Homo sapiens

PROVIDER: GSE284687 | GEO | 2025/08/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profiling of mouse polysome vs RNP fractions from testis obtained from prepuberttal and adult animals to investigate post transcriptional control mechanisms in gametes

Project description:Gametes rely heavily on post-transcriptional control mechanisms to regulate their differentiation. In eggs, the storage and selective temporal activation of maternal mRNAs is essential for normal development. In the male, transcription ceases during spermiogenesis necessitating the post-transcriptional regulation of many paternal mRNAs required for spermatid differentiation and spermatozoan function. Messenger RNAs that are being actively translated form polysomes. whereas translationally inactive mRNAs are often sequestered in ribonucleoproteins (RNPs). Here we combine polysome display and microarray analyses of RNP and polysome fractions of testes from prepubertal and adult mice to characterize the translation state of individual mRNAs as spermatogenesis proceeds.. Consistent with published reports, many post-meiotic mRNAs known to be translationally delayed shift from the RNPs into the polysomes, confirming the validity of this approach. In addition, based upon the criterion of movement from RNPs to polysomes, we detect another 742 mouse testicular genes showing dramatic shifts between RNPs and polysomes. One sub-group of 35 genes including the known translationally delayed Pgk2, are initially transcribed and translationally repressed in meiotic spermatocytes, and translated post-meiotically. This high-through-put approach defines the changing translation patterns of a large number of genes as male germ cells differentiate and identifies a new group of post-transcriptionally regulated meiotic transcripts for future study. Mouse testes from animals of 3 different ages were fractionated on a sucrose gradient and transcripts were quantified in the RNP and Polysome fractions. Transcripts were identified that changed their RNP/Polysome representation at the different developmental time points.

2007-11-23 | E-GEOD-4711 | biostudies-arrayexpress

MS analysis of GAR1 methylation immunopurified from HEK-293 Cells

Project description:The conserved box H/ACA RNPs consist of one box H/ACA RNA and 4 core proteins: Dyskerin, NHP2, NOP10 and GAR1. The assembly of the H/ACA RNPs is a stepwise process which requires several assembly factors: SHQ1, NAF1, the Survival of Motor Neuron complex SMN, and the R2TP complex. It implicates the co-transcriptional assembly of a pre-particle containing the nascent RNAs, Dyskerin, NOP10, NHP2 and NAF1. The latest keeps the H/ACA RNP inactive, and needs to be replaced by GAR1 to produce mature and functional H/ACA RNPs in the Cajal bodies. In this study, we explore in details the molecular mechanism leading to the assembly of mature box H/ACA RNPs. We performed extensive analysis of GAR1, NHP21 and NAF interactomes by quantitative stable isotope labeling by amino acids in cell culture proteomic analyses (SILAC), and revealed new assembly intermediates: 1) an early protein-only pre-H/ACA RNP complex containing the core proteins DKC1, NOP10 and NHP2, and the assembly factors SHQ1 and NAF1, and 2) a late assembly intermediates containing the RNA, the core proteins and NAF1. We showed that the SMN complex is associated with late forming H/ACA pre-RNP complexes containing GAR1. Moreover, our study identifies new proteins highly and specifically associated with GAR1, NHP2 and NAF1, reflecting their importance in box H/ACA assembly or function, such as the PRMT1 and PRMT5 arginine methylases. MS analysis of purified GAR1 revealed new sites of arginine methylations in the two GAR domains of GAR1, and showed that most of these methylated arginines exist both in mono-methylated and di-methylated forms in cells. By different methods, we showed that unmethylated GAR1 is correctly incorporated in H/ACA RNPs. Therefore, GAR1 methylation should be important for its function.

2023-05-10 | PXD026752 | Pride

SILAC APMS analysis of NAF1 interactome in HEK-293 cells

Project description:The conserved box H/ACA RNPs consist of one box H/ACA RNA and 4 core proteins: Dyskerin, NHP2, NOP10 and GAR1. The assembly of the H/ACA RNPs is a stepwise process which requires several assembly factors: SHQ1, NAF1, the Survival of Motor Neuron complex SMN, and the R2TP complex. It implicates the co-transcriptional assembly of a pre-particle containing the nascent RNAs, Dyskerin, NOP10, NHP2 and NAF1. The latest keeps the H/ACA RNP inactive, and needs to be replaced by GAR1 to produce mature and functional H/ACA RNPs in the Cajal bodies. In this study, we explore in details the molecular mechanism leading to the assembly of mature box H/ACA RNPs. MS analysis of purified GAR1 revealed new sites of arginine methylations in the two GAR domains of GAR1, and showed that most of these methylated arginines exist both in mono-methylated and di-methylated forms in cells. By different methods, we showed that unmethylated GAR1 is correctly incorporated in H/ACA RNPs. We performed extensive analysis of GAR1, NHP2 and NAF1 proteomes by quantitative stable isotope labeling by amino acids in cell culture proteomic analyses (SILAC), and revealed new assembly intermediates: 1) an early protein-only pre-H/ACA RNP complex containing the core proteins DKC1, NOP10 and NHP2, and the assembly factors SHQ1 and NAF1, and 2) a late assembly intermediates containing the RNA, the core proteins and NAF1. We showed that the SMN complex is associated with late forming H/ACA pre-RNP complexes containing GAR1. Moreover, our study identifies new proteins highly and specifically associated with GAR1, NHP2 and NAF1, suggesting their importance in box H/ACA assembly or function, such as the PRMT1 and PRMT5 arginine methylases.

2022-02-17 | PXD026747 | Pride

SILAC APMS analysis of SHQ1 interactome in HEK-293 cells

Project description:The conserved box H/ACA RNPs consist of one box H/ACA RNA and 4 core proteins: Dyskerin, NHP2, NOP10 and GAR1. The assembly of the H/ACA RNPs is a stepwise process which requires several assembly factors: SHQ1, NAF1, the Survival of Motor Neuron complex SMN, and the R2TP complex. It implicates the co-transcriptional assembly of a pre-particle containing the nascent RNAs, Dyskerin, NOP10, NHP2 and NAF1. The latest keeps the H/ACA RNP inactive, and needs to be replaced by GAR1 to produce mature and functional H/ACA RNPs in the Cajal bodies. In this study, we explore in details the molecular mechanism leading to the assembly of mature box H/ACA RNPs. MS analysis of purified GAR1 revealed new sites of arginine methylations in the two GAR domains of GAR1, and showed that most of these methylated arginines exist both in mono-methylated and di-methylated forms in cells. By different methods, we showed that unmethylated GAR1 is correctly incorporated in H/ACA RNPs. We performed extensive analysis of GAR1, NHP2 and NAF1 proteomes by quantitative stable isotope labeling by amino acids in cell culture proteomic analyses (SILAC), and revealed new assembly intermediates: 1) an early protein-only pre-H/ACA RNP complex containing the core proteins DKC1, NOP10 and NHP2, and the assembly factors SHQ1 and NAF1, and 2) a late assembly intermediates containing the RNA, the core proteins and NAF1. We showed that the SMN complex is associated with late forming H/ACA pre-RNP complexes containing GAR1. Moreover, our study identifies new proteins highly and specifically associated with GAR1, NHP2 and NAF1, suggesting their importance in box H/ACA assembly or function, such as the PRMT1 and PRMT5 arginine methylases.

2023-05-10 | PXD035330 | Pride

SILAC APMS analysis of NHP2 / Gar1 interactome in HEK-293 cells

2023-05-10 | PXD026749 | Pride

MicroRNAs control mRNA fate by compartmentalizing mRNAs based on 3’UTR length

Project description:Introduction: we conduct comprehensive transcriptomic profiling analyses on three spermatogenic cell types (pachytene spermatocytes, round and elongating spermatids) purified from adult mouse testes using RNA-seq, and we determined not only the levels of both mRNAs and all known sncRNA species, but their cytoplasmic compartmentalization as well. Method: Pachytene spermatocytes, round and elongating/elongated spermatids were purified from adult mouse testes using the STA-PUT method. We fractionated the purified spermatogenic cells into RNP, monoribosome, and polyribosome fractions using a continuous sucrose gradient ultracentrifugation method, as described. Large RNAs were isolated using the AquaRNA RNA Purification Kit (Cat#5001MT, Mo Bi Tec, Inc.), whereas small RNAs were prepared by the mirPremier™ microRNA Isolation Kit (Cat#SNC10, Sigma). Constructions of mRNA and sncRNA libraries were conducted following our published protocols (Refs) and the next-gen sequencing was performed on a Hi-Seq 2000 sequencer with SE50 at the Genomics Microarray Core Facility of the UT Southwestern Medical Center (Dallas, TX). Result:Bioinformatics analyses revealed miRNAs were mostly enriched in RNPs and RNP-enriched miRNAs preferentially target RNP-enriched mRNAs. More interestingly, we found that miRNAs could distinguish shorter and longer 3’UTR transcript based on the distance between their binding sites and the stop codon. Conclusions:Overall, our genome-wide transcriptomic and bioinformatics analyses have revealed a highly likely mechanism through which miRNAs shape the haploid male germ cell-specific transcriptome characterized by RNP-enrichment of transcripts with shorter 3’UTRs.

2016-04-18 | GSE80353 | GEO

L-bodies are novel RNA-protein condensates driving RNA transport in Xenopus oocytes

Project description:RNP granules are membrane-less compartments within cells, formed by phase separation, that function as regulatory hubs for diverse biological processes. However, the mechanisms by which RNAs and proteins interact to promote RNP granule assembly and function in vivo remain unclear. In Xenopus laevis oocytes, maternal mRNAs are transported as large RNPs to the vegetal hemisphere of the developing oocyte, where local translation is critical for proper embryonic patterning. Here, we demonstrate that vegetal transport RNPs represent a new class of cytoplasmic RNP granule, termed Localization-bodies (L-bodies). We show that L-bodies are multiphase RNP granules, containing a dynamic liquid-like protein-containing phase surrounding a non-dynamic RNA-containing substructure. Our results support a role for RNA as a critical scaffold component within these RNP granules and suggest that cis-elements within localized mRNAs may drive subcellular RNA localization through control over phase behavior.

2020-09-20 | GSE158246 | GEO

Depletion and reconstitution of 5S RNP complexes in early pre60S ribosomes

Project description:We purified pre60S ribosomes from yeast using Nsa1-FtpA as bait in Tandem Affinity Purification experiments. We tested the depletion of RPF2, using a Galactose-depletion system, to obtain ribosomal particles depleted of 5S RNP complexes. Sample A1: Control group (wild type strain) grown in YPGal; Sample A2: Control group (wild type strain) grown in YPGlu; Sample A3: Control group (Gal::HA-RPF2 strain) grown in YPGal; and Sample A4: Test group (Gal::HA-RPF2) shifted from YPGal to YPGlu for 6 hours to achieve 5S RNP depletion. Sample N1: Purified pre-60S Nsa1-associated with 5S RNP depleted after Sucrose gradient separation; Sample N2: Purified pre-60S Nsa1-associated with 5S RNP reconstituted after Sucrose gradient separation.

2023-10-24 | PXD040306 | Pride

The highly conserved intron of tyrosine tRNA is critical for m1A58 modification and controls the integrated stress response

Project description:Intron-retained tRNA

| PRJEB89406 | ENA

Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles

Project description:We explored the RNA binding properties of LINE-1 ORF1p, both free and in the L1 RNP, using a recently developed photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation technique (PAR-CLIP) to comprehensively identify ORF1p binding sites in the transcriptome of human cells (HEK293T). Our results show that ORF1p binds to a wide range of cellular mRNAs, with an enrichment for binding at the 3’ UTR. Our data also show that ORF1p binds very strongly with retrotransposable RNA, i.e., L1, Alu and SVA. PAR-CLIP analysis of L1 RNPs and free ORF1p RNA binding profiles, comparison to HuR RNA binding profile

2013-05-21 | E-GEOD-43801 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data