Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1078296 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28026310_1.fastq.gz | Fastqsanger.gz | |||
| SRR28026310_2.fastq.gz | Fastqsanger.gz | |||
| SRR28026311_1.fastq.gz | Fastqsanger.gz | |||
| SRR28026311_2.fastq.gz | Fastqsanger.gz | |||
| SRR28026312_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description:mRNAs continually change their protein partners throughout their lifetimes, yet our understanding of mRNP remodeling is limited by a lack of temporal data. Here, we present time-resolved mRNA interactome data by performing pulse metabolic labeling with photoactivatable ribonucleoside, UVA crosslinking, poly(A)+ RNA isolation, and mass spectrometry. This longitudinal approach allowed the quantification of over 700 RNA-binding proteins (RBPs) across ten distinct time points. Overall, the sequential order of mRNA binding aligns well with known functions, subcellular locations, and molecular interactions. However, we also observed numerous RBPs with unexpected dynamics: the TRanscription-EXport complex (TREX) recruited posttranscriptionally after NXF1 binding, challenging the current view of transcription-coupled mRNA export mechanism, and stress granule proteins prevalent in aged mRNPs, indicating roles in late stages of mRNA life cycle. To systematically identify mRBPs with unknown functions, we employed machine learning to compare mRNA binding dynamics with GO annotations. Our data can be explored at chronology.rna.snu.ac.kr.
2024-02-21 | GSE256124 | GEO
Project description:From synthesis to decay, mRNA changes its protein partners, yet previous studies were limited in that they profiled only the mixed pools of RNA-binding proteins (RBPs) without temporal resolution. Here, we provide time-resolved profiles of human mRNA interactome by combining pulse metabolic labeling, photoactivatable ribonucleoside crosslinking, poly(A) RNA isolation, and mass spectrometry. We captured stage-specific RBPs across 10 time points and quantified over 700 RBPs. The chronological orders of mRNA binding are generally consistent with the known functions and localizations of RBPs: pre-mRNA processing factors are detected as “early binders” while decay factors appear as “late binders”. Notably, stress granule proteins are enriched in “aged” mRNPs, suggesting their roles in the final stage of mRNA life cycle. Many late binders also interact with viral transcripts, implying their regulatory activities on viruses. Furthermore, we built a computational model to systematically identify RBPs with unexpected binding dynamics, which indicates their unknown functions. Our study reveals a dynamic landscape of mRNP remodeling, offering new functional insights into RNA-protein interaction during mRNA life cycle.
2024-02-23 | PXD039054 | Pride
Project description:The occupancy states of DNA-binding nucleosomes and subnucleosome-sized proteins (e.g. transcription factors, replication proteins, etc.) determine the chromatin accessibility landscape and provide additional regulatory context for DNA-templated processes including transcription and DNA replication. Throughout the mitotic cell division cycles, the transcriptome undergoes periodic reprogramming along with replication- and mitosis-induced global chromatin reconfiguration; however, profiling of the cell cycle-specific chromatin dynamics and understandings of its regulatory mechanisms remain limited. Here we employed high-resolution MNase-seq to factor-agnostically map the genome-wide chromatin occupancy with synchronized Saccharomyces cerevisiae cell populations, in parallel with transcriptome profiling by RNA-seq. Throughout the cell cycles, the occupancy of gene-body nucleosomes and promoter subnucleosomes (presumably TFs and polymerase) exhibit both transcription- dependent and independent periodicity, suggesting a decoupling between transcription and chromatin occupancy dynamics. The “phased” positioning of nucleosomes within gene bodies, however, is pervasively disorganized by replication fork progression, and also regulated by the intensity and cell cycle phase of transcriptional activation. Finally, we profiled the chromatin organization around replication origins throughout the complete cell cycle and revealed the chromatin context for origin efficiency.
2022-01-06 | GSE168699 | GEO
Project description:Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle
| PRJNA900198 | ENA
Project description:Small, compact genomes confer a selective advantage to viruses, yet human cytomegalovirus (HCMV) expresses the long non-coding RNAs (lncRNAs) RNA1.2, RNA2.7, RNA4.9, and RNA5.0. These lncRNAs account for majority of the viral transcriptome, but their functions remain largely unknown. Here, we showed that HCMV lncRNAs, except for RNA5.0, are required throughout the entire viral life cycle. Deletion of each lncRNA resulted in a decrease in viral progeny during lytic replication and failing to efficiently establish latent reservoirs and reactivate. Nanopore direct RNA sequencing of native lncRNA molecules revealed that each lncRNA exhibited a dynamic modification landscape, depending on the state of infection. Global analysis of the lncRNA interactome identified 32, 11, and 89 host factors that specifically bind to RNA1.2, RNA2.7, and RNA4.9, respectively. Moreover, 52 proteins commonly bound to the three lncRNAs were identified, including 11 antiviral immunity-related proteins. Our molecular analyses found that three lncRNAs are modified with N⁶-methyladenosine (m6A) and interact with m6A readers in all infection states. In-depth functional analysis revealed that m6A–mediated lncRNA stabilization as the key mechanism by which lncRNAs are maintained at high levels. Our study lays the groundwork for understanding viral lncRNA–mediated regulation of host-virus interaction throughout the HCMV life cycle.
2022-11-14 | PXD034587 | Pride
Project description:Time series data of chromatin and transcription throughout the cell cycle
| PRJNA713547 | ENA
Project description:Expression profiling of 7,530 Heterodera glycines probesets present on the Affymetrix Soybean Genome Array GeneChip throughout the life cycle of the nematode (egg, infective J2, parasitic J2, J3, J4, adult female).
2007-10-20 | E-MEXP-1110 | biostudies-arrayexpress
Project description:Small, compact genomes confer a selective advantage to viruses, yet human cyto-megalovirus (HCMV) expresses the long non-coding RNAs (lncRNAs); RNA1.2, RNA2.7, RNA4.9, and RNA5.0. Little is known about the function of these lncRNAs in the virus life cycle. Here, we dissected the functional and molecular landscape of HCMV lncRNAs. We found that HCMV lncRNAs occupy ~30 % and 50~60 % of to-tal and poly(A)+ viral transcriptome, respectively, throughout virus life cycle. RNA1.2, RNA2.7, and RNA4.9, the three abundantly expressed lncRNAs, appear to be es-sential in all infection states. Among these three lncRNAs, depletion of RNA2.7 and RNA4.9 results in the greatest defect in maintaining latent reservoir and promoting lytic replication, respectively. Moreover, we delineated the global post-transcriptional nature of HCMV lncRNAs by nanopore direct RNA sequencing and interactome analysis. We revealed that the lncRNAs are modified with N⁶-methyladenosine (m6A) and interact with m6A readers in all infection states. In-depth analysis demonstrated that m6A machineries stabilize HCMV lncRNAs, which could account for the over-whelming abundance of viral lncRNAs. Our study lays the groundwork for under-standing the viral lncRNA–mediated regulation of host-virus interaction throughout the HCMV life cycle.
2022-11-16 | GSE217713 | GEO
Project description:Small, compact genomes confer a selective advantage to viruses, yet human cyto-megalovirus (HCMV) expresses the long non-coding RNAs (lncRNAs); RNA1.2, RNA2.7, RNA4.9, and RNA5.0. Little is known about the function of these lncRNAs in the virus life cycle. Here, we dissected the functional and molecular landscape of HCMV lncRNAs. We found that HCMV lncRNAs occupy ~30 % and 50~60 % of to-tal and poly(A)+ viral transcriptome, respectively, throughout virus life cycle. RNA1.2, RNA2.7, and RNA4.9, the three abundantly expressed lncRNAs, appear to be es-sential in all infection states. Among these three lncRNAs, depletion of RNA2.7 and RNA4.9 results in the greatest defect in maintaining latent reservoir and promoting lytic replication, respectively. Moreover, we delineated the global post-transcriptional nature of HCMV lncRNAs by nanopore direct RNA sequencing and interactome analysis. We revealed that the lncRNAs are modified with N⁶-methyladenosine (m6A) and interact with m6A readers in all infection states. In-depth analysis demonstrated that m6A machineries stabilize HCMV lncRNAs, which could account for the over-whelming abundance of viral lncRNAs. Our study lays the groundwork for under-standing the viral lncRNA–mediated regulation of host-virus interaction throughout the HCMV life cycle.
2022-11-16 | GSE217710 | GEO
Project description:Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle [shortread]
| PRJNA900204 | ENA