Rtf2 is Important for Replication Fork Barrier Activity of RTS1 via Splicing of Rtf1 [cDNA-Seq]
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ABSTRACT:
PROVIDER: PRJNA791218 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17286824_1.fastq.gz | Fastqsanger.gz | |||
| SRR17286825_1.fastq.gz | Fastqsanger.gz | |||
| SRR17286826_1.fastq.gz | Fastqsanger.gz | |||
| SRR17286827_1.fastq.gz | Fastqsanger.gz | |||
| SRR17286828_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:This study investigated the role Rtf2 plays on the replication fork barrier (RFB) activity of RTS1 in S. pombe. We confirm Rtf2 is important for the full barrier activity of the RTS1-Rtf1 RFB. We show that Rtf2 does not enact its enhancing effect on RTS1 RFB activity via binding to Region A of RTS1, but instead we find it to be closely associated with several splicing factors. Analysis of cells deleted for rtf2 by cDNA-Seq reveal splicing defects specifically effecting intron retention, including for the Rtf1 transcript. We show that intron retention within rtf1 is responsible for the reduced barrier activity of RTS1 when rtf2 is deleted. This study reveals Rtf2 to be an important factor for maintaining efficient splicing within the cell.
2021-12-24 | GSE192343 | GEO
Project description:This study investigated the role Rtf2 plays on the replication fork barrier (RFB) activity of RTS1 in S. pombe. We confirm Rtf2 is important for the full barrier activity of the RTS1-Rtf1 RFB. We show that Rtf2 does not enact its enhancing effect on RTS1 RFB activity via binding to Region A of RTS1, but instead we find it to be closely associated with several splicing factors. Analysis of cells deleted for rtf2 by cDNA-Seq reveal splicing defects specifically effecting intron retention, including for the Rtf1 transcript. We show that intron retention within rtf1 is responsible for the reduced barrier activity of RTS1 when rtf2 is deleted. This study reveals Rtf2 to be an important factor for maintaining efficient splicing within the cell.
2021-12-24 | GSE192342 | GEO
Project description:Rtf2 is Important for Replication Fork Barrier Activity of RTS1 via Splicing of Rtf1
| PRJNA791210 | ENA
Project description:Rtf2 is Important for Replication Fork Barrier Activity of RTS1 via Splicing of Rtf1 [Pu-Seq]
| PRJNA791219 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2021-12-24 | GSE192344 | GEO
Project description:Arrested replication forks, when restarted by homologous recombination, result in error-prone DNA syntheses and non-allelic homologous recombination. Fission yeast RTS1 is a model fork barrier used to probe mechanisms of recombination-dependent restart. RTS1 barrier activity is entirely dependent on the DNA binding protein Rtf1 and partially dependent on a second protein, Rtf2. Human RTF2 was recently implicated in fork restart, leading us to examine fission yeast Rtf2's role in more detail. In agreement with previous studies, we observe reduced barrier activity upon rtf2 deletion. However, we identified Rtf2 to be physically associated with mRNA processing and splicing factors and rtf2 deletion to cause increased intron retention. One of the most affected introns resided in the rtf1 transcript. Using an intronless rtf1, we observed no reduction in RFB activity in the absence of Rtf2. Thus, Rtf2 is essential for correct rtf1 splicing to allow optimal RTS1 barrier activity.
| S-EPMC10473836 | biostudies-literature
Project description:Purpose: To identify gene expression in RTF2 null cells compared to WT cells Method: Total RNA for mRNA Seq, NextSeq High Output 75 SR Results: 57 genes significantly downregulated and 7 genes significantly upregulated in RTF2 deficient MEFs
2022-06-08 | GSE152047 | GEO
Project description:While hundreds of genes are induced by Type I interferons, their roles in restricting the influenza life cycle remain mostly unknown. Using a loss-of-function CRISPR screen in cells pre-stimulated with Type I interferon, we identified a small number of factors required for restricting influenza A virus replication. In addition to the known components of the interferon signaling pathway, we found a new factor, Replication Termination Factor 2 (RTF2). RTF2 restricts influenza, at least, at the nuclear stage of the viral life cycle based on several lines of evidence. First, a deficiency in RTF2 leads to higher levels of viral primary transcription, even in the presence of cycloheximide to block genome replication and secondary transcription. Second, cells that lack RTF2 have enhanced activity of a viral reporter that depends solely on four viral proteins that carry out replication and transcription in the nucleus. Third, when RTF2 protein is mislocalized outside the nucleus, it is not able to restrict replication. Furthermore, the absence of RTF2 not only led to enhanced viral transcription but also to reduced expression of anti-viral factors in response to interferon. RTF2 thus inhibits primary influenza transcription, likely acts in the nucleus, and contributes to upregulation of antiviral effectors in response to Type I interferons
2020-08-27 | GSE146403 | GEO
Project description:During heart development, an evolutionarily conserved network of cardiac transcription factors collaborate to define the precise timing and location of cardiac progenitor specification. Accumulating evidence suggests that cardiac progenitor specification is subject to transcriptional control beyond the level of transcription initiation. The PAF1C component Rtf1 is a multifunctional transcription regulatory protein that modulates pausing and elongation of RNA Pol II, as well as histone epigenetic modifications. By transient knockdown and CRISPR mutagenesis, we found that Rtf1 is essential for cardiogenesis and that without Rtf1 activity, cardiac progenitors arrest in an immature state. This role in early cardiogenesis was evolutionarily conserved between fish and mammals. We also found that Rtf1's Plus3 domain, which confers interaction with the pausing/elongation factor Spt5, was required for Rtf1's ability to support cardiac progenitor formation, while other regions of the protein were dispensable. We examined the occupancy of RNA Pol II at cardiac genes in rtf1 morphants using ChIP-seq and found that Pol II signals at the TSS of genes was reduced, suggesting a reduction in transcriptional pausing. Intriguingly, pharmacological or morpholino antisense reduction of pause release in rtf1 morphants and mutants restored the formation of cardiac cells and improved Pol II occupancy at the TSS of key cardiac genes. Our findings highlight the crucial role that transcriptional pausing plays in promoting normal levels of gene expression in a cardiac developmental context.
2023-09-22 | GSE243820 | GEO
Project description:Alternative splicing is prevalent in plants, but little is known about its regulation in the context of developmental and signaling pathways. We describe here a new factor that influences pre-mRNA splicing and is essential for embryonic development in Arabidopsis thaliana. This factor was retrieved in a genetic screen that identified mutants impaired in expression of an alternatively spliced GFP reporter gene. In addition to the known spliceosomal component PRP8, the screen retrieved a previously uncharacterized protein containing a Replication termination factor2 (Rtf2) domain defined by a C2HC2 zinc finger. The Rtf2 protein was discovered in fission yeast, where it stabilizes paused DNA replication forks by an unknown mechanism. When homozygous, a null mutation in Arabidopsis RTF2 (AtRTF2) is embryo-lethal, indicating that it encodes an essential protein. As revealed by quantitative RT-PCR, impaired expression of GFP in atrtf2 and prp8 mutants is attributable to inefficient splicing of the GFP pre-mRNA. A genome-wide analysis using RNA-seq demonstrated that 12% of total introns display a significant degree of retention in atrtf2 mutants. Intron-retaining transcripts are enriched from genes encoding proteins involved in signaling pathways and membrane transport. Affinity purification of AtRTF2 followed by mass spectrometry identified several known and predicted splicing proteins. In a yeast two-hybrid screen, AtRTF2 interacted with Exo70B1, a peripheral subunit of the exocyst, which is involved in vesicle trafficking. Considering these results and previous suggestions that Rtf2 constitutes an ubiquitin-related domain, we discuss possible roles of AtRTF2 in ubiquitin-based regulation of pre-mRNA splicing and membrane signaling to the spliceosome. Rtf2 is SDR1 (= AtRTF2) and was discovered in a genetic suppressor screen using the dms4 mutant. DMS4 was described in Kanno et al (2010) EMBO Rep. 11:65-71. Examination of whole-genome DNA methylation status in transgenic Arabidopsis plants
2014-11-14 | E-GEOD-63238 | biostudies-arrayexpress