Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA400626 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5989140_1.fastq.gz | Fastqsanger.gz | |||
| SRR5989140_2.fastq.gz | Fastqsanger.gz | |||
| SRR5989150.fastq.gz | Fastqsanger.gz | |||
| SRR5989141_1.fastq.gz | Fastqsanger.gz | |||
| SRR5989141_2.fastq.gz | Fastqsanger.gz |
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Project description:This project looks into how U1 snRNP inhibition causes a loss of telescripting through premature cleavage and polyadenylation based on the size and function of human genes.
2017-10-02 | GSE103252 | GEO
Project description:Full-length transcription in the majority of human genes depends on U1 snRNP (U1) to co-transcriptionally suppress transcription-terminating premature 3’-end cleavage and polyadenylation (PCPA) from cryptic polyadenylation signals (PASs) in introns. However, the mechanism of this U1 activity, termed telescripting, is unknown. Here, we captured a complex, comprising U1 and CPA factors (U1–CPAFs), that binds intronic PASs and suppresses PCPA. U1–CPAFs are distinct from U1-spliceosomal complexes; they include CPA’s three main subunits, CFIm, CPSF, and CstF, lack essential splicing factors, and associate with transcription elongation and mRNA export complexes. Telescripting requires U1:pre-mRNA base-pairing, which can be disrupted by U1 antisense oligonucleotide (U1 AMO), triggering PCPA. U1 AMO remodels U1–CPAFs, revealing changes, including recruitment of CPA-stimulating factors, that explain U1–CPAFs’ switch from repressive to activated states. Our findings outline U1 telescripting mechanism and demonstrate U1’s unique role as central-regulator of pre-mRNA processing and transcription.
2019-07-31 | GSE135140 | GEO
Project description:U1 snRNP regulates alternative polyadenylation in DNA damage response
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Project description:Eukaryotic pre-mRNA processing steps, including splicing and 3′ processing, are tightly coordinated, but the underlying mechanisms remain poorly understood. Previous studies proposed that the splicing factor U1 snRNP inhibits 3′ processing at intronic polyadenylation (IPA) sites through a splicing-independent mechanism, called telescripting. However, we found that global or gene-specific perturbation of splicing by targeting multiple splicing factors, including U1 snRNP, U2 snRNP, U2AF, and SF3b led to activation of 3′ processing at IPA sites. Inhibiting different splicing factors activated overlapping and distinct IPA sites and such specificity was determined, at least in part, by alterations in RNA polymerase II elongation and termination. Conversely, we showed that blocking pre-mRNA 3′ processing promoted splicing globally. These results strongly suggest that splicing and 3′ processing are competing processes that shape the transcriptome. Finally, as splicing inhibition-induced shifts to IPA site usage can lead to gene inactivation, including tumor suppressor genes, the use of general splicing inhibitors to treat human diseases may pose a significant risk.
2024-10-28 | GSE275154 | GEO
Project description:In eukaryotes, U1 small nuclear ribonucleoprotein (snRNP) forms spliceosomes in equal stoichiometry with U2, U4, U5 and U6 snRNPs; however, its abundance in human far exceeds that of the other snRNPs. Here we used antisense morpholino oligonucleotide to U1 snRNA to achieve functional U1 snRNP knockdown in HeLa cells, and identified accumulated unspliced pre-mRNAs by genomic tiling microarrays. In addition to inhibiting splicing, U1 snRNP knockdown caused premature cleavage and polyadenylation in numerous pre-mRNAs at cryptic polyadenylation signals, frequently in introns near (<5 kilobases) the start of the transcript. This did not occur when splicing was inhibited with U2 snRNA antisense morpholino oligonucleotide or the U2-snRNP-inactivating drug spliceostatin A unless U1 antisense morpholino oligonucleotide was also included. We further show that U1 snRNA–pre-mRNA base pairing was required to suppress premature cleavage and polyadenylation from nearby cryptic polyadenylation signals located in introns. These findings reveal a critical splicing-independent function for U1 snRNP in protecting the transcriptome, which we propose explains its overabundance.
2010-09-29 | GSE24179 | GEO
Project description:Transcription of the mammalian genome is pervasive, but productive transcription outside of protein-coding genes is limited by unknown mechanisms. In particular, although RNA polymerase II (RNAPII) initiates divergently from most active gene promoters, productive elongation occurs primarily in the sense-coding direction. Here we show in mouse embryonic stem cells that asymmetric sequence determinants flanking gene transcription start sites control promoter directionality by regulating promoter-proximal cleavage and polyadenylation. We find that upstream antisense RNAs are cleaved and polyadenylated at poly(A) sites (PASs) shortly after initiation. De novo motif analysis shows PAS signals and U1 small nuclear ribonucleoprotein (snRNP) recognition sites to be the most depleted and enriched sequences, respectively, in the sense direction relative to the upstream antisense direction. These U1 snRNP sites and PAS sites are progressively gained and lost, respectively, at the 5' end of coding genes during vertebrate evolution. Functional disruption of U1 snRNP activity results in a dramatic increase in promoter-proximal cleavage events in the sense direction with slight increases in the antisense direction. These data suggest that a U1-PAS axis characterized by low U1 snRNP recognition and a high density of PASs in the upstream antisense region reinforces promoter directionality by promoting early termination in upstream antisense regions, whereas proximal sense PAS signals are suppressed by U1 snRNP. We propose that the U1-PAS axis limits pervasive transcription throughout the genome. 3' end sequencing of poly (A) + RNAs in mouse ES cells with and without U1 snRNP inhibition using antisense morpholino oligonucleotides (AMO). Each with two biological replicates.
2013-06-28 | E-GEOD-46433 | biostudies-arrayexpress
Project description:The recognition of 5’ splice site (5’ ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5’ ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5’ ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5’ ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in cold-sensitive growth phenotype and moderate splicing defects. Next, we added an auxin-inducible degron to yLuc7 protein and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondria function in yeast.
2024-01-03 | GSE252348 | GEO
Project description:U1 snRNA is the small nuclear RNA that services as the backbone of U1 snRNP. Removing intron from pre-mRNA to produce mature mRNA is the core function of the U1 snRNA. As one of the most abundant small noncoding RNA in human cells – estimated to be in the region of 1x10^6 copies per human cell (Hela) – U1 snRNA level is much more abundant than the other snRNAs. However, the potential role of the different amounts of the snRNAs is still unknown. To study the function of U1 snRNA in human neurons, we used lentivirus vector to overexpression U1 snRNA. We analyzed the gene expression change and identified target genes of U1 snRNA overexpression. We uncovered a novel role of U1 snRNA in regulating gene expression in human neurons.
2020-01-01 | GSE124951 | GEO
Project description:We recently reported that serine-arginine-rich (SR) protein-mediated pre-mRNA structural remodeling generates a pre-mRNA 3D structural scaffold that is stably recognized by the early spliceosomal components. However, the intermediate steps between the free pre-mRNA and the assembled early spliceosome are not yet characterized. By probing the early spliceosomal complexes in vitro and RNA-protein interactions in vivo, we show that the SR proteins bind the pre-mRNAs cooperatively generating a substrate that recruits U1 snRNP and U2AF65 in a splice signal-independent manner. Excess U1 snRNP selectively displaces some of the SR protein molecules from the pre-mRNA generating the substrate for splice signal-specific, sequential recognition by U1 snRNP, U2AF65, and U2AF35. Our work thus identifies a novel function of U1 snRNP in mammalian splicing substrate definition, explains the need for excess U1 snRNP compared to other U snRNPs in vivo, demonstrates how excess SR proteins could inhibit splicing, and provides a conceptual basis to examine if this mechanism of splicing substrate definition is employed by other splicing regulatory proteins.
2022-07-05 | GSE188652 | GEO
Project description:We have found that depletion of the zinc finger protein ZFC3H1 inhibits the nuclear retention of these RNAs. ZFC3H1 forms a complex with MTR4 and PABPN1 (the PolyAdenylation EXosome Targeting complex (Meola et al 2016, Ogami et al 2017) and likely recruits the nuclear exosome for RNA degradation. Recently, we found that depletion of U1-70K, one protein component of the U1 snRNP spliceosomal complex, inhibits nuclear retention of 5’SS motif containing RNAs. The U1 snRNP complex recognizes and binds to the 5’SS motif and in vitro studies showed that U1-70K directly interact with a similar 5’SS motif through U1 snRNA binding (Gunderson et al 1999). Interestingly, we found that U1 snRNP is involved in targeting 5’SS motif containing mRNAs to nuclear speckles shortly following RNA transcription. In contrast, ZFC3H1 is involved in nuclear speckle localization post-transcriptionally and actively retain RNAs in these structures. Together, our results suggest a model where U1 snRNP interacts with the RNA via the 5’SS motif and targets mature mRNAs to nuclear speckles. Specifically, it suggests that misprocessed RNAs can be targeted to speckles (or other nucleoplasmic foci) and that these foci serve as a platform to recruit the nuclear exosome via ZFC3H1. Our results highlight a splicing independent role of U1 snRNP and how mRNA nuclear export function in nuclear surveillance to prevent the translation of aberrant proteins.
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