U1 snRNP regulates chromatin retention of noncoding RNAs
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ABSTRACT:
PROVIDER: PRJNA419135 | ENA |
REPOSITORIES: ENA
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Project description:U1 snRNP regulates chromatin retention of noncoding RNAs
| PRJNA554651 | ENA
Project description:Pervasive transcription in the mammalian genome produces thousands of long noncoding RNAs (lncRNAs) and promoter- or enhancer-associated unstable transcripts. They preferentially locate to chromatin, at which some regulate chromatin structure, transcription and RNA processing. While several RNA sequences responsible for nuclear localization have been identified, such as repeats in the lncRNA Xist and Alu-like elements for long RNAs, how lncRNAs as a class are enriched on chromatin remains elusive. To screen for cis-elements that contribute to RNA-chromatin localization, we developed a high-throughput method named RNA elements for subcellular localization by sequencing (REL-seq), and discovered a U1 small nuclear ribonucleoprotein (snRNP)-recognition motif being critical for chromatin localization of reporter RNAs. Across the genome, chromatin-bound lncRNAs, which are enriched with 5’ splice sites and depleted of 3’ splice sites, exhibit high levels of U1 snRNA binding compared to cytoplasm-localized protein-coding mRNAs. Acute depletion of U1 snRNA, or U1 snRNP protein component SNRNP70, drastically reduces the chromatin association of hundreds of lncRNAs and unstable transcripts without altering the overall transcription rate in cells. In addition, rapid degradation of SNRNP70 reduces the localization of both nascent and polyadenylated lncRNA transcripts to chromatin, and disrupts the nuclear-speckles and genome-wide localization of Malat1, a highly conserved and abundant lncRNA. Moreover, chromatin-bound U1 snRNP interacts with transcriptionally engaged RNA polymerase (Pol) II. Together, these results demonstrate that U1 snRNP acts widely to tether and mobilize lncRNAs to chromatin in a Pol II transcription-dependent manner. Our findings uncover a novel role of U1 snRNP beyond pre-mRNA processing and provide molecular insights into how lncRNAs are recruited to Pol II-transcribed genes and have a propensity for chromatin-associated functions.
2020-01-01 | GSE134287 | GEO
Project description:RNA subcellular localization often correlates with its function and regulation. For many long noncoding RNAs (lncRNAs) and some isoforms of coding genes, their transcripts are preferentially retained on the chromatin. However, the mechanisms controlling the chromatin retention of lncRNAs and mRNA transcripts remain largely unknown. We hypothesize that embedded RNA sequences and interacting proteins may be the cis and trans regulators governing RNA subcellular localization, respectively. To comprehensively identify the cis-regulatory elements of RNA transcript, here we have developed a high-throughput sequencing-based method named RNA elements for subcellular localization by sequencing (REL-seq). Using this method, we identified RNA sequences contribute to the chromatin retention of several transcripts. By combining REL-seq with random mutagenesis (mutREL-seq), we further narrowed down the key RNA motifs and residues in regulating their subcellular localization at base resolution. Finally, based on the RNA element we identified, we revealed and confirmed U1 snRNA targeting site contributes to RNA chromatin retention.
2020-01-01 | GSE107131 | 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: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.
2013-06-28 | GSE46433 | GEO
Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was performed to generate genome-wide binding maps of two U1-snRNP proteins: U1C and U1-70K in Trypanosoma brucei. 3 (2) biological replicates of U1C (U1-70K) -specific co-immunoprecipitated RNA after UV-crosslinking
2014-05-16 | E-GEOD-43848 | biostudies-arrayexpress
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:Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the interaction between the ubiquitin-like domain (UBL) of the protein SF3A1, a component of the U2 snRNP, with stem-loop 4 RNA (SL4) from the U1 snRNP. The complex was cross-linked and analysed both in isolation, and in broader context with components of the U1 snRNP. Cross-linking was performed using irradiation under 254 nm light, relying on the inherent reactivity of ribonucleotides.
2022-02-22 | PXD027189 | Pride
Project description:Recent proteome and transcriptome profiling of Alzheimer's disease (AD) brains reveals RNA splicing dysfunction and U1 small nuclear ribonucleoprotein (snRNP) pathology containing U1-70K and its N-terminal 40-KDa fragment (N40K). Here we present a causative role of U1 snRNP dysfunction to neurodegeneration in primary neurons and transgenic mice (N40K-Tg), in which N40K expression exerts a dominant-negative effect to downregulate full-length U1-70K. N40K-Tg recapitulates N40K insolubility, neuronal degeneration, cognitive impairment, and erroneous splicing events in synaptic pathways.
2022-08-11 | GSE196871 | GEO
Project description:Recent proteome and transcriptome profiling of Alzheimer's disease (AD) brains reveals RNA splicing dysfunction and U1 small nuclear ribonucleoprotein (snRNP) pathology containing U1-70K and its N-terminal 40-KDa fragment (N40K). Here we present a causative role of U1 snRNP dysfunction to neurodegeneration in primary neurons and transgenic mice (N40K-Tg), in which N40K expression exerts a dominant-negative effect to downregulate full-length U1-70K. N40K-Tg recapitulates N40K insolubility, neuronal degeneration, cognitive impairment, and erroneous splicing events in synaptic pathways.
2022-08-11 | GSE196872 | GEO