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The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [iCLIP]

ABSTRACT: The DEAD-box RNA helicase Dbp2p is highly conserved in eukaryotes and has been implicated in transcription, ribosome biogenesis, mRNP assembly, nuclear export, and lncRNA function. How Dbp2p functions in these seemingly unrelated biological roles is not known. An important step towards addressing this question is the determination of cellular RNA binding sites of Dbp2p. Here, we identify transcriptome-wide RNA binding sites of Dbp2p from Saccharomyces cerevisiae using denaturing tandem affinity purification followed by UV-crosslinking. We find that Dbp2p crosslinks to mRNAs and ribosomal RNAs, and most markedly to non-coding RNAs, including snoRNA, snRNAs, and tRNAs. In snoRNAs, Dbp2p preferentially interacts with sites near the 3’ ends. These sites closely correspond to regions where RNA-DNA hybrids (R-loop) form, and to binding sites of the RNA helicase Sen1p, a component of the Nrd1-Nab3-Sen1 (NNS) complex, which functions in transcription termination and 3' processing of non-coding RNAs in yeast. We also show that Dbp2p interacts in an RNA-independent manner with Sen1p in vivo. We further observe Dbp2p crosslinks to tRNAs and other RNAs also at sites where RNA-loops form. Collectively, our data link Dbp2p to diverse non-coding RNAs, to Sen1p, and to R-loops. The transcriptome-wide connection to R-loops provides a unifying theme for seemingly unrelated cellular roles of Dbp2p.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE113488 | GEO | 2018/04/22

REPOSITORIES: GEO

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The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [RNA-Seq]

Project description:The DEAD-box RNA helicase Dbp2p is highly conserved in eukaryotes and has been implicated in transcription, ribosome biogenesis, mRNP assembly, nuclear export, and lncRNA function. How Dbp2p functions in these seemingly unrelated biological roles is not known. An important step towards addressing this question is the determination of cellular RNA binding sites of Dbp2p. Here, we identify transcriptome-wide RNA binding sites of Dbp2p from Saccharomyces cerevisiae using denaturing tandem affinity purification followed by UV-crosslinking. We find that Dbp2p crosslinks to mRNAs and ribosomal RNAs, and most markedly to non-coding RNAs, including snoRNA, snRNAs, and tRNAs. In snoRNAs, Dbp2p preferentially interacts with sites near the 3’ ends. These sites closely correspond to regions where RNA-DNA hybrids (R-loop) form, and to binding sites of the RNA helicase Sen1p, a component of the Nrd1-Nab3-Sen1 (NNS) complex, which functions in transcription termination and 3' processing of non-coding RNAs in yeast. We also show that Dbp2p interacts in an RNA-independent manner with Sen1p in vivo. We further observe Dbp2p crosslinks to tRNAs and other RNAs also at sites where RNA-loops form. Collectively, our data link Dbp2p to diverse non-coding RNAs, to Sen1p, and to R-loops. The transcriptome-wide connection to R-loops provides a unifying theme for seemingly unrelated cellular roles of Dbp2p.

2018-04-22 | GSE113487 | GEO

The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [RNA-Seq]

Project description:The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [RNA-Seq]

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The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops

Project description:The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops

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The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [iCLIP]

Project description:The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [iCLIP]

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3´-end sequencing of poly(A)+ RNA in wild-type Saccharomyces cerevisiae and nuclear exosome mutant strains

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Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria

Project description:During transcription the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout budding yeast genome. In wild-type strains, R-loops were readily detected over the 35S rDNA region transcribed by Pol I and over the 5S rDNA transcribed by Pol III. In strains lacking RNase H activity, R-loops were elevated over other Pol III genes notably tRNAs, SCR1 and U6 snRNA, and were also associated with the cDNAs of endogenous TY1 retrotransposons, which showed increased rates of mobility to the 5?-flanking regions of tRNA genes. Unexpectedly, R-loops were also associated with mitochondrial genes in the absence of RNase H1, but not of RNase H2. Finally, R-loops were detected on highly expressed protein-coding genes in the wild-type, notably over the second exon of spliced ribosomal protein genes. ChIP-seq of RNA-DNA hybrids using antibody S9.6

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Characterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression

Project description:Chromatin-associated RNAs have diverse roles in the nucleus. However, their mechanisms of action are poorly understood, in part due to the inability to identify proteins that specifically associate with chromatin-bound RNAs. Here, we address this problem for a subset of chromatin-associated RNAs that form R-loops—RNA-DNA hybrid structures that include a displaced strand of single-stranded DNA. R-loops generally form co-transcriptionally and have important roles in regulation of gene expression, immunoglobulin class switching, and other processes. However, unresolved R-loops can lead to DNA damage and chromosome instability. To identify factors that may bind and potentially regulate R-loop accumulation or mediate R-loop-dependent functions, we used a comparative immunoprecipitation/mass spectrometry approach, with and without RNA-protein crosslinking, to identify a stringent set of R-loop-binding proteins in mouse embryonic stem cells. We identified 365 R-loop-interacting proteins, which were highly enriched for proteins with predicted RNA-binding functions. We characterized several R-loop-interacting proteins of the DEAD-box family of RNA helicases and found that these proteins localize to the nucleolus and, to a lesser degree, the nucleus. Consistent with their localization patterns, we found that these helicases are required for ribosomal RNA processing and regulation of gene expression. Surprisingly, depletion of these helicases resulted in misregulation of highly overlapping sets of protein-coding genes, including many genes that function in differentiation and development. We conclude that R-loop-interacting DEAD-box helicases have non-redundant roles that are critical for maintaining the normal embryonic stem cell transcriptome.

2021-09-17 | PXD022697 | Pride

Back-spliced RNA from Retrotransposon Binds to Centromere and Regulates Centromeric Chromatin Loops in Maize

Project description:In most plants, centromeric DNA contains highly repetitive sequences, including tandem repeats and retrotransposons; however, the roles of these sequences in the structure and function of the centromere are unclear. Here, we found that retrotransposon-derived back-spliced RNA can bind to the centromere through R-loops and regulate the formation of centromeric chromatin loops. Multiple RNA sequences from centromeric retrotransposons (CRMs) were enriched in maize (Zea mays) centromeres and back spliced RNA from CRM1 were detected. We identified three types of circular CRM1 RNAs with the same back-splicing site based on the back-spliced sequences. These circular RNAs bound to the centromere through R-loops. Two R-loop sites inside a single circular RNA promoted the formation of chromatin loops in CRM1 regions. When RNAi was used to target the back-spliced site of the circular CRM1 RNAs, the levels of R-loops and chromatin loops formed by these circular RNAs decreased, while the levels of R-loops produced by linear RNAs with similar binding sites increased. Linear RNAs with only one R-loop site could not promote chromatin loop formation. Higher levels of R-loops and lower levels of chromatin loops in the CRM1 regions of RNAi plants led to a reduced localization of the centromeric H3 variant (CENH3). Our work reveals that centromeric chromatin organization by circular CRM1 RNAs via R-loops and chromatin loops. R-loops are integral components of centromeric chromatin. Proper centromere structure is essential for CENH3 localization. CRM1 elements may have helped to build a suitable chromatin environment during centromere evolution.

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