Ontology highlight
ABSTRACT:
PROVIDER: PRJNA705592 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13810700_1.fastq.gz | Fastqsanger.gz | |||
| SRR13810700_2.fastq.gz | Fastqsanger.gz | |||
| SRR13810800_1.fastq.gz | Fastqsanger.gz | |||
| SRR13810800_2.fastq.gz | Fastqsanger.gz | |||
| SRR13810900_1.fastq.gz | Fastqsanger.gz |
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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.
2020-01-01 | GSE137701 | GEO
Project description:We systemically investigated the circRNA profiles among the subcellular fractions of HepG2 cell, including nucleus, cytoplasm, mitochondria, ribosome, cytosol and exosome. Our studies reveals the wide distribution of circRNAs among the subcellular fractions except the mitochondria. Further comparative analysis indicate the differential subcellular distributions in expression, length, GC content, classification, alternative circularization and function of the parental genes. Through analyzing the binding motifs distribution of the transport-related RBPs among the subcellular circRNAs, we found that the different subcellular distribution characteristics of circRNAs might be resulted from the RBP-mediated selective transportation. It also implies that the circRNAs may follow the same transportation mechanism as linear RNAs: the RBPs specially recognize, bind to and transport the RNAs with the corresponding binding motifs, regardless of circular or linear RNAs. Our researches not only facilitate better understanding of the life history and molecular behavior of circRNA in cell, but also contribute to the exploration for new biological functions of circRNA.
2019-01-16 | GSE107169 | GEO
Project description:Many cellular RNAs localize to specific subcellular compartments. Currently, methods to systematically study subcellular RNA localization are limited and lagging behind proteomic approaches. Here, we combined APEX2-mediated proximity biotinylation of proteins with PAR-CLIP to simultaneously profile the proteome and the transcriptome bound by RNA binding proteins in any given subcellular compartment. Our approach is fractionation-independent and does not rely on additional RNA manipulation and labeling steps, thus making it easy to apply. Furthermore, it enables to study the locali-zation of RNA processing intermediates, as well as the identification of regulatory RNA cis-acting elements occupied in different cellular compartments. In a proof-of-concept study we studied RNA and protein localization in the nucleus, cytoplasm and at cell-cell interfaces using Proximity-CLIP. These experiments revealed among other in-sights frequent transcriptional readthrough continuing for several kilobases down-stream of the canonical cleavage and polyadenylation site, a differential binding pat-tern of nuclear and cytoplasmic mRNAs, as well as the localization of mRNAs contain-ing 3’UTR CUG sequence elements at cell-cell interfaces, of which many encode regulatory proteins.
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Project description:The subcellular localization patterns of RNAs are controlled by regulatory elements contained within them. However, for most localized RNAs, the identities of these elements are unknown. We had previously identified several localization elements that are necessary and sufficient for robust, kinesin-dependent RNA targeting to microtubule plus ends in a variety of cell types. Yet the characteristics of these elements that are critical for function remained unclear. To address this, we systematically created tens of thousands of mutant localization elements and quantified their ability to regulate subcellular RNA localization in neuronal cells. We found that the minimally active size of these localization elements is large, approximately 200 nt. These elements contain multiple important subsequences, with some being completely intolerant of any changes and others being tolerant to a shuffling of nucleotide order but not to changes in nucleotide composition. Using single molecule microscopy, we verified these findings in primary rat neurons. These results demonstrate that highly active mammalian RNA localization elements are large, complex, and multipartite and lay a foundation for further mechanistic studies of their function.
2026-06-09 | GSE334718 | GEO
Project description:RNA molecules are localized to subcellular regions through interactions between localization-regulatory cis-elements and trans-acting RNA binding proteins (RBPs). However, the identities of RNAs whose localization is regulated by a specific RBP as well as the impacts of that RNA localization on cell function have generally remained unknown. Here, we demonstrate that the RBP HNRNPA2B1 acts to keep specific RNAs out of neuronal projections. Using subcellular fractionation, high-throughput sequencing, and single molecule RNA FISH, we find that hundreds of RNAs demonstrate markedly increased abundance in neurites in HNRNPA2B1 knockout cells. These RNAs often encode motor proteins and are enriched for known HNRNPA2B1 binding sites and motifs in their 3′ UTRs. The speed and processivity of microtubule-based transport is impaired in these cells, specifically in their neurites. HNRNPA2B1 point mutations that increase its cytoplasmic abundance relative to wildtype lead to stronger suppression of both RNA mislocalization and transport defects than seen with wildtype HNRNPA2B1. We further find that the subcellular localizations of HNRNPA2B1 target RNAs are sensitive to perturbations of RNA decay machinery, suggesting that it is HNRNPA2B1’s known role in regulating RNA stability that may explain these observations. These findings establish HNRNPA2B1 as a negative regulator of neurite RNA abundance and link the subcellular activities of motor proteins with the subcellular abundance of the RNAs that encode them.
2024-08-20 | GSE275212 | 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.
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Project description:The distribution of RNA in human embryonic stem cells (hESC) and the function of RNA localization in maintaining hESC pluripotency and differentiation are currently unknown. Here, by isolating five subcellular components of hESCs and differentiated cells, we uncovered the global subcellular RNA localization in hESC. For protein-coding mRNA, different transcripts of the same gene exhibit an “isoform switch” between subcellular components, which is regulated by localization cis-elements in their variable regions. For noncoding RNA, multiple sequence features such as polyA tail, length, and GC content jointly regulate their subcellular localization. In addition, we found that some developmental genes can be transcribed in advance and confined to chromatin in undifferentiated hESCs. Finally, we revealed significant changes in overall RNA distribution, mapped RNA dynamic localization atlas, and characterized different dynamic RNA localization patterns during hESC differentiation into mesoderm. The multiple RNA localization patterns we revealed will provide some new enlightenment for hESC stemness maintenance and differentiation.
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Project description:The pervasive expression of circular RNA from protein coding loci is a recently discovered feature of many eukaryotic gene expression programs. Computational methods to discover and quantify circular RNA are essential to the study of the mechanisms of circular RNA biogenesis and potential functional roles they may play. In this paper, we present a new statistical algorithm that increases the sensitivity and specificity of circular RNA detection.by discovering and quantifying circular and linear RNA splicing events at both annotated exon boundaries and in un-annotated regions of the genome Unlike previous approaches which rely on heuristics like read count and homology between exons predicted to be circularized to determine confidence in prediction of circular RNA expression, our algorithm is a statistical approach. We have used this algorithm to discover general induction of circular RNAs in many tissues during human fetal development. We find that some regions of the brain show marked enrichment for genes where circular RNA is the dominant isoform. Beyond this global trend, specific circular RNAs are tissue specifically induced during fetal development, including a circular isoform of NCX1 in the developing fetal heart that, by 20 weeks, is more highly expressed than the linear isoform as well as beta-actin. In addition, while the vast majority of circular RNA production occurs at canonical U2 (major spliceosome) splice sites, we find the first examples of developmentally induced circular RNAs processed by the U12 (minor) spliceosome, and an enriched propensity of U12 donors to splice into circular RNA at un-annotated, rather than annotated, exons. Together, our algorithm and its results suggest a potentially significant role for circular RNA in human development. 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kit.
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Project description:High-throughput RNA sequencing methods coupled with specialized bioinformatic analyses have recently uncovered tens of thousands of unique circular (circ)RNAs, but their complete sequences, genes of origin, and functions are largely unknown. Given that circRNAs lack free ends and are thus relatively stable, their association with microRNAs (miRNAs) and RNA-binding proteins (RBPs) can influence gene expression programs. While exoribonuclease treatment is widely used to degrade linear RNAs and enrich circRNAs in RNA samples, it does not efficiently eliminate linear RNAs. Here, we describe a novel method for the isolation of highly pure circRNA populations involving RNase R treatment followed by Polyadenylation and poly(A)+ RNA Depletion (RPAD), which removes linear RNA to near completion. High-throughput sequencing of RNA prepared using RPAD from human cervical carcinoma HeLa cells and mouse C2C12 myoblasts led to two surprising discoveries: (1) many circRNA isoforms share an identical backsplice sequence but have different body sizes and sequences, and (2) thousands of novel intronic circular RNAs (IcircRNAs) are expressed in cells, including many IcircRNAs that do not follow gt/ag splicing patterns. In sum, isolating high-purity circRNAs using the RPAD method can enable quantitative and qualitative analyses of circRNA types and sequence composition, paving the way for the elucidation of circRNA functions.
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