Similar Datasets
Project description:Probe SLERT secondary structure by SHAPE-MaP in PA1 cell line
2021-05-11 | GSE174140 | GEO
Project description:To refine the authentic CENP-C binding sites of lnc-CCTT and globally map lnc-CCTT secondary structure, we also performed SHAPE-MaP (selective 2’-hydroxyl acylation analyzes by primer extension and mutational profiling), which uses hydroxyl-selective electrophiles to modify the 2’-hydroxyl groups of unbound single-stranded nucleotides, in HeLa cells both ex vivo and in vivo. Lnc-CCTT secondary structure was modeled by combination SHAPE data from cell-free ex vivo with pairing probabilities. As expected, nucleotides 43-79 nt, a determinant for RNA-DNA triplex formation, exhibited a continuous single-strandedness, which may be prone to binding DNA. More importantly, only nucleotides 118-177 nt, which was folded into a stem-loop structure in the secondary structure, showed a significant reduced SHAPE reactivities in cell when comparing to cell-free state, suggesting this region could be attributed to interaction with protein components.
2022-04-20 | GSE149529 | GEO
Project description:RNA secondary structure is crucial for RNA mentalism, including transcription, splicing, translation, RNA-binding protein interaction as well as turnover. The kink-turn (K-turn) structure motif is is an RNA three-dimensional (3D) structure that exists in all three primary phylogenetic domains and plays vital roles in RNA metabolism. In order to investigate the K-turn secondary structure in vivo, we combined SHAPE-Map and our RIP-PEN-seq to profile the RNA structure of 15.5K-interacted RNAs.
2023-04-10 | GSE220470 | GEO
Project description:MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here we employed SHAPE-MaP, a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. By comparing the structures with high-throughput processing data, we determined the optimal structural features of pri-miRNAs. The sequence determinants are influenced substantially by their structural contexts. Moreover, we identified an element termed the bulged GWG motif (bGWG) with a 3′ bulge in the lower stem, which promotes processing. Our structure-function mapping better annotates the determinants of pri-miRNA processing and offers practical implications for designing small hairpin RNAs and predicting the impacts of miRNA mutations.
2024-01-31 | GSE254361 | GEO
Project description:Six transcripts of the gene SERPINA1 (serpin family A member 1) were sequenced via SHAPE-MaP to obtain their secondary structure profiles. For each transcript, SHAPE-MaP includes a sample treated with 1M7 reagent ('p'), a minus reagent negative control ('m'), and a denatured control ('d'). The 1M7 reagent preferentially reacts with unpaired bases in RNA and subsequently induces mutations during the reverse transcription step of library preparation. After sequencing and alignment, the 'mutational profiles' of the 'p', 'd' and 'm' samples are used to calculate the SHAPE reactivity of each base in the transcript. SHAPE reactivity correlates to the tendency of a base to be paired as part of a secondary structure.
2016-11-01 | GSE81525 | GEO
Project description:We show that DANCE-MaP permits measurement of state-specific per-nucleotide reactivities, direct secondary structure PAIRs, and tertiary RINGs for RNA structural ensembles. Here, we demonstrate DANCE-MaP on the V. vulnificus add riboswitch.
2022-03-23 | GSE182552 | GEO
Project description:SHAPE-MaP structure probing experiment was performed on SARS-CoV-2 infected Vero cells at 4 days post infection with two biological replicates. For each replciate, SHAPE-MaP includes a sample treated with 2-methylnicotinic acid imidazolide acid (modified) or a minue reagent (unmodified). NAI preferentially reacts with unpaired bases in RNA, forming acylated bases. These modifications are encoded as mutation during reverse transcripatse and library preparation. After sequencing and alignment, the reactivity profiles of 'modified' and 'unmodified' samples are used to calculate SHAPE reactivity of each base
2021-01-11 | GSE154171 | GEO
Project description:There is increasing evidence that the architecture of long non-coding RNAs – just like that of proteins – is hierarchically organized into independently folding sub-modules with distinct functions. Studies characterizing the cellular activities of such modules, however, are rare. The lncRNA growth arrest specific 5 (Gas5) is a key regulator of cell survival in response to stress and nutrient availability. We used SHAPE-MaP to probe the structure of Gas5 in vitro and in cellulo. The results show that Gas5 contains three separate structural modules including the previously predicted steroid receptor binding hairpin motif. Functional assays show that the newly identified modules act independently in leukemic T cells. The 5’ terminal module with low secondary structure content affects basal survival and slows the cell cycle, whereas the highly structured core module mediates the effects of mTOR inhibition on cell growth. Disruption of specific secondary structures within the modules abolish their function in cells. These results highlight the central role of Gas5 in regulating cell survival and reveals how a single lncRNA transcript utilizes a modular structure-function relationship to respond to a variety of cellular stresses under various cellular conditions.
2021-04-07 | PXD018584 | Pride
Project description:Complete in vivo SHAPE-MaP structure of the SARS-CoV-2 genome
| PRJNA645342 | ENA
Project description:SHAPE-MaP probing of RNA structures in E. coli cells
| PRJEB23974 | ENA