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Structural atlas of human primary microRNAs generated by SHAPE-MaP

ABSTRACT: Structural atlas of human primary microRNAs generated by SHAPE-MaP

PROVIDER: PRJNA1070250 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27748786_1.fastq.gz	Fastqsanger.gz
	SRR27748786_2.fastq.gz	Fastqsanger.gz
	SRR27748787_1.fastq.gz	Fastqsanger.gz
	SRR27748787_2.fastq.gz	Fastqsanger.gz
	SRR27748788_1.fastq.gz	Fastqsanger.gz

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Structural atlas of human primary microRNAs generated by SHAPE-MaP

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

BTV Shape Map

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Project description:Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [SHAPE-MaP]

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Complete in vivo SHAPE-MaP structure of the SARS-CoV-2 genome

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

RIP-PEN-SHAPE-MaP for 15.5K-interacted RNAs

Project description:RIP-PEN-SHAPE-MaP for 15.5K-interacted RNAs

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Project description:Enhanced DMS-MaP enables superior RNA structural analysis

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RIP-PEN-SHAPE-MaP for 15.5K-interacted RNAs

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.

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