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Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation

ABSTRACT: Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation

PROVIDER: PRJNA270325 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1534952.fastq.gz	Fastqsanger.gz
	SRR1534953.fastq.gz	Fastqsanger.gz
	SRR1534954.fastq.gz	Fastqsanger.gz
	SRR1534955.fastq.gz	Fastqsanger.gz
	SRR1534956.fastq.gz	Fastqsanger.gz

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Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation [iCLIP]

Project description:Visualizing the physical basis for molecular behavior inside living cells is a grand challenge in biology. RNAs are central to biological regulation, and RNA’s ability to adopt specific structures intimately controls every step of the gene expression program.1 However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles predominantly viewed only two of four nucleotides that make up RNA.2,3 Here we present a novel biochemical approach, In Vivo Click SHAPE (icSHAPE), that enables the first global view of RNA secondary structures of all four bases in living cells. icSHAPE of embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguishes different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved in vitro, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA binding or modification proteins that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N6-methyladenosine (m6A) modification genome-wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.

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Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation [icSHAPE]

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Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation

Project description:This SuperSeries is composed of the SubSeries listed below.

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Project description:Numerous indirect, genetic approaches in various experimental systems have implicated dynamic alternative non-B DNA structures in human physiology and disease. Nevertheless, direct detection of dynamic DNA structures in vivo remains a challenge. To address this problem, we developed a new methods to visualize ssDNA containing alternative DNA structures. We described an uncharted landscape of dynamic alternative DNA structures formed by DNA cruciform and DNA triplexes (H-DNA) that contribute to genome instability.

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Project description:Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability

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In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding

Project description:Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates’ secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the RNA folding events. Our results suggest that cotranscriptional RNA folding in vivo is a mixture of cooperative folding events, in which local RNA secondary structure elements are formed as they get transcribed, and non-cooperative events, in which 5΄-halves of long-range helices get sequestered into transient non-native interactions until their 3΄ counterparts have been transcribed. Together our work provides the first transcriptome-scale overview of RNA cotranscriptional folding in a living organism.

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Project description:Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability [END-seq]

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