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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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RNA Structure01:19

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Related Experiment Video

Updated: Apr 4, 2026

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
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Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

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Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.

Kyle E Watters1, Timothy R Abbott1, Julius B Lucks2

  • 1School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.

Nucleic Acids Research
|September 10, 2015
PubMed
Summary
This summary is machine-generated.

A new method, in-cell SHAPE-Seq, reveals how RNA structure impacts gene expression within bacterial cells. This tool links RNA sequence, structure, and function, aiding molecular and synthetic biology research.

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Area of Science:

  • Molecular Biology
  • Synthetic Biology
  • RNA Biology

Background:

  • Non-coding RNAs (ncRNAs) utilize structural conformations to regulate gene expression via interactions with cellular machinery.
  • Understanding the structure-function relationship of ncRNAs is crucial for both comprehending biological processes and engineering novel RNA-based systems.

Purpose of the Study:

  • To develop and validate a high-throughput method for simultaneously probing RNA structure and gene expression within living bacterial cells.
  • To investigate the structure-function dynamics of RNA regulatory mechanisms in Escherichia coli.
  • To compare in-cell versus in vitro RNA folding.

Main Methods:

  • Development of in-cell SHAPE-Seq, a high-throughput technique combining in-cell RNA structure probing with gene expression measurement.
  • Application of in-cell SHAPE-Seq to study translational regulatory RNAs in Escherichia coli.
  • Characterization of endogenous ncRNAs (5S rRNA, RNase P, btuB riboswitch) in cellular contexts.

Main Results:

  • Nucleotides involved in RNA-RNA interactions show increased accessibility when binding partners are absent.
  • Quantitative correlations were established between RNA structural changes and gene expression levels.
  • In-cell and in vitro RNA structures showed high similarity for synthetic RNAs but significant divergence for RNAs with complex cellular interactions.

Conclusions:

  • In-cell SHAPE-Seq provides a powerful and accessible tool for dissecting RNA sequence-structure-function relationships in vivo.
  • The method facilitates a deeper understanding of endogenous ncRNA function and enables the engineering of novel RNA-based genetic controls.
  • Cellular context significantly influences the structure of complex interacting RNAs compared to in vitro conditions.