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Related Concept Videos

RNA Structure01:19

RNA Structure

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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.
Different Types of RNA Have the Same Basic Structure
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RNA Structure01:23

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Overview
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-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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Ribosome Profiling02:24

Ribosome Profiling

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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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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Related Experiment Video

Updated: Mar 21, 2026

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

Zhipeng Lu1, Qiangfeng Cliff Zhang2, Byron Lee1

  • 1Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.

Cell
|May 17, 2016
PubMed
Summary

We developed PARIS, a novel method to map RNA structures in living cells. This technique reveals widespread complex RNA structures and interactions, offering new insights into the RNA structurome and interactome.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • RNA base pairing is crucial for its diverse biological functions.
  • Understanding RNA structure and interactions is essential for deciphering cellular processes.

Purpose of the Study:

  • To develop a method for global mapping of RNA duplexes in living cells with high resolution.
  • To investigate the landscape of RNA structures and interactions across the transcriptome.

Main Methods:

  • Developed PARIS (psoralen crosslinking for RNA interactions and structures), a method utilizing reversible psoralen crosslinking.
  • Applied PARIS to map RNA duplexes at near base-pair resolution in human and mouse cell types.
  • Utilized PARIS data to guide phylogenetic analysis of RNA structures.

Main Results:

  • Identified frequent long-range RNA structures and higher-order architectures within the transcriptome.
  • Revealed pervasive alternative RNA conformations at the individual-molecule level.
  • Discovered conserved long-range and alternative RNA structures, including complex duplexes in XIST lncRNA essential for X chromosome inactivation.

Conclusions:

  • PARIS provides a versatile tool for global mapping of the RNA structurome and interactome.
  • The study uncovered extensive and complex RNA structures and interactions previously uncharacterized.
  • PARIS-based structural insights aid in understanding RNA function, evolution, and regulation, exemplified by XIST RNA's role in epigenetic silencing.