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Related Concept Videos

Riboswitches01:56

Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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Transcriptional Regulation: Riboswitches01:23

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Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Ribozymes02:47

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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.
Applications of ribosome profiling
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Related Experiment Video

Updated: Jul 12, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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Ribocentre-switch: a database of riboswitches.

Fan Bu1,2, Xiaowei Lin3,4, Wenjian Liao3,4

  • 1Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.

Nucleic Acids Research
|October 19, 2023
PubMed
Summary

Riboswitches are RNA molecules that regulate gene expression by changing shape when binding to small molecules. The Ribocentre-switch database offers a comprehensive resource for studying these regulatory elements and their functions.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Bioinformatics

Background:

  • Riboswitches are RNA regulatory elements in mRNA's untranslated regions.
  • They possess an aptamer domain for small molecule binding and an expression platform for gene control.
  • Ligand binding induces conformational changes, regulating downstream gene expression.

Purpose of the Study:

  • To systematically compile and present riboswitch structures and ligand-binding functions.
  • To introduce Ribocentre-switch, a comprehensive database for riboswitch research.

Main Methods:

  • Database curation from over 430 references.
  • Inclusion of riboswitch sequences, structures, functions, ligand-binding pockets, and applications.
  • Data compilation for 56 known and 26 orphan riboswitches.

Main Results:

  • The Ribocentre-switch database contains 89,591 sequences.
  • It provides detailed information on riboswitch characteristics and biological roles.
  • Facilitates comparison and identification of potential riboswitch candidates.

Conclusions:

  • Ribocentre-switch serves as a valuable resource for understanding RNA conformational changes in response to ligand signaling.
  • The database aids in the comparative analysis of riboswitches.
  • It supports the identification of novel riboswitch candidates for further study.