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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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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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Regulation of Nuclear Protein Sorting01:45

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Nuclear protein sorting regulates nucleus composition and gene expression, crucial for determining the fate of a eukaryotic cell. Hence, the entry and exit of molecules across the nuclear envelope is a tightly controlled process. Nuclear protein sorting can be inhibited by one of the following ways: 1) masking cargo signal sequences, 2) modifying the nuclear receptor's affinity for cargo, 3) controlling the nuclear pore size, 4) retaining the cargo during its transit to the cytosol or the...
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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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Updated: Mar 13, 2026

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
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RNA Structure Switches RBP Binding.

Zheng Luo1, Qin Yang1, Li Yang2

  • 1Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China.

Molecular Cell
|October 22, 2016
PubMed
Summary
This summary is machine-generated.

RNA sequence motifs alone do not determine RNA-binding protein (RBP) interactions. RNA secondary structure also significantly impacts RBP binding, acting as a repressive factor in both in vitro and in vivo conditions.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • RNA-binding proteins (RBPs) play crucial roles in gene regulation.
  • Predicting RBP binding sites typically relies on identifying specific RNA sequence motifs.
  • The contribution of RNA structure to RBP binding remains incompletely understood.

Purpose of the Study:

  • To investigate the role of RNA secondary structure in RBP binding beyond sequence specificity.
  • To determine if RNA structure influences RBP association in vitro and in vivo.

Main Methods:

  • Computational analysis of RNA sequences and structures.
  • In vitro binding assays.
  • In vivo experiments to assess RBP-RNA interactions.

Main Results:

  • RNA sequence motifs alone are insufficient to fully explain RBP binding.
  • RNA secondary structure exhibits a repressive effect on RBP association.
  • This structural repression is observed under both in vitro and in vivo experimental conditions.

Conclusions:

  • RNA secondary structure is a critical determinant of RBP binding, complementing sequence-based recognition.
  • Understanding the interplay between RNA sequence and structure is essential for accurate prediction of RBP-RNA interactions.
  • This finding has implications for understanding gene regulation and developing therapeutic strategies targeting RNA-protein interactions.