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Types of RNA01:23

Types of RNA

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
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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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Experimental RNAi02:15

Experimental RNAi

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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
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Conservative Site-specific Recombination and Phase Variation02:53

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Related Experiment Video

Updated: Jun 21, 2025

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing
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Re-engineered guide RNA enables DNA loops and contacts modulating repression in E. coli.

Yunshi Yang1, Iris Rocamonde-Lago1, Boxuan Shen1,2

  • 1Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Stockholm 17177, Sweden.

Nucleic Acids Research
|July 16, 2024
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Summary

Researchers developed a dual guide RNA (dgRNA) that links two single guide RNAs. This innovation enables targeting distant DNA regions, offering a minimal system for remodeling chromosomal conformation using dCas9 and RNA.

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Area of Science:

  • Molecular Biology
  • Synthetic Biology
  • Genetics

Background:

  • Single guide RNA (sgRNA) in CRISPR systems functions as both an information carrier and a structural scaffold.
  • The guide region of sgRNA is crucial for DNA recognition and typically not considered modular.
  • Modifications to the scaffold region exist, but the guide region's modularity remains unexplored.

Purpose of the Study:

  • To investigate the DNA binding and loop-induction capabilities of a novel dual guide RNA (dgRNA).
  • To explore the potential of dgRNA as a modular system for targeting distal genomic regions.
  • To assess the minimal system requirements for inducing DNA contacts and remodeling chromosomal conformation.

Main Methods:

  • Designed and synthesized a chimera of two sgRNAs joined by an RNA linker, termed dgRNA.
  • Studied the sequence bi-specificity of dgRNA to understand its DNA binding properties.
  • Utilized a LacZ reporter system in E. coli to test dgRNA activity in vivo, specifically loop-mediated gene inhibition.

Main Results:

  • The RNA linker in dgRNA facilitates bringing distal parts of double-stranded DNA into proximity.
  • dgRNA demonstrated effective targeting of distal genomic regions, comparable to established methods.
  • Loop-mediated gene inhibition was successfully recapitulated in E. coli using the dgRNA system.

Conclusions:

  • dgRNA functions as a sequence bi-specific molecule capable of inducing DNA contacts.
  • The dgRNA system, requiring only dCas9 and RNA, offers a minimal approach to remodel chromosomal conformation.
  • This technology holds potential for applications in various organisms requiring targeted genomic manipulation.