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Related Concept Videos

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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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Prokaryotes can control gene expression through operons—DNA sequences consisting of regulatory elements and clustered, functionally related protein-coding genes. Operons use a single promoter sequence to initiate transcription of a gene cluster (i.e., a group of structural genes) into a single mRNA molecule. The terminator sequence ends transcription. An operator sequence, located between the promoter and structural genes, prohibits the operon’s transcriptional activity if bound by...
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The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
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Identifying candidate structured RNAs in CRISPR operons.

Brayon J Fremin1,2, Nikos C Kyrpides1,2

  • 1Department of Energy, Joint Genome Institute, Berkeley, CA, USA.

RNA Biology
|May 2, 2022
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Summary
This summary is machine-generated.

Researchers discovered 156 novel structured RNAs in CRISPR-Cas systems using comparative genomics. This includes new CRISPR direct repeats and a tracrRNA, aiding in classifying CRISPR arrays.

Keywords:
CRISPRcomparative genomicsstructured RNA

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Ubiquitous and Tissue-specific RNA Targeting in Drosophila Melanogaster using CRISPR/CasRx
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Area of Science:

  • Genomics and Molecular Biology
  • CRISPR-Cas Systems
  • Noncoding RNA Structure

Background:

  • Noncoding RNAs with secondary structures are crucial for CRISPR-Cas immune systems.
  • Many structured RNAs within these systems remain undiscovered.
  • Comparative genomics offers a powerful approach for identifying novel RNA structures.

Purpose of the Study:

  • To identify novel structured RNAs within a large dataset of CRISPR-Cas systems.
  • To characterize new CRISPR direct repeats and trans-activating CRISPR RNAs (tracrRNAs).
  • To explore the potential overlap of structured RNAs with coding regions.

Main Methods:

  • Employed a large-scale comparative genomics approach.
  • Analyzed 36,111 CRISPR-Cas systems to predict structured RNAs.
  • Investigated overlaps between predicted RNA structures and coding genes.

Main Results:

  • Predicted 156 novel candidate structured RNAs.
  • Identified 46 new CRISPR direct repeat models and 1 tracrRNA model.
  • Discovered overlaps with coding genes, including Cas genes and potential cas9 regions.
  • Demonstrated tracrRNA antirepeat sequence utility for classifying CRISPR arrays into type II-C systems.

Conclusions:

  • Unbiased identification of structured RNAs is vital for understanding CRISPR-Cas diversity.
  • Novel structured RNAs, including tracrRNAs, can be found within coding regions.
  • The identified tracrRNA aids in accurate classification of CRISPR-Cas type II-C systems.