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Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events

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Flanking Sequence Cotranscriptionally Regulates Twister Ribozyme Activity.

Lauren N McKinley^1,2, Reuben G Kern^2,3, Sarah M Assmann^2,4

¹Depatment of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States.

|December 22, 2023

Summary

This summary is machine-generated.

Flanking sequences can regulate twister ribozyme activity by forming inactive ribozymogens. This regulation can be controlled externally, offering potential in gene expression and synthetic biology.

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

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Published on: August 9, 2019

Area of Science:

Molecular Biology
Biochemistry
RNA Biology

Background:

Ribozymes are RNA molecules with catalytic activity, but their regulatory mechanisms are less understood than protein enzymes.
Twister ribozymes, a class of nucleolytic RNAs, have known catalytic properties, but their regulation within native sequences is understudied.
Naturally occurring ribozymes are not isolated and their activity can be influenced by adjacent genomic sequences.

Purpose of the Study:

To investigate the regulatory role of flanking sequences on twister ribozyme activity in rice (Oryza sativa).
To identify specific twister ribozymes whose activity is modulated by their native genomic context.
To explore potential mechanisms of ribozyme regulation and external control applicable to synthetic biology.

Main Methods:

Analysis of published RNA-sequencing data sets from rice.
Structure probing techniques to investigate RNA conformation.
Cotranscriptional cleavage assays to measure ribozyme activity.
Oligonucleotide-mediated rescue experiments.

Main Results:

Differential regulation of twister ribozymes by flanking sequences was observed.
The Osa 1-2 ribozyme showed no interaction with flanking sequences.
Flanking sequences of Osa 1-3 and Osa 1-8 ribozymes formed inactive ribozymogen conformations, attenuating self-cleavage.
Antisense oligonucleotide addition rescued the activity of the Osa 1-3 ribozymogen.

Conclusions:

Flanking sequences play a significant role in differentially regulating twister ribozyme activity in vivo.
Ribozymogen formation represents a plausible mechanism for natural ribozyme regulation.
External control of ribozymogens, demonstrated with antisense oligonucleotides, has implications for synthetic biology and gene regulation.