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Restarting Stalled Replication Forks

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...

Chromatin Structure Regulates pre-mRNA Processing

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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...

Transcription Attenuation in Prokaryotes

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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
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Related Experiment Video

Updated: May 21, 2025

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Guanine quadruplexes mediate mitochondrial RNA polymerase pausing.

Ryan J Snyder¹, Uma Shankar¹, Don Delker²

¹Epigenetics and RNA Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.

|May 13, 2025

Summary

This summary is machine-generated.

RNA guanine quadruplexes regulate mitochondrial transcription by pausing RNA polymerase. Stabilizing these structures in nascent RNA diminishes gene expression and cellular respiration.

Keywords:

Guanine quadruplex Mitochondria Proximal tubule RNA polymerase pausing Transcription

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Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

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Published on: September 19, 2017

Area of Science:

Molecular Biology
Genetics
Biochemistry

Background:

Nucleic acids possess functional secondary structures beyond primary sequences, influencing transcription.
Guanine-rich sequences form stable guanine quadruplexes via non-canonical base pairing.
While DNA guanine quadruplexes are linked to transcription regulation, the role of RNA guanine quadruplexes is less understood.

Purpose of the Study:

Investigate the impact of guanine quadruplexes in nascent RNA on mitochondrial transcription.
Determine the role of RNA guanine quadruplexes in regulating mitochondrial RNA polymerase (POLRMT) pausing.

Main Methods:

Precision nuclear run-on assay to map POLRMT pausing sites in human cells.
In vitro primer extension assays to assess quadruplex-mediated pausing.
Cell-based assays using a quadruplex-stabilizing agent (RHPS4) to evaluate transcriptional effects.

Main Results:

Over 400 POLRMT pausing sites were identified on the mitochondrial genome, often downstream of guanine-rich regions.
Nascent RNA guanine quadruplexes were shown to mediate POLRMT pausing in vitro.
Stabilization of RNA guanine quadruplexes disrupted mitochondrial transcription, reduced cellular respiration, and caused ATP stress.

Conclusions:

RNA guanine quadruplex-mediated pausing is a key regulator of POLRMT transcription and mitochondrial function.
Modulating quadruplex dynamics in nascent RNA, not DNA, is sufficient to control mitochondrial gene expression.