Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.8K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.8K
The Eukaryotic Promoter Region02:40

The Eukaryotic Promoter Region

16.2K
The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
16.2K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.4K
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...
6.4K
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

7.3K
Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
7.3K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

9.2K
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
9.2K
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

888
The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
888

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Enhanced and selective oxygen reduction by iron porphyrin with a biguanide residue in the second coordination sphere.

Chemical science·2026
Same author

Midterm Clinical and Echocardiographic Outcomes After Transcatheter Aortic Valve Replacement in Patients With Severe Bicuspid Aortic Valve Stenosis.

Journal of the American Heart Association·2026
Same author

The RNA binding protein ZFP36L2 displays tissue-selective mRNA targeting in mice.

RNA biology·2026
Same author

Pyridoxal-Based Selective Chemo Sensor for Colorimetric and Fluorescent Detection of Copper Ions and Imaging in Live Cells.

Journal of fluorescence·2026
Same author

Green tea catechin EGCG attenuates hippocampal atrophy and cognitive impairment in obesity via autophagy signaling.

NPJ science of food·2026
Same author

One-Pot LAMP-Coupled CRISPR/Cas12b Assay Enables Sensitive Detection of <i>Helicobacter pylori</i>.

Biology·2026

Related Experiment Video

Updated: Jun 21, 2025

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

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

Published on: August 9, 2019

6.6K

An intricate balancing act: Upstream and downstream frameshift co-regulatory elements.

Samuel Lee1, Shuting Yan1, Abhishek Dey2

  • 1Department of Chemistry, New York University, New York, 10003, NY, U.S.A.

Biorxiv : the Preprint Server for Biology
|July 9, 2024
PubMed
Summary

Targeting SARS-CoV-2 ribosomal frameshifting offers a therapeutic strategy. This study reveals how the 5' attenuator hairpin (AH) and 3' frameshift element (FSE) interact, influencing viral protein synthesis and replication.

Keywords:
RNAframeshiftgraph theory

More Related Videos

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

8.3K
Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
11:36

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

2.0K

Related Experiment Videos

Last Updated: Jun 21, 2025

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

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

Published on: August 9, 2019

6.6K
HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

8.3K
Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
11:36

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

2.0K

Area of Science:

  • Virology and Molecular Biology
  • RNA Structure and Dynamics
  • Computational Biology

Background:

  • Ribosomal frameshifting is crucial for SARS-CoV-2 replication.
  • The 5' stem-loop (attenuator hairpin, AH) and 3' frameshift element (FSE) are key RNA regions.
  • The interplay between AH and FSE in SARS-CoV-2 frameshifting remains unclear.

Purpose of the Study:

  • To investigate the RNA folding and conformational landscape of SARS-CoV-2 frameshifting elements.
  • To elucidate the relationship between the 5' AH and 3' FSE.
  • To identify potential therapeutic targets by understanding the frameshifting mechanism.

Main Methods:

  • Graph-theory-based modeling (RNA-As-Graphs, RAG) to represent RNA secondary structures.
  • Analysis of conformational landscapes and length-dependent folding.
  • Design and testing of four mutants to probe the roles of AH, AS1, and FSE.

Main Results:

  • AH coexists with specific 3' FSE pseudoknots (3_6, 3_3) but not others (e.g., 3_5).
  • Alternative Stem 1 (AS1) can disrupt FSE pseudoknots and promote alternative folds.
  • Mutational analysis confirmed that pseudoknot strength is inversely related to AS1 strength, and vice versa.

Conclusions:

  • A sequence of length-dependent folds governs SARS-CoV-2 frameshifting.
  • The interaction between 5' AH and 3' FSE is complex and influences viral replication.
  • Understanding these structural dynamics offers new avenues for antiviral therapeutic development.