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

Nucleosome Remodeling02:54

Nucleosome Remodeling

9.3K
Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
9.3K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.1K
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.
The recognition sites for Cre recombinase called LoxP...
6.1K
RNA Splicing01:32

RNA Splicing

56.6K
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
56.6K
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

5.9K
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,...
5.9K
Long-patch Base Excision Repair01:02

Long-patch Base Excision Repair

7.1K
Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
7.1K
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

30.0K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
30.0K

You might also read

Related Articles

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

Sort by
Same author

Beta-Adrenergic Stimulation and <i>MYH7</i> G256E Mutant Gene Dosage Drive Hypertrophic Cardiomyopathy Phenotype Penetrance.

bioRxiv : the preprint server for biology·2026
Same author

Human RNA ligase 1 as a novel regulator of ribosome function and translation under oxidative stress.

Nucleic acids research·2026
Same author

The vacuolar tauopathy-associated mutation D395G confers redox sensitivity to p97/VCP.

bioRxiv : the preprint server for biology·2026
Same author

PPa1 insufficiency drives lysosomal storage disease and inflammatory macrophage expansion in the bone marrow.

bioRxiv : the preprint server for biology·2026
Same author

Non-hydrolyzable acetyllysine analogs to study protein acetylation in vitro and in cells.

Nature communications·2026
Same author

The Structural Basis for Pacs1-Wdr37 Complex Assembly and Stability.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: Aug 18, 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

6.7K

Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.

Victor Emmanuel Cruz1, Kamil Sekulski1, Nagesh Peddada1

  • 1Department of Biophysics, UT Southwestern Medical Center - ND10.124B, Dallas, TX, USA.

Nature Structural & Molecular Biology
|December 9, 2022
PubMed
Summary

DEAD-box ATPases like Spb4 remodel RNA during ribonucleoprotein assembly. Cryo-EM structures reveal how Spb4 unwinds RNA, driving rRNA organization for efficient assembly.

More Related Videos

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
10:52

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

8.2K
Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells
10:06

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

Published on: April 26, 2017

9.0K

Related Experiment Videos

Last Updated: Aug 18, 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

6.7K
Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
10:52

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

8.2K
Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells
10:06

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

Published on: April 26, 2017

9.0K

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • DEAD-box ATPases are crucial for RNA biology, yet their in vitro activity doesn't fully explain their complex roles in ribonucleoprotein (RNP) assembly.
  • These enzymes are vital for large-scale RNA remodeling during RNP biogenesis.

Purpose of the Study:

  • To elucidate the mechanism by which the DEAD-box ATPase Spb4 remodels rRNA during 60S ribosomal biogenesis.
  • To understand how Spb4's RNA unwinding activity contributes to accurate RNP assembly.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) to determine structures of 60S ribosomal biogenesis intermediates.
  • Structural analysis to identify interactions and conformational states of Spb4.

Main Results:

  • Cryo-EM structures revealed Spb4 mediating context-specific RNA unwinding and extensive rRNA secondary structure remodeling.
  • Spb4 was observed in a post-catalytic, high-energy intermediate stabilized by multiple interactions.
  • This intermediate drives the organization of a critical three-way junction in rRNA domain IV.

Conclusions:

  • Spb4 utilizes limited RNA strand separation to provide non-equilibrium directionality in RNP assembly.
  • This mechanism ensures efficient and accurate assembly of complex ribonucleoprotein structures.