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

Chromatin Structure and RNA Splicing02:41

Chromatin Structure and RNA Splicing

2.6K
2.6K
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

6.6K
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...
6.6K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

3.0K
3.0K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

8.9K
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...
8.9K
Ribosome Profiling02:24

Ribosome Profiling

3.2K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.2K
RNA Stability01:53

RNA Stability

31.7K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
31.7K

You might also read

Related Articles

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

Sort by
Same author

Scalable, fast and accurate differential gene expression testing from millions of cells of multiple patients.

Nature communications·2026
Same author

How do theme park attributes influence visitors' positive emotions? Nonlinear effects and spatial heterogeneity in Shanghai's theme parks.

PloS one·2026
Same author

Derivation and Pluripotency Validation of Six iPSC Lines From Amniotic Fluid Carrying Intermediate α-Thalassemia Genotypes (--<sup>3.7</sup>/α<sup>SEA</sup> and --<sup>4.2</sup>/α<sup>SEA</sup>).

Stem cells international·2026
Same author

Associations between physical activity and mortality in chronic obstructive pulmonary disease population with comorbidities: a prospective cohort.

Journal of thoracic disease·2026
Same author

Multi-omics analysis reveals polyethylene microplastics-induced gill damage, metabolic disruption and immune dysregulation in Lateolabrax maculatus.

Comparative biochemistry and physiology. Part D, Genomics & proteomics·2026
Same author

Extending differential gene expression testing to handle genome aneuploidy in cancer.

PLoS computational biology·2026

Related Experiment Video

Updated: May 7, 2026

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using &#967;CRAC
09:15

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Published on: May 9, 2020

6.1K

CRAK-Velo: chromatin accessibility kinetics integration improves RNA velocity estimation.

Nour El Kazwini1, Mingze Gao2, Idris Kouadri Boudjelthia1

  • 1Theoretical and Scientific Data Science, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy.

Genome Biology
|May 5, 2026
PubMed
Summary

We introduce CRAK-Velo, a new model for RNA velocity analysis in single-cell data. It integrates chromatin accessibility to reveal gene regulatory processes and improve cell-type identification.

Keywords:
Chromatin accessibilityRNA velocityRegion kinetics

More Related Videos

RNA-Associated Chromatin DNA-DNA Interaction Method
11:01

RNA-Associated Chromatin DNA-DNA Interaction Method

Published on: April 30, 2026

77
Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil Ers4tU
11:46

Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil Ers4tU

Published on: August 22, 2019

13.2K

Related Experiment Videos

Last Updated: May 7, 2026

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using &#967;CRAC
09:15

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Published on: May 9, 2020

6.1K
RNA-Associated Chromatin DNA-DNA Interaction Method
11:01

RNA-Associated Chromatin DNA-DNA Interaction Method

Published on: April 30, 2026

77
Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil Ers4tU
11:46

Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil Ers4tU

Published on: August 22, 2019

13.2K

Area of Science:

  • Computational biology
  • Genomics
  • Molecular biology

Background:

  • RNA velocity is a powerful tool for analyzing single-cell transcriptomic data.
  • Connecting RNA velocity to regulatory mechanisms remains a challenge.

Purpose of the Study:

  • To develop a novel model, CRAK-Velo, that integrates chromatin accessibility with RNA velocity estimation.
  • To provide biologically consistent developmental flow estimates and enable accurate cell-type deconvolution.
  • To elucidate regulatory processes by examining gene-chromatin region interactions.

Main Methods:

  • Developed CRAK-Velo, a semi-mechanistic model.
  • Integrated chromatin accessibility data into RNA velocity estimation.
  • Applied the model to single-cell transcriptomic data.

Main Results:

  • CRAK-Velo provides biologically consistent estimates of developmental trajectories.
  • The model achieves accurate cell-type deconvolution.
  • Identified regulatory processes through gene-chromatin region interactions.

Conclusions:

  • CRAK-Velo enhances RNA velocity analysis by incorporating chromatin accessibility.
  • The model offers insights into gene regulation and cell fate decisions.
  • This approach advances the understanding of dynamic cellular processes from single-cell data.