Related Experiment Video
Updated: May 7, 2026
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
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.
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.
Related Concept Videos
02:41Chromatin Structure and RNA Splicing
2.6K
2.6K
02:41Chromatin 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...
The chromatin structure, especially...
6.6K
02:36RNA Polymerase II Accessory Proteins
3.0K
3.0K
02:36RNA 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
02:24Ribosome 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...
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
01:53RNA 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