Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

You might also read

Related Articles

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

Sort by

Same author

Genome-wide mapping of Cas9-induced sister chromatid exchange across single and over 200 genomic targets.

bioRxiv : the preprint server for biology·2026

Same author

Lesions initiating spontaneous mitotic crossover are minimally subject to non-homologous end joining.

bioRxiv : the preprint server for biology·2026

Same author

Genome-wide chromatin recording resolves dynamic cell state changes.

bioRxiv : the preprint server for biology·2026

Same author

Ribosome biogenesis bottlenecks reveal vulnerabilities in cancer.

bioRxiv : the preprint server for biology·2026

Same author

High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq.

Nucleic acids research·2026

Same author

Chromatin folding principles underlying the generation of antibody diversity.

Molecular cell·2026

Same journal

iMUT-seq mapping of DSB-induced mutations with high sensitivity at single-nucleotide resolution.

Nature protocols·2026

Same journal

An assay to quantify sexual commitment and stage conversion in the human malaria parasite Plasmodium falciparum.

Nature protocols·2026

Same journal

Author Correction: Direct inoculation of bioreactor-controlled stirred suspension culture with cryopreserved human pluripotent stem cells.

Nature protocols·2026

Same journal

High-throughput measurements of protein domain functions using magnetic separation.

Nature protocols·2026

Same journal

Inducing physiological polarity and performing gene editing using CRISPR-Cas9 in human trophoblast organoids.

Nature protocols·2026

Same journal

Photocatalytic low-temperature defluorination of PTFE.

Nature protocols·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Oct 7, 2025

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial

Sofia A Quinodoz^1,2, Prashant Bhat^1,3, Peter Chovanec¹

¹Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

Nature Protocols

|January 11, 2022

Summary

This summary is machine-generated.

Split-Pool Recognition of Interactions by Tag Extension (SPRITE) maps complex DNA interactions within the nucleus. This method aids in understanding gene regulation by revealing how DNA packaging influences cell-type-specific gene expression.

More Related Videos

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

Related Experiment Videos

Last Updated: Oct 7, 2025

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

Area of Science:

Genomics
Molecular Biology
Cell Biology

Background:

Cell-type-specific gene expression is crucial for cellular function.
Understanding DNA packaging's role in gene regulation requires advanced interaction mapping techniques.

Purpose of the Study:

To present a detailed protocol for the Split-Pool Recognition of Interactions by Tag Extension (SPRITE) method.
To enable researchers to map higher-order DNA interactions within the nucleus and study their influence on gene regulation.

Main Methods:

SPRITE involves cross-linking interacting DNA, RNA, and protein molecules.
Iterative split-and-pool barcoding is used to tag spatially proximal DNA molecules.
Sequencing and computational analysis of barcoded DNA fragments reconstructs interaction networks.

Main Results:

SPRITE accurately maps pairwise DNA interactions and higher-order spatial contacts.
The method can capture interactions among thousands of simultaneously interacting molecules.
A detailed experimental protocol and an automated computational pipeline are provided.

Conclusions:

SPRITE is a powerful tool for investigating the relationship between nuclear architecture and gene regulation.
The provided protocol and pipeline facilitate the application of SPRITE in diverse research settings.
This method advances our understanding of how DNA packaging influences cell-specific gene expression.