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

Lloren&#231; Rovirosa; Laureano Tom&#225;s-Daza; Blanca Urmeneta; Alfonso Valencia; Biola M. Javierre

doi:10.3791/65316

Un flux de travail intégré pour étudier l’architecture spatio-temporelle du génome centrée sur le...

JoVE Journal
Genetics

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JoVE Journal Genetics

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

Un flux de travail intégré pour étudier l’architecture spatio-temporelle du génome centrée sur le promoteur dans des populations cellulaires rares

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11:36 min

April 21, 2023

DOI: 10.3791/65316-v

Llorenç Rovirosa*¹, Laureano Tomás-Daza*^1,2, Blanca Urmeneta¹, Alfonso Valencia^2,3, Biola M. Javierre^1,4

¹Josep Carreras Leukaemia Research Institute, ²Barcelona Supercomputing Center, ³Catalan Institution for Research and Advanced Studies (ICREA), ⁴Institute for Health Science Research Germans Trias i Pujol

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Overview

This study explores how low input Capture Hi-C (liCHi-C) can identify gene promoter interactions with distal regulatory elements in rare cell types. The method enhances the understanding of gene regulation and chromatin interactions in the nucleus.

Key Study Components

Area of Science

Gene regulation
Chromatin organization
Cell type analysis

Background

Gene expression is influenced by interactions between promoters and regulatory elements.
Previous methods struggled to analyze rare cell types.
Understanding chromatin interactions is crucial for insights into gene regulation.
liCHi-C offers a novel approach to study these interactions.

Purpose of Study

To investigate chromatin interactions in the nucleus.
To link non-coding mutations with affected genes.
To analyze chromosome rearrangements in clinical samples.

Methods Used

Low input Capture Hi-C (liCHi-C) protocol.
Exploration of 3D chromatin organization.
Analysis of primary stem cells and tumor samples.
Reduction of input materials and costs for data acquisition.

Main Results

Successful identification of gene interactions in rare cell types.
Linkage of non-coding mutations to potential gene targets.
Detection of chromosome rearrangements in tumor samples.
Enhanced understanding of gene expression regulation in malignant transformation.

Conclusions

liCHi-C expands the capabilities of 3D chromatin analysis.
It allows for the exploration of previously unmeasurable cell types.
This method provides valuable insights into gene regulation mechanisms.

Frequently Asked Questions

What is low input Capture Hi-C?

Low input Capture Hi-C (liCHi-C) is a method used to study chromatin interactions at a low material input, enabling analysis of rare cell types.

How does liCHi-C improve gene regulation studies?

liCHi-C allows researchers to identify interactions between gene promoters and regulatory elements in cell types that were previously difficult to analyze.

What types of samples can be analyzed with this method?

The method can be applied to primary stem cells, tumor samples, and other relevant clinical samples.

What are the implications of this research?

This research provides insights into gene expression regulation, particularly in the context of diseases such as cancer.

Can liCHi-C detect chromosome rearrangements?

Yes, liCHi-C can detect chromosome rearrangements, including translocations in tumor samples.

What is the significance of studying 3D chromatin organization?

Studying 3D chromatin organization helps to understand the spatial regulation of gene expression and its implications in health and disease.

L’expression des gènes est régulée par les interactions des promoteurs de gènes avec les éléments régulateurs distaux. Ici, nous décrivons comment la capture Hi-C à faible entrée (liCHi-C) permet l’identification de ces interactions dans des types de cellules rares, qui étaient auparavant non mesurables.

Avec liCHi-C, la principale question à laquelle nous essayons de répondre est de savoir comment la chromatine interagit dans le noyau, et donc, de comprendre une nouvelle couche de régulation des gènes. Nous avons prouvé avec liCHi-C que nous pouvons explorer l’organisation du génome d’un échantillon donné, relier la mutation non codante associée à la maladie aux gènes potentiels affectés et détecter les réarrangements chromosomiques, tels que la translocation, par exemple, dans les échantillons tumoraux. Nous pouvons maintenant explorer l’organisation chromatique 3D des types de cellules cicatricielles, telles que les cellules souches primaires ou les échantillons cliniques pertinents.

Notre protocole réduit les matériaux d’entrée ainsi que le temps et le coût nécessaires pour obtenir des données de qualité afin d’explorer l’organisation du génome à la résolution du fragment de restriction. liCHi-C étend la portée du champ d’organisation de la chromatine 3D, ce qui nous permet d’explorer de nouveaux types de cellules auparavant impossibles à analyser. Grâce au liCHi-C, la communauté scientifique peut explorer la régulation particulière de l’expression génique.

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