Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.
Methods
; 142: 59-73, 2018 06 01.
Article
en En
| MEDLINE
| ID: mdl-29382556
ABSTRACT
The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods.
Palabras clave
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Mapeo Cromosómico
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Imagenología Tridimensional
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Desoxirribonucleasa I
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Imagen Molecular
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Secuenciación de Nucleótidos de Alto Rendimiento
Idioma:
En
Revista:
Methods
Asunto de la revista:
BIOQUIMICA
Año:
2018
Tipo del documento:
Article
País de afiliación:
Estados Unidos