BAT Hi-C maps global chromatin interactions in an efficient and economical way.
Methods
; 170: 38-47, 2020 01 01.
Article
em En
| MEDLINE
| ID: mdl-31442560
ABSTRACT
Chromosome Conformation Capture (3C)-based technologies, such as Hi-C, have represented a significant breakthrough in investigating the structure and function of higher-order genome architecture. However, the mapping of global chromatin interactions remains challenging across many biological conditions due to high background noise and financial constraints, especially for small laboratories. Here, we describe the Bridge linker-Alul-Tn5 Hi-C (BAT Hi-C) method, which is a simple and efficient method for delineating chromatin conformational features of mouse embryonic stem (mES) cells and uncover DNA loops. This protocol combines Alul fragmentation and biotinylated linker-mediated proximity ligation to obtain kilobase (kb) resolution with a marked increase in the amount of unique read pairs. The protocol also includes chromatin isolation to reduce background noise and Tn5 tagmentation to cut down on preparation time. Importantly, with only one-third sequencing depth, our method revealed the same spectrum of chromatin contacts as in situ Hi-C. BAT Hi-C is an economical (i.e., approximately $40 for library preparation) and straightforward (total hands-on time of 3â¯days) tool that is ideal for the in-depth analysis of long-range chromatin looping events in a genome-wide fashion.
Palavras-chave
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Cromatina
/
Mapeamento Cromossômico
/
Genômica
Tipo de estudo:
Health_economic_evaluation
Limite:
Animals
Idioma:
En
Ano de publicação:
2020
Tipo de documento:
Article