| Chapter title |
Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome.
|
|---|---|
| Chapter number | 6 |
| Book title |
DNA-Protein Interactions
|
| Published in |
Methods in molecular biology, January 2023
|
| DOI | 10.1007/978-1-0716-2847-8_6 |
| Pubmed ID | |
| Book ISBNs |
978-1-07-162846-1, 978-1-07-162847-8
|
| Authors |
Lim, Hee-Woong, Iwafuchi, Makiko, Hee-Woong Lim, Makiko Iwafuchi |
| Abstract |
Genomic DNA wraps around core histones to form nucleosomes, which provides steric constraints on how transcription factors (TFs) can interact with gene regulatory sequences. It is increasingly apparent that well-positioned, accessible nucleosomes are an inherent feature of active enhancers and can facilitate cooperative TF binding, referred to as nucleosome-mediated cooperativity. Thus, profiling chromatin and nucleosome properties (accessibility, positioning, and occupancy) on the genome is crucial to understand cell-type-specific gene regulation. Here we describe a simplified protocol to profile accessible nucleosomes in the mammalian genome using low-level and high-level micrococcal nuclease (MNase) digestion followed by genome-wide sequencing. |
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