Instructors and contact information
- Haibo Liu (Department of Animal Science, Iowa State University, Ames, IA, 50010, USA. email@example.com)
- Jianhong Ou (Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA. Jianhong.firstname.lastname@example.org)
- Lihua Julie Zhu (Corresponding author, Department of Molecular, Cell and Cancer Biology, Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, Worcester, MA, 01655, USA. Julie.Zhu@umassmed.edu)
Introduction to the ATAC-seq technology
In eukaryotes, nucleosomes are basic DNA packaging units, each of which consists of a nucleosome core particle (NPC), linker DNA and linker histone H1. The NPC is composed of ~147 bp of DNA wrapped around a histone core octamer, spaced from adjacent NPCs by a linker DNA of ~20-90 bp. Linker histones binds additional 20 bp of linker DNA at its entry/exit points to a NPC to stabilize nucleosome conformation and higher-order chromatin assembly. Nucleosomes can be hierarchically assembled into higher-order structures, eventually into chromatin or even chromosomes1,2 (Figure 1, adapted from Nature Education 1(1):26). In cells, different genomic regions are packaged with different accessibility to transcriptional machinery. Most notably, promoters and enhancers of actively transcribed genes are devoid of histone interaction, which are called “open” chromatin regions (Figure 2, adapted from Wang et al3). Thus, the interplay between histones and DNA serves as an important layer for controlling gene expression4,5. Therefore, it is important to determine the chromatin accessibility to better understand gene expression regulation in cells.