Genome-wide maps of chromatin accessibility in Irf8+/+ and Irf8-/- mice LT-HSC cells

We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 1000–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with the nucleosome. Using ATAC-seq maps of chromatin accessibility in Irf8+/+ and Irf8-/- LT-HSC cells, we demonstrated the genome-wide activity of cis-regulatory elements (CREs) perturbation in IRF8 deficient mice bone marrow LT-HSC. Overall design: Examination of the genome-wide activity of cis-regulatory elements (CREs) using Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) in Irf8+/+ and Irf8-/- mice LT-HSC cells.