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Fig. 4 | Genome Biology

Fig. 4

From: Identification of transcription factor binding sites using ATAC-seq

Fig. 4

Nucleosome architecture and strand-specific cleavage profiles. a Tn5 digests open chromatin regions left/right of the TF binding (regulatory region) or in nucleosome linkers. Nucleosome-free fragments will generate reads with (Nfr type I) or without (Nrf type II) the TF bound to DNA. As sequencing is performed from the 5 to 3 ends, Nfr type I fragments will always generate forward reads on the left (orange) and reverse reads on the right (blue) relatively to the TF binding site. DNA fragments from 1N decomposition with a cleavage event in the regulatory region will either include (1N Type II) or not (1N Type I) a TF. 1N Type III are produced by cleavage events between two neighboring linkers. b Bias-corrected average cleavage profile around CTCF ChIP-seq peaks for Omni-ATAC in GM12878 cells for fragments with distinct number of nucleosomes. Strand bias can be estimated as the ratio of reads in forward (orange) and reverse (blue) around intervals between nucleosomes and CTCF. c Decomposition of Nfr, 1N and 2N fragments by types clarifies the origin of strand cleavage bias. Numbers in orange (blue) indicate amount of reads in the forward (reverse) strand at each interval

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