![]() ![]() SRR891269 and SRR891270 are ATAC-seq data for two biological replicates of 50K cells from EBV-transformed lymphoblastoid cell line GM12878. The function matplot is for summarizing the signal distribution around TSSs using a density plot.ĪTAC-seq datasets from two different studies were downloaded from the ENA Sequence Read Archive (SRA). And the function featureAlignedHeatmap is for generating a heatmap showing signal distribution around TSSs. 21 The function enrichedFragments is for calculating signals around TSSs using the split BAM objects. Typical nucleosome density distributions around TSSs of actively transcribed genes and active enhancers are shown in Figure 9, adapted from Baldi. By contrast, the promoters of genes that are not actively expressed in a given cell type exhibit much tighter association with histones, which prevents transcription factors from activating transcription and contributes to gene repression. ![]() These regions of “open” chromatin are usually occupied by transcription factors that facilitate gene transcription. ![]() Previous studies have shown that transcriptionally active elements, such as promoters and enhancers, are defined by short regions of DNA that are devoid of direct histone interactions. Plotting global signal distribution around transcriptional start sites (TSSs) # bamQC bamQC( bamFile, outPath = NULL) # $totalQNAMEs The tagged DNA fragments are then amplified and simultaneously sequencing adapters and indices compatible to Illumina sequencing platforms are added by using PCR with optimized cycles (Figure 4, adapted from Buenrostro et al 7). Briefly, hyperactive Tn5 transposases preloaded with adapters are first added to simultaneously tag and fragment open chromatin in nuclei (500~50,000) isolated from fresh or cryopreserved tissues/cells at nearly native states, a process called tagmentation. 7 Compared to other methods, such as MNase-seq, FAIRE-seq and DNase-seq, ATAC-seq allows comparable or even higher signal-to-noise ratio, but requires much less amount of the biological materials and time to process. 6 Among these methods, ATAC-seq (an assay for Transposase-Accessible Chromatin using sequencing) is a rapid and sensitive method for profiling chromatin accessibility. In recent years, a few methods have been developed to profile genome-wide chromatin accessibility (Figure 3, adapted from Tsompana and Buck 6) For review, see Tsompana and Buck. 4,5 Therefore, it is important to determine the chromatin accessibility to better understand gene expression regulation in cells. Thus, the interplay between histones and DNA serves as an important layer for controlling gene expression. 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 al 3). In cells, different genomic regions are packaged with different accessibility to transcriptional machinery. Nucleosomes can be hierarchically assembled into higher-order structures, eventually into chromatin or even chromosomes 1,2 (Figure 1, adapted from Nature Education 1(1):26). ![]() 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. 147 bp of DNA wrapped around a histone core octamer, spaced from adjacent NPCs by a linker DNA of ca. In eukaryotes, nucleosomes are basic DNA packaging units, each of which consists of a nucleosome core particle (NPC), linker DNA and linker histone H1. ![]()
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