MNase-seq uses an endo-exonuclease that degrades the accessible linker DNA between nucleosomes and reveals the position of nucleosomes by sequencing the protected DNAs. High-throughput sequencing techniques such as MNase-seq, chemical mapping, DNase-seq, FAIRE-seq, and ATAC-seq have been developed to assess genome-wide chromatin structure. Thus, the chromatin accessibility plays a critical role in regulating gene expression pattern. It is known that precise location of a nucleosome relative to transcriptional target sites can significantly influence factor binding. The dense nucleosome regions (nucleosome occupied regions, NOR) are tightly packed, whereas the loose nucleosome regions (nucleosome free regions, NFR) are more accessible to transcription factors.
Nucleosomes are arranged into regularly spaced arrays, separated by unwrapped linker DNA whose length varies among species and cell types.
Eukaryotic genomes are packed into nucleoprotein called chromatin whose basic unit is the nucleosome, which comprises a histone octamer wrapped around 147 base pairs of DNA.
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