DNase-Seq

DNase-Seq (DNase I hypersensitive sites sequencing) is a method in molecular biology used to identify the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I.[1][2] FAIRE-Seq is a successor of DNase-Seq for the genome-wide identification of accessible DNA regions in the genome. Both the protocols for determining open chromatin region have their own bias depending on underlying nucleosome structure. Such as FAIRE-seq provides higher tag-count at non-promoter regions.[3] On the other hand, Dnase-seq signal is higher at promoter regions, however DNase-seq has been shown to have better sensitivity than FAIRE-seq even at non-promoter regions.[3]

References

  1. ↑ Crawford, GE; Holt, IE, Whittle, J, Webb, BD, Tai, D, Davis, S, Margulies, EH, Chen, Y, Bernat, JA, Ginsburg, D, Zhou, D, Luo, S, Vasicek, TJ, Daly, MJ, Wolfsberg, TG, Collins, FS (January 2006). "Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS).". Genome Research 3 (1): 230. doi:10.1101/gr.4074106. PMC 1356136. PMID 16344561.
  2. ↑ Madrigal, P; Krajewski, P (October 2012). "Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data.". Front Genet 16 (1): 123–31. doi:10.3389/fgene.2012.00230. PMC 3484326. PMID 23118738.
  3. ↑ 3.0 3.1 Prabhakar S., Vibhor Kumar; Rayan NA; Kraus P; Lufkin T; Ng HH (July 2013). "Uniform, optimal signal processing of mapped deep-sequencing data.". Nature Biotechnology 31 (7): 615–22. doi:10.1038/nbt.2596. PMID 23770639.

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