Nucleosome Positioning Prediction In Functional Region Of Human And Yeast Genome

Nucleosome is the basic building block of eukaryotic chromatin, the location of histoneoctamer on the DNA sequence is called nucleosome positioning. The nucleosomepositioning plays a central role in diverse cellular processes such as DNA transcription,replication and repair. The research on nucleosome positioning is a hot topic in epigenetics.This article includes the following three aspects.1. Insulator in chromosome is a DNA sequence element that can protect genes fromaffecting of its external enhancer and non-active chromatin structure. The GC content ofinsulator was calculated and average nucleosome occupancy was also calculated in the1000bp of upstream and downstream of start site and termination site of insulator. Theresults showed that the GC content in the insulator is higher than the average level in human,and the nucleosome average occupancy is higher in insulator than blanks both insulator. Theinsulator sequence in which GC content is higher benefits the bending of DNA sequence andform a compact nucleosome around histone octamer, and the insulator in which thenucleosome occupancy is higher is beneficial to isolate two transcriptional function region.2. The promoter is a DNA sequence that promotes gene transcription and is recognizedby RNA polymerase. The promoter is an essential component of gene transcription, and thearrangement of nucleosome influences gene transcription. The RNA polymerase combiningpromoter causes transcription in the promoter region lacking nucleosome. We calculated thenucleosome average occupancy of upstream and downstream of promoter in S.cerevisiaeand the results showed that there is nucleosome free region in the upstream of the promoter,indicating that this region may be recognized by transcription factors.3. E. coli is a prokaryote and the nucleosome isn’t existed in chromatin. However,chromatin of E. coli can form the nucleosome in vitro. In this paper, k-mer frequency ofnucleosome core sequence and linker sequence of E.coli was calculated. By comparing thepreference of the k-mer frequency of nucleosome core sequence and linker sequence inE.coli, S.cerevisiae and human genome, we found that that the linker DNAs are moreconservative than nucleosome DNAs.