| In eukaryotic cells,nucleosome is an important component of chromatin,and it involves all the biological functions associated with DNA,such as transcription regulation,DNA replication and reparation.The precise position of nucleosome is the key to execute its biological function,and nucleosome positioning is determined by many factors,such as chromatin remodeling factor,DNA binding protein,DNA sequences preferences.With the development of chromatin immunoprecipitation-chip(ChIP-chip)and chromatin immunoprecipitation-sequencing(CHIP-seq),nucleosome positioning map has been given in many organisms.Nucleosome structure is conserved in eukaryotes,the nucleosome core particle comprises 147 base pairs of DNA wrapped around an octamer of histone proteins,and the octamer of histone proteins are also conserved.However,there are differences of genome background among different organisms,and DNA sequence preferences of nucleosomes have made a significant contribution to the nucleosome organization,and it is unclear that whether the sequence preferences of nucleosomes are the same in different organisms,and whether there is concerted evolution in nucleosome sequences.Further,nucleosome has played a crucial role in gene transcription regulation,and lots of researches focus on the nucleosomes around TSS,but how to find the +1/-1 nucleosomes theoretically based on the TSS need to be studied,and it is unclear whether the nucleosome organization around TSS and the sequence structure of NFR are related to gene expression levels.The translation regulation mechanism based on nucleosome is very complex,and the gene transcriptional regulation network involved in nucleosomes should be continuously improved.So,three aspects were discussed in this paper based on the single base pair resolution maps of nucleosome positions of Saccharomyces cerevisiae,Schizosaccharomyces pombe and Drosophila.First,evolutionary analysis was analyzed in nucleosome core sequences of three organisms.Second,nucleosome distribution around TSS and its relation to gene expression were analyzed in Saccharomyces cerevisiae.Third,through the analysis of sequence characteristics of ±1 nucleosomes in there organisms,the differences of gene expression regulation mechanism by nucleosome in different organisms were discussed.(1)In the evolutionary analysis of nucleosome sequences,New Symmetric Relative Entropy was applied innovatively to analyze the nucleosome sequences in S.cerevisiae,S.pombe and Drosophila.NSRE distributions could well reflect the characteristic differences of nucleosome sequences among three organisms,and the differences were mainly reflected in the nucleosome dyad region.Single nucleotide(1-mer)makes major contribution to the constitutive property of nucleosome sequence,and the degree of sequence dependence to nucleosome is Drosophila>S.pombe>S.cerevisiae.These differences indicate a concerted evolution in the sequence usage of nucleosome.Through the analysis of base composition of nucleosome core sequences,it reflects that no matter in which organism,there are always two special sites in nucleosome core sequences:one is A-rich and T-poor,and the other is just opposite.Further analysis indicate that base A&T have made a majority of contribution to NSRE distribution characteristics of all nucleosome core sequences in three organisms,and the dependence degree on base A&T for dyad peaks in three organisms is conserved.For further discussing the usage biases of motif in nucleosome sequences,we analyzed the nucleosome sequences in three organisms respectively by Characteristic Parameter obtained by the information of CGO,CG1 and CG2 subset.It is reflected that,the motifs in CG1 constitute the skeleton of nucleosome sequence,and motifs in CGO and CG2 are the factors that regulate the characteristics of nucleosome,and the usage biases of motif in nucleosome sequences are derived from these two types of motifs.(2)In the study of nucleosome distributions around transcription start site,based on the single-base pair resolution map of nucleosome positions in S.cerevisiae,we used two types of position definitions for ±1 nucleosomes to analyze nucleosome distribution patterns on TSS flanking regions.While the position definition based on TSS directly,nucleosome distributions on the downstream of TSS were bimodal,and it could not reflect the functional distributions of nucleosomes.Then we re-demarcated ±1 nucleosomes,the nucleosome on the TSS or the nearest to TSS was defined as +1 nucleosome,then nucleosome distribution around TSS was analyzed.It reflects that about 2/3 genes have striking NFR and about 1/3 have non-striking NFR.In striking NFR genes,the length and the order structure of NFR display a positive correlation with gene expression levels.In non-striking NFR genes,the position of-1 nucleosome has obvious conservative property and does not correlate with gene expression levels.(3)In the study of translation regulation mechanism based on nucleosome,first,the nucleosome sequences of S.cerevisiae,S.pombe and Drosophila were analyzed by New Symmetric Relative Entropy.It reflects that the sequence characteristics of ±1 nucleosomes in S.cerevisiae are different from other two organisms,and these differences are mainly reflected in two aspects:① the entropy is higher in the region close to TSS of ±1 nucleosome sequence in S.cerevisiae,and in the other two organisms,the ± 1 nucleosomes have no such characteristics.② in Drosophila and S.pombe,±1 nucleosomes have the same way in base frequency usage for NSRE:base A&T are major determinants for NSRE distribution characteristics,and base C&G are nearly useless.But in S.cerevisiae,there are some differences:base C&G have also taken part in the construction of NSRE distribution characteristics,though it only exists in the flanking region of nucleosome sequence but not in the dyad region.Through the analysis of nucleosome sequences by Characteristic Parameter,it indicates that the translation regulation mechanism based on nucleosome in S.cerevisiae is different from that in other two organisms.In Drosophila and S.pombe,the translation regulation involves multiple nucleosomes,but in S.cerevisiae,it mainly depends on the slide of±1 nucleosomes.Further analysis shows that the Characteristic Parameter construct by the information of CGO motif could well characterize the sequence potential energy difference,and this sequence potential energy difference could well describe the slide tendency of nucleosome. |
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