| Based on8-mer and second order information redundancy, the article analyzed the evolution diversity and function of8-mer in Human DNA、the function differences between nucleosome core sequence and nucleosome linker sequences in Yeast、the local feature of nucleosome core sequence in Yeast and interactions of nucleosome DNA with histones. The study were divided into four parts, and the concrete content are as follows.1、The DNA sequences of Human Chromosome1were classified into intergenic, CDS,5’UTR,3’UTR and intron sequences.8-mer frequencies were calculated for the5kinds of sequences. Distributions of their frequencies of appearance shows that mono-peak distribution is appeared in CDS, similar mono-peak distributions are appeared in5’UTR,3’UTR and clear3-peak distributions are appeared in intergenic and intron sequences. All of the8-mers were classified into3motif sub-sets according to8-mers that include two or larger than two dinucleotides, one dinucleotide and zero dinucleotide and drawed the8-mer distributions again. We found that three CG motif sets of8-mers form independent distributions and the center of3distributions are same as the center of8-mer3peak distributions of the total8-mers. According to the classification of the other15dinucleotides, the three motif sets of8-mers do not form independent distributions. Moreover, relative frequencies of dinucleotides and tri-nucleotides of three CG motif sets of8-mers were calculated. Relative frequency distributions of dinucleotides and tri-nucleotides in five DNA sequences are nearly identical for CG2motif set, similar for CGi motif set and clear diversity for CGo motif set. Our results show that CG2and CGi motif sets of8-mers have conservative property in DNA evolution and have convergence usage in the five kinds of sequences. Otherwise, CGo motif set of8-mers show the diversity in DNA evolution and has divergence usage in the five kinds of sequences.2、According to nucleosome positioning map of single-base precision of Yeast genome-wide16chromosomes which Brogaard and others published in Nature in2012, extracted nucleocome core sequences and nucleosome linker sequences from Yeast genome-wide16chromosomes. Calculated Relative Frequency (RF) of k-mer (k=4,5,6, and8) of two kinds of sequence. Found the longer k-mer the stronger usage offset, and only part of8-mer which existed strong usage offset showed the usage difference. Calculated the logarithmic ratio of Relative Frequency (LRF) of k-mer, and arranged them from small to large. Found only8-mer showed symmetrical distribution, and a part of8-mer usage were far more than linker sequence, a part of8-mer usage were far less than linker sequence. Computed LRF of8-mer with RF of core sequence which were from small to big. Found8-mer usage differences mainly occurred in the area whose RF were low. LRF of k-mer were arranged according to the increasing order of RF of core sequence. Found only usage difference of8-mer was particularly significant. Calculated G+C and dinucleotide content of local8-mer around0,10000,20000,30000,40000,50000and60000, and repeated this step in the biggest and smallest8-mer. Found the G+C content gradually decreases with the increase of RF. Core sequence was more prefered for GG and CC dinucleosides, linker sequence was more prefered for GC dinucleoside. The usage of CG dinucleoside in linker sequence was always higher than core sequence. Analyzing results show that the nucleosome motif which could performed function was at least8bp, and sequence characteristics of motif which contained CG dinucleotide should be closely related with nucleosome core sequence.3、According to nucleosome positioning map of single-base precision of Yeast genome-wide16chromosomes which Brogaard and others published in Nature in2012, respectively extracted+1and-1、+2and-2nucleosome sequences near the all TSS or TTS in Yeast chromosome2, and respectively extracted all nucleosome sequences in Chromosome2、CDS region and intergenic region of Yeast chromosome2. Expand the histone octamer on nucleosome core sequence. Found that arrangement of histone are asymmetric. According to the asymmetriy of histone arrangement and frequency distribution of AA/TA/AT/TT dinucleoside geted by Kristin, each kind of nucleosome sequences were classified into5groups, and calculated their the second order information redundancy. Because the second order information redundancy relate to sequence length and C+G content, for5group sequences of each kind of nucleosome, every group sequences respectively randomly generated100groups random sequences, and random sequences have uniform length and A+T content with the original sequences. Then calculated the second-order information redundancy of random sequences (average of second order information redundancy of100random sequences). Used the second-order information redundancy of the original sequences to divide second-order information redundancy of random sequences and geted logarithmic results. Found that under the dynamic balance-1and-2nucleosomes (TSS and TTS) have the trend to move towards the3’end;+1and+2(TSS and TTS) nucleosomes have the trend to move towards the5’end.4、According to nucleosome positioning map which Brogaard and others geted, according to the above method extracted the same10kinds of nucleosome sequence in the yeast genome. In order to insure that the random fluctuation of10kinds of nucleosome sequences are uniform, each kind of nucleosome took6363. For each kind of nucleosome, aligned unique nucleosomes, and calculated the second order information redundancy of each kind of nucleosome. Found that the distribution second order information redundancy though clutter but exists asymmetry distribution on both sides of nucleosome center cite. Because the second order information redundancy reflects the strength of interaction between nucleosome sequence and histone, so its asymmetry reveal the intrinsic reason of nucleosome motion. Smoothed the distribution of the second order information redundancy of each kind of nucleosome. Distribution of the second order information redundancy exist prominent asymmetry after smoothing. The study showed that under the dynamic balance+1and+2(TSS and TTS) nucleosomes have the trend to move towards the5’end;-1(TSS and TTS) and-2(TTS) nucleosomes have the trend to move towards the3’end;-2(TSS) nucleosomes have the trend to move towards the5’end;... |
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