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10-11 bp periodicities in complete genomes reflect protein structure and DNA folding.

机译:完整基因组中的10-11 bp周期性反映蛋白质结构和DNA折叠。

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MOTIVATION: Completely sequenced genomes allow for detection and analysis of the relatively weak periodicities of 10-11 basepairs (bp). Two sources contribute to such signals: correlations in the corresponding protein sequences due to the amphipatic character of alpha-helices and the folding of DNA (nucleosomal patterns, DNA supercoiling). Since the topological state of genomic DNA is of importance for its replication, recombination and transcription, there is an immediate interest to obtain information about the supercoiled state from sequence periodicities. RESULTS: We show that correlations within proteins affect mainly the oscillations at distances below 35 bp. The long-ranging correlations up to 100 bp reflect primarily DNA folding. For the yeast genome these oscillations are consistent in detail with the chromatin structure. For eubacteria and archaea the periods deviate significantly from the 10.55 bp value for free DNA. These deviations suggest that while a period of 11 bp in bacteria reflects negative supercoiling, the significantly different period of thermophilic archaea close to 10 bp corresponds to positive supercoiling of thermophilic archaeal genomes. AVAILABILITY: Protein sets and C programs for the calculation of correlation functions are available on request from the authors (see http://itb.biologie.hu-berlin.de).
机译:动机:完全测序的基因组可以检测和分析10-11个碱基对(bp)相对较弱的周期性。有两个来源促成此类信号:由于α螺旋的两性特征和DNA折叠(核小体模式,DNA超螺旋),相应的蛋白质序列具有相关性。由于基因组DNA的拓扑状态对其复制,重组和转录至关重要,因此迫切需要从序列周期性中获取有关超螺旋状态的信息。结果:我们显示蛋白质内的相关性主要影响35 bp以下距离处的振荡。高达100 bp的长期相关性主要反映了DNA折叠。对于酵母基因组,这些振荡在细节上与染色质结构一致。对于真细菌和古细菌,该时期显着偏离了游离DNA的10.55 bp。这些偏差表明,虽然细菌中11 bp的时间段反映了负超螺旋,但是接近10 bp的嗜热古细菌的显着不同时期对应于嗜热古细菌基因组的正超卷曲。可用性:可以根据作者的要求提供用于计算相关函数的蛋白质集和C程序(请参见http://itb.biologie.hu-berlin.de)。

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