Predicting recombination hotspots in yeast based on DNA sequence and chromatin structure
作者单位：School of MathematicsPhysics and Biological EngineeringInner Mongolia University of Science and Technology The Institute of Bioengineering and TechnologyInner Mongolia University of Science and Technology
会议名称：《第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学》
会议日期：2012年
学科分类：0710[理学-生物学] 07[理学] 08[工学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 0836[工学-生物工程] 090102[农学-作物遗传育种]
关 键 词：Recombination hotspots Nucleosome IDQD
摘 要：Background:Meiotic recombination does not occur evenly across the genome,but instead occurs at relatively high frequencies in some genomic regions(hotspots) and relatively low frequencies in others(coldspots).Recombination depends not only on sequence features, but also on chromatin *** and characterization of hotspots and coldspots are considerably significant for that information about hotspots/coldspots would shed light on the mechanism of recombination and genome *** of high-resolution recombination rates using genetic experiments is time-consuming and ***,it is necessary to develop computational methods to predict recombination rates or recombination hotspots in the *** far,there is no model for predicting recombination hotspots in which chromatin structure is *** this study,we analyzed the correlation between recombination and nucleosome occupancy,and presented a model for predicting recombination hotspots based on the sequence and nucleosome occupancy in yeast. Methods:The relationship between recombination and nucleosome occupancy is estimated by Pearson correlation.A model based on IDQD(increment of diversity combined with quadratic discriminant) algorithm using tetranucleotide frequencies in sequences and nucleosome occupancy as features is developed to predict recombination hotspots/coldspots in yeast. Results:Our results show that the regions with high nucleosome occupancy have high recombination rate in the yeast *** correlation between genome-wide recombination rate and nucleosome occupancy is significant(R-0.151,P0.001).The prediction accuracy of hotspots based on sequence alone is 80%.The prediction accuracy increased to 81.6%when nucleosome occupancy is used as an additional feature. Conclusion:Our data show that recombination is significantly positively correlated with nucleosome occupancy in the yeast genome,and hotspots prediction accuracy is improved when nucleosom