Sequence-dependent geometric flexibility of core promoter regions in human genome
作者单位：The National Research Center for Animal Transgenic BiotechnologyInner Mongolia University School of Physical Science and TechnologyInner Mongolia University
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] 071007[理学-遗传学]
关 键 词：Human promoter DNA structural flexibility Transcription initiation regulation Promoter prediction
摘 要：Background:The general framework of promoter mechanism is dependent on protein- DNA interaction in which the different transcription factors(TFs) bind on the promoter region to enable its *** many studies have been taken on this area,the mechanism of transcription regular is still *** it is necessary to investigate promoter sequences in higher dimensions than the sequence alone. Dataset and Methods:The 4263 CpG related and 1683 non-CpG related human promoters were downloaded from the UCSC Genome Browser(http://***/). The sequences with 400 lbp length from 2000bp upstream to 2000bp downstream of the transcription start sites(TSSs the 0th sites) were selected as the core *** on the physical potentials derived from quantum chemical calculations of atomic molecular dynamics (MD) simulations,In this study we introduced physical structural variables by defining three displacements(rise,shift and slide) and three rotation angles(twist,roll and tilt) for each dinucleotide to describe transcription initiation of human promoter. Results:Using 16 experimental parameters of nearest-neighbor dinucleotides based on the structural models,we converted the core-promoter sequence into a string of numerical values for studying the structural *** analysis results reveal that there are significant difference of structural patterns between the CpG related and non-CpG related promoter region,which indicated that the thermodynamic mechanism of transcription initiation for CpG related and non-CpG gene may be *** clearly observed that the structure profiles of CpG related promoter have the enhanced stiffness or flexibility than the non-CpG related promoter,particular in the shift profile and the twist *** believe that the six flexibility parameters will be helpful for further elucidating the transcription initiation regulation and improving the identification accuracy of human promoter.