DNA Deformations and Interactions with Transcription Fac

DNA 变形及其与转录因子的相互作用

基本信息

项目摘要

During the last fiscal year, we have developed and applied our knowledge-based elastic model of DNA to two closely related problems: positioning of nucleosomes and differential p53-induced regulation of transcription. (1) A novel mechanism of DNA folding in chromatin: Implications for nucleosome positioning. The bending of DNA in nucleosome is accompanied by the lateral displacements of adjacent base pairs, which are usually neglected. We have found, however, that the shear deformation, called Slide, plays a much more important role in DNA folding than was ever imagined. Remarkably, the large Slide deformations imposed on DNA by histones govern both the DNA superhelical trajectory and the positioning of nucleosomes. The energy cost of these deformations is sequence specific - the high-affinity nucleosomal sequences are aligned such that the most easily deformed base-pair steps (TA and CA:TG) occur at sites of large positive Slide and negative Roll (the minor groove bending). Our findings agree with the results of in vitro sequence selection (SELEX) experiments. An important feature of our approach is incorporating all the essential degrees of freedom of 'real' DNA, as opposed to conventional 'elastic rod' model - the latter ignores the lateral Slide displacements of base pairs, and as a result, fails to account for the preferable positioning of the pyrimidine-purine (YR) steps. The close correspondence between the predicted locations of YR dimers and the observed YR sites on high-affinity nucleosomal sequences demonstrates the potential advantage of our 'structural' approach in the prediction of nucleosome positioning. Next, we will use this approach for the analysis of positioning of the linker histones. (2) DNA bending in the tetrameric p53 complex: Sequence analysis in the chromatin context. The tumor suppressor protein p53 acts as a transcription factor when bound to DNA response elements (RE), usually consisting of two decamers RRR-CWWG-YYY separated by a variable spacer (W=A or T; in most cases, the central tetramer is CATG). Earlier, we predicted significant DNA bending and overtwisting upon binding to p53. This year, two dimeric p53-DNA complexes have been resolved crystallographically; both demonstrate CATG bending into the major groove, in accord with our prediction. The p53 core domains are positioned on the outer side of the DNA loop that is important for p53 interaction with the nucleosomal DNA. In other words, wrapping DNA around the histone core can facilitate p53 binding by exposing the cognate DNA site in the bent conformation favorable for the p53-DNA recognition. The functional importance of these findings is best illustrated by comparing the high affinity of p53 to RE associated with cell cycle arrest (CCA-sites), with the low affinity to RE associated with apoptosis (Apo-sites). This difference cannot be explained by the p53-DNA binding constants measured for free DNA. Therefore, we examined the long-range genomic environment of these p53 response elements. Unexpectedly, the Apo-sites are clustered around the transcription start sites (TSS) of the target genes and located within GC-rich regions, while the CCA-sites are scattered further away from the TSS and located in AT-rich regions. Based on our analysis of the high-affinity nucleosomal sequences, we conclude that stable, positioned nucleosomes are likely to form near the CCA-sites, but not near the Apo-sites. Thus, the different nucleosomal organization of the two sets of p53 response elements may be a key factor affecting p53-DNA binding (increasing, in agreement with experimental results, the p53 affinity to the CCA-sites and decreasing its affinity to the sites associated with apoptosis). This example emphasizes direct correlation between the selection of p53-induced tumor suppression pathway (apoptosis or cell cycle arrest) and structural organization of the corresponding p53-binding sites in chromatin.
在上一个财政年度,我们已经开发和应用我们的知识为基础的弹性模型的DNA两个密切相关的问题:定位的核小体和差异p53诱导的转录调控。(1)染色质中DNA折叠的新机制:对核小体定位的影响。核小体中DNA的弯曲伴随着相邻碱基对的侧向位移,而这种位移通常被忽略。然而,我们已经发现,剪切变形,称为滑动,在DNA折叠中起着比想象中更重要的作用。值得注意的是,组蛋白对DNA施加的大的滑动变形控制着DNA超螺旋轨迹和核小体的定位。这些变形的能量消耗是序列特异性的-高亲和力核小体序列被对齐,使得最容易变形的碱基对步骤(TA和CA:TG)发生在大的正滑动和负滚动(小沟弯曲)的位点。我们的发现与体外序列选择(SELEX)实验的结果一致。我们的方法的一个重要特征是结合了"真实的" DNA的所有基本自由度,而不是传统的"弹性杆"模型-后者忽略了碱基对的侧向滑动位移,因此,未能解释嘧啶-嘌呤(YR)步骤的优选定位。YR二聚体的预测位置和高亲和力核小体序列上观察到的YR位点之间的密切对应关系表明了我们的“结构”方法在预测核小体定位中的潜在优势。接下来,我们将使用这种方法来分析连接组蛋白的定位。(2)四聚体p53复合物中的DNA弯曲:染色质背景下的序列分析。肿瘤抑制蛋白p53在与DNA反应元件(RE)结合时充当转录因子,所述DNA反应元件通常由两个十聚体RRR-CWWG-YYY组成,所述十聚体由可变间隔区(W = A或T;在大多数情况下,中心四聚体是CATG)分隔。早些时候,我们预测了与p53结合后显著的DNA弯曲和过度扭曲。今年,两个二聚体p53-DNA复合物已被解析结晶,都证明CATG弯曲到大沟,在雅阁与我们的预测。p53核心结构域位于DNA环的外侧,这对于p53与核小体DNA的相互作用是重要的。换句话说,将DNA包裹在组蛋白核心周围可以通过暴露有利于p53-DNA识别的弯曲构象中的同源DNA位点来促进p53结合。通过比较p53对与细胞周期停滞相关的RE的高亲和力(CCA位点)和对与细胞凋亡相关的RE的低亲和力(Apo位点),最好地说明了这些发现的功能重要性。这种差异不能用游离DNA的p53-DNA结合常数来解释。因此,我们研究了这些p53反应元件的长程基因组环境。出乎意料的是,Apo位点聚集在靶基因的转录起始位点(TSS)周围并位于GC富集区域内,而CCA位点远离TSS分散并位于AT富集区域内。根据我们对高亲和力核小体序列的分析,我们得出结论,稳定、定位的核小体可能在CCA位点附近形成,但在Apo位点附近不形成。因此,两组p53反应元件的不同核小体组织可能是影响p53-DNA结合的关键因素(与实验结果一致,增加p53对CCA位点的亲和力,并降低其对与凋亡相关的位点的亲和力)。本实施例强调了p53诱导的肿瘤抑制途径(细胞凋亡或细胞周期停滞)的选择与染色质中相应p53结合位点的结构组织之间的直接相关性。

项目成果

期刊论文数量(7)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Iodine-125 radioprobing of E. coli RNA polymerase transcription elongation complexes.
大肠杆菌 RNA 聚合酶转录延伸复合物的碘 125 放射性探测。
  • DOI:
    10.1016/s0076-6879(03)71007-6
  • 发表时间:
    2003
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Karamychev,ValeriN;Tatusov,Alexei;Komissarova,Natalia;Kashlev,Mikhail;Neumann,RonaldD;Zhurkin,VictorB;Panyutin,IgorG
  • 通讯作者:
    Panyutin,IgorG
DNA trajectory in the Gal repressosome.
Gal 阻抑体中的 DNA 轨迹。
  • DOI:
    10.1101/gad.1209404
  • 发表时间:
    2004
  • 期刊:
  • 影响因子:
    10.5
  • 作者:
    Semsey,Szabolcs;Tolstorukov,MichailY;Virnik,Konstantin;Zhurkin,VictorB;Adhya,Sankar
  • 通讯作者:
    Adhya,Sankar
Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin.
通过 2-氨基嘌呤或 6-甲基异黄蝶呤的荧光监测分子内三链 DNA 结构的形成。
  • DOI:
    10.1093/nar/gkh158
  • 发表时间:
    2004
  • 期刊:
  • 影响因子:
    14.9
  • 作者:
    Shchyolkina,AnnaK;Kaluzhny,DmitryN;Borisova,OlgaF;Hawkins,MaryE;Jernigan,RobertL;Jovin,ThomasM;Arndt-Jovin,DonnaJ;Zhurkin,VictorB
  • 通讯作者:
    Zhurkin,VictorB
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Victor Zhurkin其他文献

Victor Zhurkin的其他文献

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{{ truncateString('Victor Zhurkin', 18)}}的其他基金

p53-induced Regulation of Transcription in the Chromatin Context
p53 诱导的染色质转录调节
  • 批准号:
    9153693
  • 财政年份:
  • 资助金额:
    --
  • 项目类别:
p53-induced Regulation of Transcription in the Chromatin Context
p53 诱导的染色质转录调节
  • 批准号:
    7733278
  • 财政年份:
  • 资助金额:
    --
  • 项目类别:
p53-induced Regulation of Transcription in the Chromatin Context
p53 诱导的染色质转录调节
  • 批准号:
    9556386
  • 财政年份:
  • 资助金额:
    --
  • 项目类别:
DNA Folding in Chromatin at the Supra-nucleosome Level
核小体上水平的染​​色质 DNA 折叠
  • 批准号:
    10014465
  • 财政年份:
  • 资助金额:
    --
  • 项目类别:
p53-induced Regulation of Transcription in the Chromatin Context
p53 诱导的染色质转录调节
  • 批准号:
    10014467
  • 财政年份:
  • 资助金额:
    --
  • 项目类别:
DNA Folding in Chromatin and Interaction with Transcription Factors
染色质中的 DNA 折叠及其与转录因子的相互作用
  • 批准号:
    8157498
  • 财政年份:
  • 资助金额:
    --
  • 项目类别:
DNA Deformations and Interactions with Transcription Fac
DNA 变形及其与转录因子的相互作用
  • 批准号:
    7291749
  • 财政年份:
  • 资助金额:
    --
  • 项目类别:
DNA Folding in Chromatin and Interaction with Transcription Factors
染色质中的 DNA 折叠及其与转录因子的相互作用
  • 批准号:
    8552858
  • 财政年份:
  • 资助金额:
    --
  • 项目类别:
p53-induced Regulation of Transcription in the Chromatin Context
p53 诱导的染色质转录调节
  • 批准号:
    7965754
  • 财政年份:
  • 资助金额:
    --
  • 项目类别:
p53-induced Regulation of Transcription in the Chromatin Context
p53 诱导的染色质转录调节
  • 批准号:
    8349201
  • 财政年份:
  • 资助金额:
    --
  • 项目类别:

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Crumple Dynamics and Interactions Mediating Elastic Deformations of Structures
调节结构弹性变形的压皱动力学和相互作用
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DNA 变形及其与转录因子的相互作用
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