基于位置权重矩阵的核小体识别及功能分析

为研究高通量的人类CD4+T细胞的核小体定位模式,使用迭代算法对核小体定位模式进行分类,并利用位置权重矩阵方法分别构建稳定核小体定位序列、动态核小体定位序列和连接区序列模型,通过十倍交叉验证评估模型性能,并与Segal方法与弯曲度方法进行比较,发现位置权重矩阵方法在敏感性、精度和准确性方面都具有一定优越性。同时采用滑窗法在全基因组选取候选序列进行核小体识别,挖掘核小体定位相关基因,并进行基因生物学进程功能富集分析,发现稳定与动态核小体、真实与潜在核小体对应的基因所参与调控的生物学过程各有不同,但也有一些生物学过程为不同类别核小体所共有,例如对细胞内大分子的调控功能。     

核小体定位研究进展

核小体定位在诸如转录调控、DNA复制和修复等多种细胞过程中起着重要作用。基因组上核小体位置的确定涉及DNA、转录因子、组蛋白修饰酶和染色质重塑复合体之间的相互作用。核小体定位、组蛋白修饰、染色质重塑等问题已成为目前遗传学研究的热点——表观遗传学——的重要研究内容。文章从核小体定位基本概念、核小体定位与基因表达调控的关系、核小体定位实验研究和理论预测工作等几个方面总结了核小体定位的最新研究进展。     

酿酒酵母YPH499 Ⅲ号染色体上ARS形成核小体能力的比较

核小体定位是复制起始调控的重要因素,但是核小体定位是如何调控真核生物的复制起始,目前还不是很清楚。研究酵母Ⅲ号染色体上的不同活性复制起始序列形成核小体能力对探究真核生物DNA复制起始机制有着重要的生物学意义。酿酒酵母Ⅲ号染色体上的10个复制起始序列分为高活性和低活性两组复制起始序列,利用核小体体外组装技术,将回收纯化的高活性和低活性复制起始序列分别与组蛋白八聚体在体外进行梯度盐透析组装形成核小体,并进行Biotin标记检测,然后用Image J软件分析不同复制起始序列组装形成核小体能力的强弱。结果表明,用Image J软件对核小体组装能力强弱进行分析:ARS304ARS303ARS313ARS302ARS306ARS314,ARS305,ARS307,ARS309,ARS315。低活性复制起始序列较高活性复制起始序列更易形成核小体;复制起始位点偏好出现于核小体缺乏区。     

基于DNA变形能的核小体定位预测方法研究进展

真核细胞中,作为染色质基本结构单元的核小体参与调控基因的转录、DNA复制、重组以及RNA剪接等诸多生物学过程。阐明核小体定位机制并准确预测核小体在染色体上的位置对解读染色质结构与功能有重要生物学意义。在过去30多年时间里,研究人员发展了多种预测核小体位置的方法。最理想的方法应考虑DNA序列、组蛋白修饰和染色质重塑等影响核小体定位的诸多因素,然而现实中,捕捉主要因素的模型也往往具有很高的鲁棒性和实用价值。DNA序列偏好性是在全基因组尺度上影响核小体定位的最重要因素之一,因此基于DNA序列的核小体定位预测方法也最常见。这种方法可大致分为两类,即基于DNA序列信息的生物信息学模型和基于DNA变形能的生物物理学模型。本文重点介绍生物物理学模型近些年取得的主要进展。     

两种模式生物核小体定位比较研究

在对两种模式生物酵母与果蝇胚胎期核小体定位进行研究时,发现不同物种间以及同一物种中不同表达模式基因上的核小体分布呈现出差显著异性。在总体上,转录起始位点附近的酵母核小体NFR区域比果蝇的NFR短。经基因中心对齐后,酵母与果蝇胚胎期沉默型基因的核小体缺失区域的两个边界中间处共同呈现了一个明确有着均匀间隔的核小体数n,且随着基因长度L的变长其周期性特性逐渐变模糊,但果蝇的图谱表现的更为复杂。结果表明,从单细胞酵母生物到多细胞果蝇生物间基因组的进化过程中,核小体组织的演化既有变异性,也具有保守性。     

人类基因组核苷酸多态性位点核小体定位分析

研究人类基因组核苷酸多态性位点周围核小体的定位,对于分析核苷酸的变异机制有重要意义.分析了人类基因组单核苷酸多态性(SNP)位点、简单插入位点、插入删除位点和删除位点的分布规律,以及这些位点周围的核小体定位特征.结果表明:转录起始位点下游的核苷酸多态性位点分布呈现约211 bp的周期特征,单核苷多态位点另有一个146 bp的周期;约211 bp的周期与转录起始位点下游核小体的分布周期204 bp非常接近,146 bp的周期恰是核小体核心DNA的长度.这些结果说明核小体与多态性位点的分布关系密切.进一步研究证实,单核苷酸多态性位点多分布于核心DNA上,且多位于核心DNA的两端,这使得单核苷酸多态性位点具有146 bp周期,而插入、插入删除、删除多态性位点多分布于核小体排开区域,间隔约为204 bp.转录起始位点下游核小体等间隔的规则分布使得多态性位点的分布也具有周期性.研究表明,相对于核小体,不同类型变异发生的位置不同,核小体定位在基因组多态性位点的形成过程中具有重要作用.     

基于遗传算法酵母核小体定位性质预测

在DNA序列上,定位模糊的特殊核小体与定位良好的普通核小体同时存在于染色体区域内,但由于二者的化学性质差异不明显,区分较为困难。本文针对实验核小体在真核基因转录起始位点周围的分布规律和保守性建立了一个核小体分布模型,并在前人所做的预测核小体位置的工作基础上,利用遗传算法寻找模型上不同性质核小体的分布中心,构建核小体定位性质判别准则,最终确定了转录起始位点上、下游定位良好和模糊核小体的位置。     

核小体定位的转录调控功能研究进展

核小体是真核生物染色质的基本组成单位,组蛋白八聚体在DNA 双螺旋上精确位置称为核小体定位．核小体定位已被证实在基因转录调控、DNA复制与修复、调控进化等过程中扮演着重要的角色．随着染色质免疫共沉淀-芯片(ChIP-chip)与染色质免疫共沉淀-测序(ChIP-seq)等高通量技术的出现,已测定了多种模式生物全基因组核小体定位图谱,掀起了一股核小体定位及其功能的研究热潮,并取得了一定的成果．本文介绍了核小体定位的概念,总结了核小体在启动子与编码区域内定位的基本模式．在此基础上,综述了核小体定位在转录起始、转录延伸、基因表达模式多样化以及可变剪接等方面的功能研究进展．     

核小体定位与RNA剪接

根据核小体定位序列和缺失序列的碱基分布特征,应用多样性增量二次判别方法(IDQD)构建模型对这两类序列进行了区分,受试者操作特性曲线下的面积达到了0.958．应用这一模型研究了核小体在人类基因组剪接位点(GT/AG)邻近序列中的分布方式,发现外显子所对应的DNA序列通常倾向参与核小体的形成,并且由它所转录的RNA统计上具有较强的刚性,而剪接位点及其邻近的内含子对应的DNA序列则避免参与核小体的形成,所转录的RNA统计上具有较强的柔性．进一步还发现,DNA序列的核小体定位/缺失和RNA的刚性/柔性具有统计相关性,为从机制上解释为何前体RNA剪接事件与DNA序列中的核小体定位信息有关提供了依据．     

酿酒酵母人造纤维小体的研究进展

纤维素乙醇的统合生物加工过程(consolidated bioprocessing,CBP)是将(半)纤维素酶生产、纤维素水解和乙醇发酵过程组合,通过一种微生物完成的生物加工过程。CBP有利于降低生物转化过程的成本,受到研究者的普遍关注。酿酒酵母(Saccharomyces cerevisiae)作为传统的乙醇生产菌株,是极具潜力的CBP底盘细胞。纤维小体是某些厌氧微生物细胞表面由纤维素酶系与支架蛋白组成的大分子复合物,它能高效降解木质纤维,在酿酒酵母表面展示纤维小体已成为构建CBP细胞的研究热点。笔者综述了人造纤维小体在酿酒酵母细胞表面展示组装的研究进展,重点阐述了纤维小体各元件的设计和改造,并针对酿酒酵母分泌途径的改造,提出提高人造纤维小体分泌组装的可能性策略。     

In vitro assay of squalene epoxidase of Saccharomyces cerevisiae

We describe a simple assay for measuring squalene epoxidase specific activity in Saccharomyces cerevisiae cell-free extracts, by using [14C] farnesyl pyrophosphate as substrate. Cofactor requirements for activity are FAD and NADPH or NADH, NADPH being the preferred reduced pyridine nucleotide. Squalene epoxidase activity is localized in microsomal fraction and no supernatant soluble factor is required for maximum activity. Microsomal fraction converted farnesyl pyrophosphate into squalene, squalene 2,3-epoxide and lanosterol, showing that squalene 2,3-epoxide-lanosterol cyclase is also a microsome-bound enzyme. We show also that squalene epoxidase activity is not inhibited by ergosterol or lanosterol, but that enzyme synthesis is induced by oxygen.     

In vitro reactions of vacuole inheritance in Saccharomyces cerevisiae

Vacuole inheritance is temporally coordinated with the cell cycle and is restricted spatially to an axis between the maternal vacuole and the bud. The new bud vacuole is founded by a stream of vacuole-derived membranous vesicles and tubules which are transported from the mother cell into the bud to form the daughter organelle. We now report in vitro formation of vacuole-derived tubules and vesicles. In semi-intact cells, formation of tubulovesicular structures requires ATP and the proteins encoded by VAC1 and VAC2, two genes which are required for vacuole inheritance in vivo. Isolation of vacuoles from cell lysates before in vitro incubation reveals that formation of tubulovesicular structures requires cytosol as well as ATP. After forming tubulovesicular structures, isolated vacuoles subsequently increase in size. Biochemical assays reveal that this increase results from vacuole to vacuole fusion, leading to mixing of organellar contents. Intervacuolar fusion is sensitive to the phosphatase inhibitors microcystin-LR and okadaic acid, suggesting that protein phosphorylation/dephosphorylation reactions play a role in this event.     

Nucleosome depletion alters the chromatin structure of Saccharomyces cerevisiae centromeres.

Saccharomyces cerevisiae centromeric DNA is packaged into a highly nuclease-resistant chromatin core of approximately 200 base pairs of DNA. The structure of the centromere in chromosome III is somewhat larger than a 160-base-pair nucleosomal core and encompasses the conserved centromere DNA elements (CDE I, II, and III). Extensive mutational analysis has revealed the sequence requirements for centromere function. Mutations affecting the segregation properties of centromeres also exhibit altered chromatin structures in vivo. Thus the structure, as delineated by nuclease digestion, correlated with functional centromeres. We have determined the contribution of histone proteins to this unique structural organization. Nucleosome depletion by repression of either histone H2B or H4 rendered the cell incapable of chromosome segregation. Histone repression resulted in increased nuclease sensitivity of centromere DNA, with up to 40% of CEN3 DNA molecules becoming accessible to nucleolytic attack. Nucleosome depletion also resulted in an alteration in the distribution of nuclease cutting sites in the DNA surrounding CEN3. These data provide the first indication that authentic nucleosomal subunits flank the centromere and suggest that nucleosomes may be the central core of the centromere itself.     

Nucleosome positioning,nucleotide excision repair and photoreactivation in Saccharomyces cerevisiae

The position of nucleosomes on DNA participates in gene regulation and DNA replication. Nucleosomes can be repressors by limiting access of factors to regulatory sequences, or activators by facilitating binding of factors to exposed DNA sequences on the surface of the core histones. The formation of UV induced DNA lesions, like cyclobutane pyrimidine dimers (CPDs), is modulated by DNA bending around the core histones. Since CPDs are removed by nucleotide excision repair (NER) and photolyase repair, it is of paramount importance to understand how DNA damage and repair are tempered by the position of nucleosomes. In vitro, nucleosomes inhibit NER and photolyase repair. In vivo, nucleosomes slow down NER and considerably obstruct photoreactivation of CPDs. However, over-expression of photolyase allows repair of nucleosomal DNA in a second time scale. It is proposed that the intrinsic abilities of nucleosomes to move and transiently unwrap could facilitate damage recognition and repair in nucleosomal DNA.     

Structure-based Analysis of DNA Sequence Patterns Guiding Nucleosome Positioning in vitro

Abstract

Recent studies of genome-wide nucleosomal organization suggest that the DNA sequence is one of the major determinants of nucleosome positioning. Although the search for underlying patterns encoded in nucleosomal DNA has been going on for about 30 years, our knowledge of these patterns still remains limited. Based on our evaluations of DNA deformation energy, we developed new scoring functions to predict nucleosome positioning. There are three principal differences between our approach and earlier studies: (i) we assume that the length of nucleosomal DNA varies from 146 to 147 bp; (ii) we consider the anisotropic flexibility of pyrimidine-purine (YR) dimeric steps in the context of their neighbors (e.g., YYRR versus RYRY); (iii) we postulate that alternating AT-rich and GC-rich motifs reflect sequence-dependent interactions between histone arginines and DNA in the minor groove. Using these functions, we analyzed 20 nucleosome positions mapped in vitro at single nucleotide resolution (including clones 601, 603, 605, the pGUB plasmid, chicken β-globin and three 5S rDNA genes). We predicted 15 of the 20 positions with 1-bp precision, and two positions with 2-bp precision. The predicted position of the ‘601’ nucleosome (i.e., the optimum of the computed score) deviates from the experimentally determined unique position by no more than 1 bp—an accuracy exceeding that of earlier predictions.

Our analysis reveals a clear heterogeneity of the nucleosomal sequences which can be divided into two groups based on the positioning ‘rules’ they follow. The sequences of one group are enriched by highly deformable YR/YYRR motifs at the minor-groove bending sites SHL ±3.5 and ±5.5, which is similar to the α-satellite sequence used in most crystallized nucleosomes. Apparently, the positioning of these nucleosomes is determined by the interactions between histones H2A/H2B and the terminal parts of nucleosomal DNA. In the other group (that includes the ‘601’ clone) the same YR/YYRR motifs occur predominantly at the sites SHL ±1.5. The interaction between the H3/H4 tetramer and the central part of the nucleosomal DNA is likely to be responsible for the positioning of nucleosomes of this group, and the DNA trajectory in these nucleosomes may differ in detail from the published structures.

Thus, from the stereochemical perspective, the in vitro nucleosomes studied here follow either an X-ray-like pattern (with strong deformations in the terminal parts of nucleosomal DNA), or an alternative pattern (with the deformations occurring predominantly in the central part of the nucleosomal DNA). The results presented here may be useful for genome-wide classification of nucleosomes, linking together structural and thermodynamic characteristics of nucleosomes with the underlying DNA sequence patterns guiding their positions.     

The DNA Sequence-dependence of Nucleosome Positioning in vivo and in vitro

Abstract

The contribution of histone-DNA interactions to nucleosome positioning in vivo is currently a matter of debate. We argue here that certain nucleosome positions, often in promoter regions, in yeast may be, at least in part, specified by the DNA sequence. In contrast other positions may be poorly specified. Positioning thus has both statistical and DNA-determined components. We further argue that the relative affinity of the octamer for different DNA sequences can vary and therefore the interaction of histones with the DNA is a ‘tunable’ property.