A RhoGDP dissociation inhibitor spatially regulates growth in root hair cells

Root hairs are cellular protuberances extending from the root surface into the soil; there they provide access to immobile inorganic ions such as phosphate, which are essential for growth. Their cylindrical shape results from a polarized mechanism of cell expansion called tip growth in which elongation is restricted to a small area at the surface of the hair-forming cell (trichoblast) tip. Here we identify proteins that spatially control the sites at which cell growth occurs by isolating Arabidopsis mutants (scn1) that develop ectopic sites of growth on trichoblasts. We cloned SCN1 and showed that SCN1 is a RhoGTPase GDP dissociation inhibitor (RhoGDI) that spatially restricts the sites of growth to a single point on the trichoblast. We showed previously that localized production of reactive oxygen species by RHD2/AtrbohC NADPH oxidase is required for hair growth; here we show that SCN1/AtrhoGDI1 is a component of the mechanism that focuses RHD2/AtrbohC-catalysed production of reactive oxygen species to hair tips during wild-type development. We propose that the spatial organization of growth in plant cells requires the local RhoGDI-regulated activation of the RHD2/AtrbohC NADPH oxidase.     

cdx4 mutants fail to specify blood progenitors and can be rescued by multiple hox genes

Organogenesis is dependent on the formation of distinct cell types within the embryo. Important to this process are the hox genes, which are believed to confer positional identities to cells along the anteroposterior axis. Here, we have identified the caudal-related gene cdx4 as the locus mutated in kugelig (kgg), a zebrafish mutant with an early defect in haematopoiesis that is associated with abnormal anteroposterior patterning and aberrant hox gene expression. The blood deficiency in kgg embryos can be rescued by overexpressing hoxb7a or hoxa9a but not hoxb8a, indicating that the haematopoietic defect results from perturbations in specific hox genes. Furthermore, the haematopoietic defect in kgg mutants is not rescued by scl overexpression, suggesting that cdx4 and hox genes act to make the posterior mesoderm competent for blood development. Overexpression of cdx4 during zebrafish development or in mouse embryonic stem cells induces blood formation and alters hox gene expression. Taken together, these findings demonstrate that cdx4 regulates hox genes and is necessary for the specification of haematopoietic cell fate during vertebrate embryogenesis.     

The Polycomb complex PRC2 and its mark in life

Polycomb group proteins maintain the gene-expression pattern of different cells that is set during early development by regulating chromatin structure. In mammals, two main Polycomb group complexes exist - Polycomb repressive complex 1 (PRC1) and 2 (PRC2). PRC1 compacts chromatin and catalyses the monoubiquitylation of histone H2A. PRC2 also contributes to chromatin compaction, and catalyses the methylation of histone H3 at lysine 27. PRC2 is involved in various biological processes, including differentiation, maintaining cell identity and proliferation, and stem-cell plasticity. Recent studies of PRC2 have expanded our perspectives on its function and regulation, and uncovered a role for non-coding RNA in the recruitment of PRC2 to target genes.     

植物根尖干细胞微环境的遗传调控

干细胞微环境是平衡干细胞自我更新、多向分化和压力响应的微环境.近年来,通过大量的突变体筛选和现代的影像技术,植物根尖干细胞微环境特化和维持的调控机制取得了很大进展.该文着重概述转录因子网络、激素信号转导、染色质因子和基因组组织因子在调控根尖干细胞微环境中的作用.     

束花石斛和黄花石斛的光合特性研究

研究了大花组的束花石斛和黄花石斛的光合生理,结果表明,2种石斛叶片的解剖结构为异面叶,气孔仅分布在下表面,具气孔盖,叶脉维管束鞘不含叶绿体,无花环型结构,具C3植物特征.2种石斛的光补偿点(LCP)和光饱和点(LSP)分别为5～10μmol/(m2.s)和850～900μmol/(m2.s),最大光合速率(Pn)约为6μmol/(m2.s);CO2补偿点和饱和点分别为80～90μmol/mol和800μmol/mol;光合作用的最适温度在26～30℃.Pn日变化为双峰型曲线,首峰出现在11:00左右,最大光合速率在5～6μmol/(m2.s),次峰出现在15:00左右,夜间不吸收CO2.PEPCase活性低,RuBPCase和GO酶活性较高.以上结果表明,束花石斛和黄花石斛光合作用碳同化途径属C3植物类型,具有半阴生植物的特点.     

Rhizobium--plant signal exchange.

Initial stages in the Rhizobium-legume symbiosis can be thought of as a reciprocal molecular conversation: transmission of a gene inducer from legume host to bacterium, with ensuing bacterial synthesis of a morphogen that is transmitted to the plant, switching the developmental fate of the legume root. These signal molecules have a key role in determining bacterium-host specificity and the purified Nod factor compounds provide useful new tools to probe plant cell function.     

中国沙棘营养器官结构特征及其与生境关系的研究

对中国沙棘初生结构的分化和次生生长过程进行了观察。发现沙棘根系角质层发达，外被粘质物，外皮层细胞的细胞壁大量栓质化。根瘤的形成与木质部和皮层有密切关系，弗兰克氏菌的侵入刺激皮层形成大量的薄壁细胞，向外突出形成根瘤。茎的皮层外部细胞较小，排列整齐，细胞壁厚，表皮外有很厚的角质层和一定量的蜡质。叶的结构更加体现了抗旱、耐寒植物的特点，栅栏组织发达，排列紧密，海绵组织不发达，细胞间隙较大，气孔深陷，且具有角质层和密而叠置的星状毛及鳞片等。这些均为生活在旱、寒环境里表现出的适应性。     

植物根尖分生组织干细胞调控模式

静止中心(QC)形成和干细胞区特化是植物根尖分生组织确立的标志。静止中心位于根尖分生组织中心,干细胞围绕在静止中心细胞周围。依赖于生长素的PLT途径和不依赖于生长素的SCR/SHR途径共同发挥维持静止中心细胞稳定的作用。静止中心和干细胞区的柱干细胞之间存在类似于WUS/CLV3的WOX5/ACR4/CLE40的反馈抑制调节途径,该调节途径维持着静止中心细胞和柱干细胞之间的平衡。静止中心和其他类型干细胞之间也可能存在类似的反馈抑制调节途径。生长素、细胞分裂素、赤霉素等植物激素信号在根干细胞功能发挥方面也起到重要作用,与各种基因一起组成根分生组织干细胞调控网络。     

基于广义线性模型的基因表达水平预测

组蛋白修饰是生物体中普遍存在的一种现象,能够以不同的调控方式影响基因表达,且随着高通量测序技术的飞速发展,大量的测序数据使得探究组蛋白修饰信号与基因表达水平之间的内在联系成为可能.由于基因表达数据存在零膨胀现象,提出了一种基于广义线性模型框架的主从模型,能够以较高精度从组蛋白修饰信号预测基因表达水平.首先通过人类全基因组注释文件中的基因位点信息,筛选出包含完整基因位点信息的表达数据;其次,根据基因位点信息,定位并提取出组蛋白修饰数据中基因特定位点的特征信息,构建设计矩阵;最后结合响应变量数据零膨胀的特点,构建主从模型,以GM12878细胞系为例,与现有的多种回归算法进行对比,验证了所提模型的有效性.     

Determinants of nucleosome organization in primary human cells

Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate chromatin remodelling mechanisms have evolved that govern nucleosome organization at promoters, regulatory elements, and other functional regions in the genome. Analyses of chromatin landscape have uncovered a variety of mechanisms, including DNA sequence preferences, that can influence nucleosome positions. To identify major determinants of nucleosome organization in the human genome, we used deep sequencing to map nucleosome positions in three primary human cell types and in vitro. A majority of the genome showed substantial flexibility of nucleosome positions, whereas a small fraction showed reproducibly positioned nucleosomes. Certain sites that position in vitro can anchor the formation of nucleosomal arrays that have cell type-specific spacing in vivo. Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells.     

Three-dimensional chromatin distribution in neuroblastoma nuclei shown by confocal scanning laser microscopy

The relationship between cell shape and function has long been of interest. However, although the behaviour of the cytoskeleton during the cell cycle has been studied extensively variations in the shape and three-dimensional substructure of the nucleus are less well documented. The spatial distribution of chromatin has previously been studied by a mathematical analysis of the optical densities of stained nuclei, allowing an indirect derivation of the three-dimensional distribution of chromatin. More direct information on chromatin organization can be obtained from electron-microscopic serial sections, although this is very laborious. Using an iterative deconvolution algorithm, Agard and Sedat achieved a degree of optical sectioning in conventional fluorescence microscopy and reconstructed the three-dimensional arrangement of polytene chromosomes. We report here on the three-dimensional structure of cultured mammalian cells as visualized by confocal scanning laser microscopy (CSLM). The exceptionally short depth of field of this imaging technique provides direct optical sectioning which, together with its higher resolution, makes CSLM extremely useful for studying the three-dimensional morphology of biological structures.     

DNA triplet repeats mediate heterochromatin-protein-1-sensitive variegated gene silencing

Gene repression is crucial to the maintenance of differentiated cell types in multicellular organisms, whereas aberrant silencing can lead to disease. The organization of DNA into chromatin and heterochromatin is implicated in gene silencing. In chromatin, DNA wraps around histones, creating nucleosomes. Further condensation of chromatin, associated with large blocks of repetitive DNA sequences, is known as heterochromatin. Position effect variegation (PEV) occurs when a gene is located abnormally close to heterochromatin, silencing the affected gene in a proportion of cells. Here we show that the relatively short triplet-repeat expansions found in myotonic dystrophy and Friedreich's ataxia confer variegation of expression on a linked transgene in mice. Silencing was correlated with a decrease in promoter accessibility and was enhanced by the classical PEV modifier heterochromatin protein 1 (HP1). Notably, triplet-repeat-associated variegation was not restricted to classical heterochromatic regions but occurred irrespective of chromosomal location. Because the phenomenon described here shares important features with PEV, the mechanisms underlying heterochromatin-mediated silencing might have a role in gene regulation at many sites throughout the mammalian genome and modulate the extent of gene silencing and hence severity in several triplet-repeat diseases.     

Chromatin organization is a major influence on regional mutation rates in human cancer cells

Cancer genome sequencing provides the first direct information on how mutation rates vary across the human genome in somatic cells. Testing diverse genetic and epigenetic features, here we show that mutation rates in cancer genomes are strikingly related to chromatin organization. Indeed, at the megabase scale, a single feature—levels of the heterochromatin-associated histone modification H3K9me3—can account for more than 40% of mutation-rate variation, and a combination of features can account for more than 55%. The strong association between mutation rates and chromatin organization is upheld in samples from different tissues and for different mutation types. This suggests that the arrangement of the genome into heterochromatin- and euchromatin-like domains is a dominant influence on regional mutation-rate variation in human somatic cells.