去泛素化酶与基因表达调控

泛素化是常见的蛋白质翻译后修饰方式之一,其参与了生物体内细胞分裂与分化、生长发育、转录调节、损伤应激、免疫应答等多方面的生理活动.近年来,泛素研究领域的重要成员之一——去泛素化酶(deubiquitylating enzymes)被不断发现和报道.作为一类可以移除泛素的异肽酶类,去泛素化酶具有结构和功能的多样性.基因表达调控一直是分子遗传学的研究热点,系统整理和总结去泛素化酶与基因表达调控的关系具有重要意义.本文综述了去泛素化酶与基因表达调控的关系,包括去泛素化酶与染色质稳态维持、细胞周期调控和DNA损伤修复等三个方面,并对该领域未来的研究方向进行了预测和讨论.     

植物胚胎发生基因调控的研究进展

植物胚胎发生是指单细胞的受精卵经过一系列受控的细胞分裂和分化,发育为成熟的多细胞种胚的过程,也是一个基因有序的选择性表达调控的过程。主要从胚胎发生的3个时期即原胚期——极性建成、球形胚-心形胚过度期——区域形态建成、器官形成与成熟期——分生组织形成及发育等方面对基因调控的研究进展作一简要综述。     

Creation of the whole human genome microarray

Several companies have recently announced the availability of products that enable a scientist to probe gene expression from the entire human genome on a single DNA microarray. This review will focus on the underlying technological trends that have made this achievement possible, the particular methodologies which are employed to create such microarrays and the implications of the whole human genome microarray for future biological studies. The single genome array represents an important milestone on the path to unraveling the complexity of the cellular networks that control living processes. The microarrays being designed today may, however, become distant ancestors to the whole human genome arrays of the future as our understanding of the functioning of the human genome increases.     

Through a genome, darkly: comparative analysis of plant chromosomal DNA

Plant nuclear genomes encompass a wide range of variation in size and nucleotide composition with diverse arrangements of chromosomal segments, repetitive sequences and distribution of genes. Comparative genomic analysis may be undertaken at different levels of organisation, which are reflected in this review, together with a focus on the genetic and functional significance of the observed variation. Patterns of genome organisation have been revealed which reflect the different underlying mechanisms and constraints driving change. Thus comparative issues of genome size, nucleotide sequence composition and genome heterogeneity are provided as a background to understanding the different levels of segmental and repetitive sequence duplication and distribution of genes. The extent of synteny and collinearity revealed by recent genetic and sequence comparisons is discussed, together with a consideration of problems associated with such analyses. The possible origins and mechanisms of variation in genome size and organisation are covered, including the prevalence of duplication at different levels of organisation. The likely genetic, functional and adaptive consequences of replicated loci are discussed with evidence from comparative studies. The scope for comparative analysis of epigenetic plant genome variation is considered. Finally, opportunities for applying comparative genomics to isolating genes and understanding complex crop genomes are addressed.     

CELL POSITION-DEPENDENT RECIPROCAL FEEDBACK REGULATION OF TYPE I COLLAGEN GENE EXPRESSION IN CULTURED HUMAN SKIN FIBROBLASTS

In order to investigate possible cell positional effects on the gene expression of human dermal fibroblasts, the authors cultured the cells on non-coated polystyrene culture dishes, type I collagen-coated dishes, or collagen gels formed by type I collagen, or suspended them in type I collagen gels and measured collagen synthesis by the cells. The production rate of type I collagen was similar whether cells were cultured on non-coated polystyrene or on type I collagen-coated dishes, but it was suppressed significantly when the cells were placed within the collagen gel matrix. Time-dependent expression of genes for α1(I) and α2(I) collagen chains was measured by Northern blot analysis. A significant increase in mRNA levels for these chains was observed when the cells were cultured for three days on type I collagen-coated dishes or on collagen gels. On the other hand, a significant decrease in the mRNA levels was observed after 2 days and later, when the cells were cultured within type I collagen gel matrix. These results indicate that human dermal fibroblasts recognize their position on or in type I collagen (extracellular matrix) and respond by changing their expression patterns of type I collagen chain genes. The results of the kinetics of gene expression also suggest that upregulation and downregulation of type I collagen genes are controlled by different mechanisms.     

DNA甲基化异常与肿瘤耐药

肿瘤耐药是导致肿瘤化疗失败的主要原因, 其产生机制复杂多样, 是多种因素共同作用的结果。近年来, 表观遗传改变在肿瘤耐药中的作用日益受到关注。DNA甲基化是一种重要的表观遗传修饰, 在调节基因表达和维持基因组稳定性中扮演着重要角色。原发性或获得性耐药的肿瘤细胞大多伴随DNA异常甲基化, 越来越多的证据显示, DNA甲基化异常是肿瘤细胞耐药表型产生的重要机制。文章就DNA甲基化异常与肿瘤细胞耐药的关系及相关作用机制进行了综述。     

Aberrant CpG methylation of the TFAP2A gene constitutes a mechanism for loss of TFAP2A expression in human metastatic melanoma

Metastatic melanoma is a deadly treatment-resistant form of skin cancer whose global incidence is on the rise. During melanocyte transformation and melanoma progression the expression profile of many genes changes. Among these, a gene implicated in several steps of melanocyte development, TFAP2A, is frequently silenced; however, the molecular mechanism of TFAP2A silencing in human melanoma remains unknown. In this study, we measured TFAP2A mRNA expression in primary human melanocytes compared to 11 human melanoma samples by quantitative real-time RT-PCR. In addition, we assessed CpG DNA methylation of the TFAP2A promoter in these samples using bisulfite sequencing. Compared to primary melanocytes, which showed high TFAP2A mRNA expression and no promoter methylation, human melanoma samples showed decreased TFAP2A mRNA expression and increased promoter methylation. We further show that increased CpG methylation correlates with decreased TFAP2A mRNA expression. Using The Cancer Genome Atlas, we further identified TFAP2A as a gene displaying among the most decreased expression in stage 4 melanomas vs. non-stage 4 melanomas, and whose CpG methylation was frequently associated with lack of mRNA expression. Based on our data, we conclude that TFAP2A expression in human melanomas can be silenced by aberrant CpG methylation of the TFAP2A promoter. We have identified aberrant CpG DNA methylation as an epigenetic mark associated with TFAP2A silencing in human melanoma that could have significant implications for the therapy of human melanoma using epigenetic modifying drugs.     

甲基化修饰在细菌表观调控中的功能

为了适应复杂多变的生存环境,微生物通常需要在保证基因组序列不变的前提下不断调整胞内代谢网络。表观调控可以在不改变DNA序列的情况下对基因表达进行调控,因此成为细菌中重要的调控方式。作为一种DNA修饰,DNA甲基化修饰是生物体中最常见的表观调控工具。在本文中我们全面、深入解析了两种孤儿甲基转移酶:DNA腺嘌呤甲基转移酶(DNA adenine methyltransferase,Dam)和细胞周期调控甲基转移酶(Cell cycle-regulated methyltransferase,Ccr M)在原核生物中的表观调控功能。我们主要探讨了DNA甲基化参与的细胞生理过程包括DNA复制起始、DNA错配修复、基因表达调控、致病性和相变异等方面。同时,我们结合三维基因组研究技术基因组结构捕获(Chromosome conformation capture,3C)技术和新型DNA磷硫酰化修饰讨论了该领域的发展前景。     

从少量转染细胞中同时快速提取总RNA和基因组DNA

采用4mol / L LiCl将DNA和RNA分相,建立了同时从少量转染细胞中快速提取细胞总RNA和大分子基因组DNA的方法.与以前的方法相比,本法快速、简便、经济,尤其适合应用在哺乳动物细胞基因表达与调控的研究中．     

DNA甲基化在动植物遗传育种中的研究进展

DNA甲基化是真核生物表观遗传学重要的机制之一,对基因转录水平的表达具有重要的调控作用。近年来,DNA甲基化在动植物遗传育种领域的研究引起了人们广泛的关注。我们从DNA甲基化与基因的表达调控、动植物基因组的甲基化状态、甲基敏感扩增片段多态性方法、DNA甲基化与杂种优势,以及DNA甲基化与分子标记等方面,简要综述了国内外有关DNA甲基化在动植物遗传育种研究中的进展,着重于全基因组DNA甲基化模式在动植物遗传育种中的相关研究和应用。     

Aberrant CpG methylation of the TFAP2A gene constitutes a mechanism for loss of TFAP2A expression in human metastatic melanoma

Metastatic melanoma is a deadly treatment-resistant form of skin cancer whose global incidence is on the rise. During melanocyte transformation and melanoma progression the expression profile of many genes changes. Among these, a gene implicated in several steps of melanocyte development, TFAP2A, is frequently silenced; however, the molecular mechanism of TFAP2A silencing in human melanoma remains unknown. In this study, we measured TFAP2A mRNA expression in primary human melanocytes compared to 11 human melanoma samples by quantitative real-time RT-PCR. In addition, we assessed CpG DNA methylation of the TFAP2A promoter in these samples using bisulfite sequencing. Compared to primary melanocytes, which showed high TFAP2A mRNA expression and no promoter methylation, human melanoma samples showed decreased TFAP2A mRNA expression and increased promoter methylation. We further show that increased CpG methylation correlates with decreased TFAP2A mRNA expression. Using The Cancer Genome Atlas, we further identified TFAP2A as a gene displaying among the most decreased expression in stage 4 melanomas vs. non-stage 4 melanomas, and whose CpG methylation was frequently associated with lack of mRNA expression. Based on our data, we conclude that TFAP2A expression in human melanomas can be silenced by aberrant CpG methylation of the TFAP2A promoter. We have identified aberrant CpG DNA methylation as an epigenetic mark associated with TFAP2A silencing in human melanoma that could have significant implications for the therapy of human melanoma using epigenetic modifying drugs.