现代系统生物技术与图式遗传学

基因组程序化表达调控与生物体形态结构发生的相互对应是图式遗传学和系统生物技术研究复杂生物系统的核心。基因-蛋白质表达与神经-内分泌信号,构成生物系统发生演变的双向调控过程是生物信息控制系统的结构、功能和演变的基础。细胞信号传导与基因差异表达调控是从基因、细胞到器官的细胞动力学转换系统,是基因、蛋白质、脂类等生物高分子相互作用与细胞再生、分化、迁移、凋亡的程序化调控节律,也就是基因定位图谱-细胞定位图谱的基因组-蛋白质组与生物体的细胞节律-形态的发生转换过程。     

Applications of single cell RNA sequencing to research of stem cells

Stem cells(SCs) with their self-renewal and pluripotent differentiation potential,show great promise for therapeutic applications to some refractory diseases such as stroke, Parkinsonism, myocardial infarction, and diabetes. Furthermore, as seed cells in tissue engineering, SCs have been applied widely to tissue and organ regeneration. However, previous studies have shown that SCs are heterogeneous and consist of many cell subpopulations. Owing to this heterogeneity of cell states, gene expression is highly diverse between cells even within a single tissue,making precise identification and analysis of biological properties difficult, which hinders their further research and applications. Therefore, a defined understanding of the heterogeneity is a key to research of SCs. Traditional ensemble-based sequencing approaches, such as microarrays, reflect an average of expression levels across a large population, which overlook unique biological behaviors of individual cells, conceal cell-to-cell variations, and cannot understand the heterogeneity of SCs radically. The development of high throughput single cell RNA sequencing(scRNA-seq) has provided a new research tool in biology, ranging from identification of novel cell types and exploration of cell markers to the analysis of gene expression and predicating developmental trajectories. scRNA-seq has profoundly changed our understanding of a series of biological phenomena. Currently, it has been used in research of SCs in many fields, particularly for the research of heterogeneity and cell subpopulations in early embryonic development. In this review, we focus on the scRNA-seq technique and its applications to research of SCs.     

Physical forces modulate cell differentiation and proliferation processes

Currently, the predominant hypothesis explains cellular differentiation and behaviour as an essentially genetically driven intracellular process, suggesting a gene‐centrism paradigm. However, although many living species genetic has now been described, there is still a large gap between the genetic information interpretation and cell behaviour prediction. Indeed, the physical mechanisms underlying the cell differentiation and proliferation, which are now known or suspected to guide such as the flow of energy through cells and tissues, have been often overlooked. We thus here propose a complementary conceptual framework towards the development of an energy‐oriented classification of cell properties, that is, a mitochondria‐centrism hypothesis based on physical forces‐driven principles. A literature review on the physical–biological interactions in a number of various biological processes is analysed from the point of view of the fluid and solid mechanics, electricity and thermodynamics. There is consistent evidence that physical forces control cell proliferation and differentiation. We propose that physical forces interfere with the cell metabolism mostly at the level of the mitochondria, which in turn control gene expression. The present perspective points towards a paradigm shift complement in biology.     

New technologies to study helminth development and host-parasite interactions

How parasites develop and survive, and how they stimulate or modulate host immune responses are important in understanding disease pathology and for the design of new control strategies. Microarray analysis and bulk RNA sequencing have provided a wealth of data on gene expression as parasites develop through different life-cycle stages and on host cell responses to infection. These techniques have enabled gene expression in the whole organism or host tissue to be detailed, but do not take account of the heterogeneity between cells of different types or developmental stages, nor the spatial organisation of these cells. Single-cell RNA-seq (scRNA-seq) adds a new dimension to studying parasite biology and host immunity by enabling gene profiling at the individual cell level. Here we review the application of scRNA-seq to establish gene expression cell atlases for multicellular helminths and to explore the expansion and molecular profile of individual host cell types involved in parasite immunity and tissue repair. Studying host-parasite interactions in vivo is challenging and we conclude this review by briefly discussing the applications of organoids (stem-cell derived mini-tissues) to examine host-parasite interactions at the local level, and as a potential system to study parasite development in vitro. Organoid technology and its applications have developed rapidly, and the elegant studies performed to date support the use of organoids as an alternative in vitro system for research on helminth parasites.     

The large-scale evolution by generating new genes from gene duplication; similarity and difference between monoploid and diploid organisms

On the basis of the concept of biological activity, the large-scale evolution by generating new genes from gene duplication is theoretically compared between the monoploid organism and the diploid organism. The comparison is carried out not only for the process of generating one new gene but also for the process of generating two or more kinds of new genes from successive gene duplication. This comparison reveals the following difference in evolutionary pattern between the monoploids and diploids. The monoploid organism is more suitable to generate one or two new genes step by step but its successive gene duplication is obliged to generate smaller sizes of genes by the severer lowering of biological activity or self-reproducing rate. This is consistent with the evolutionary pattern of prokaryotes having steadily developed chemical syntheses, O₂-releasing photosynthesis and O₂-respiration in the respective lineages. On the other hand, the diploid organism with the plural number of homologous chromosome pairs has a chance to get together many kinds of new genes by the hybridization of variants having experienced different origins of gene duplication. Although this strategy of hybridization avoids the severe lowering of biological activity, it takes the longer time to establish the homozygotes of the more kinds of new genes. During this long period, furthermore different types of variants are accumulated in the population, and their successive hybridization sometimes yields various styles of new organisms. This evolutionary pattern explains the explosive divergence of body plans that has occasionally occurred in the diploid organisms, because the cell differentiation is a representative character exhibited by many kinds of genes and its evolution to the higher hierarchy constructs body plans.     

Stem cell dogmas in the genomics era

Recently, much excitement has been generated by strong suggestions that stem cells isolated from diverse somatic tissues may have a previously unsuspected degree of developmental or differentiation plasticity. For example, a hematopoietic stem cell may be capable of producing mature liver cells, muscle tissue or even neurons. Similarly, central nervous system stem cells or muscle stem cells may be capable of producing mature blood cell populations. These observations have called into question several fundamental dogmas of developmental biology. In addition, these observations offer extraordinary promise in the clinical setting. It is of paramount importance to rigorously assess the suggested plasticity phenomena using precise clonal analysis. In order to explore the plasticity phenomena in more direct ways, it is necessary to develop in vitro systems where such behavior can be recapitulated in a well-defined setting. Finally, stem cell plasticity will be governed, at least in part, by cell-autonomous mechanisms: that is, those mediated by the panel of gene products expressed in stem cells. Therefore, it is necessary to identify the complete gene expression profile that defines the stem cell.     

An abstract cell model that describes the self-organization of cell function in living systems

The principal aim of systems biology is to search for general principles that govern living systems. We develop an abstract dynamic model of a cell, rooted in Mesarovi? and Takahara's general systems theory. In this conceptual framework the function of the cell is delineated by the dynamic processes it can realize. We abstract basic cellular processes, i.e., metabolism, signalling, gene expression, into a mapping and consider cell functions, i.e., cell differentiation, proliferation, etc. as processes that determine the basic cellular processes that realize a particular cell function. We then postulate the existence of a 'coordination principle' that determines cell function. These ideas are condensed into a theorem: If basic cellular processes for the control and regulation of cell functions are present, then the coordination of cell functions is realized autonomously from within the system. Inspired by Robert Rosen's notion of closure to efficient causation, introduced as a necessary condition for a natural system to be an organism, we show that for a mathematical model of a self-organizing cell the associated category must be cartesian closed. Although the semantics of our cell model differ from Rosen's (M,R)-systems, the proof of our theorem supports (in parts) Rosen's argument that living cells have non-simulable properties. Whereas models that form cartesian closed categories can capture self-organization (which is a, if not the, fundamental property of living systems), conventional computer simulations of these models (such as virtual cells) cannot. Simulations can mimic living systems, but they are not like living systems.     

miRNA的生物形成及调控基因表达机制

微RNA(microRNA,miRNA)通过调节靶基因的表达水平影响细胞分化、增殖、凋亡等特性,在生物的生长发育和疾病发生发展中发挥重要的作用。将miRNA用于基因功能研究,药物靶点验证,基因治疗等领域有非常好的前景。揭示miRNA的生成和加工过程以及miRNA调节靶基因基因表达水平的作用机制对于阐述miRNA在生理病理过程中的作用有重要意义。因此,本文对miRNA的发生,成熟以及作用机制的研究进展作综述。     

Type II arginine methyltransferase PRMT5 regulates gene expression of inhibitors of differentiation/DNA binding Id2 and Id4 during glial cell differentiation

PRMT5 is a type II protein arginine methyltranferase that catalyzes monomethylation and symmetric dimethylation of arginine residues. PRMT5 is functionally involved in a variety of biological processes including embryo development and circadian clock regulation. However, the role of PRMT5 in oligodendrocyte differentiation and central nervous system myelination is unknown. Here we show that PRMT5 expression gradually increases throughout postnatal brain development, coinciding with the period of active myelination. PRMT5 expression was observed in neurons, astrocytes, and oligodendrocytes. siRNA-mediated depletion of PRMT5 in mouse primary oligodendrocyte progenitor cells abrogated oligodendrocyte differentiation. In addition, the PRMT5-depleted oligodendrocyte progenitor and C6 glioma cells expressed high levels of the inhibitors of differentiation/DNA binding, Id2 and Id4, known repressors of glial cell differentiation. We observed that CpG-rich islands within the Id2 and Id4 genes were bound by PRMT5 and were hypomethylated in PRMT5-deficient cells, suggesting that PRMT5 plays a role in gene silencing during glial cell differentiation. Our findings define a role of PRMT5 in glial cell differentiation and link PRMT5 to epigenetic changes during oligodendrocyte differentiation.     

Epigenetic mechanisms that regulate cell identity

Individual cell fate decisions can vary according to changes in gene expression in response to environmental, developmental, or metabolic cues. This plasticity is tightly regulated during embryonic development and mediated by the exquisitely coordinated activation and repression of groups of genes. Genes that become repressed are immersed in a condensed chromatin environment that renders them refractory to stimulation. This mechanism is responsible for both the loss of cell plasticity during differentiation and the preservation of cell identity. Understanding the molecular events involved in the establishment and maintenance of these restrictive domains will benefit the design of strategies for cellular reprogramming, differentiation, and cancer treatment.     

Allele-specific gene expression and epigenetic modifications and their application to understanding inheritance and cancer

Epigenetic information is characterized by its plasticity during development and differentiation as well as its stable transmission during mitotic cell divisions in somatic tissues. This duality contrasts to genetic information, which is essentially static and identical in every cell in an organism with only a few exceptions such as immunoglobulin genes in lymphocytes. Epigenetics is traditionally perceived as a means to regulate gene expression without a change in DNA sequence. This, however, does not exclude a potential role for genetic variations in providing differential backgrounds on which epigenetic modulations and their regulatory consequences are achieved. An effective approach to investigating the interplay between genetic variations and epigenetic variations is through allele-specific analysis of epigenetics and gene expression. Such studies have generated many new insights into functions of genetic variations, mechanisms of gene expression regulation, and the role of mutations and epigenetic alterations in human cancer. This article is part of a Special Issue entitled: Chromatin in time and space.     

Roles of cell-intrinsic and microenvironmental factors in photoreceptor cell differentiation

Photoreceptor differentiation requires the coordinated expression of numerous genes. It is unknown whether those genes share common regulatory mechanisms or are independently regulated by distinct mechanisms. To distinguish between these scenarios, we have used in situ hybridization, RT-PCR, and real-time PCR to analyze the expression of visual pigments and other photoreceptor-specific genes during chick embryo retinal development in ovo, as well as in retinal cell cultures treated with molecules that regulate the expression of particular visual pigments. In ovo, onset of gene expression was asynchronous, becoming detectable at the time of photoreceptor generation (ED 5-8) for some photoreceptor genes, but only around the time of outer segment formation (ED 14-16) for others. Treatment of retinal cell cultures with activin, staurosporine, or CNTF selectively induced or down-regulated specific visual pigment genes, but many cognate rod- or cone-specific genes were not affected by the treatments. These results indicate that many photoreceptor genes are independently regulated during development, are consistent with the existence of at least two distinct stages of gene expression during photoreceptor differentiation, suggest that intrinsic, coordinated regulation of a cascade of gene expression triggered by a commitment to the photoreceptor fate is not a general mechanism of photoreceptor differentiation, and imply that using a single photoreceptor-specific "marker" as a proxy to identify photoreceptor cell fate is problematic.     

miRNA与细胞分化的研究进展

microRNA(miRNA)是一类长度为22nt的内源性的参与转录后调节的单链非编码小RNA。近年来的研究表明,miRNA在基因表达调控方面具有广泛和普遍的作用,参与了生物体发生发育、细胞增殖、细胞分化等生物学过程,尤其是其在干细胞的自我更新与多向分化的调节作用日益受到关注。我们查阅近年有关文献,介绍了miRNA的生成、作用机制、研究方法,论述及其对真核生物细胞分化的调控作用。     

Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch

We study the plasticity of a delayed stochastic model of a genetic toggle switch as a multipotent differentiation pathway switch, at the single cell and cell population levels, by observing distributions of differentiation pathways choices of genetically homogeneous cell populations. Assuming a model of stochastic pathway determination of cell differentiation that is regulated by the proteins of the switch, we vary the proteins’ expression level and degradation rates, which cells are known to be able to regulate, to vary mean level, noise, and bias of the proteins’ expression levels. It is shown that small changes in each of these dynamical features significantly and distinctively affects the dynamics of the switch at the single cell level and thus, the cell differentiation patterns. The regulation of these features allows cells to regulate their pluripotency and cell populations’ distribution of lineage choice, suggesting that the stochastic switch has high plasticity regarding differentiation pathway choice regulation, thus providing adaptability to environmental stresses and changes.     

糖组学研究技术及其进展

多细胞生物机体内,蛋白质糖基化是一个重要后修饰事件 . 蛋白质的糖链不仅仅是区别细胞种类的标志,且与众多的生物现象有关,如细胞发育、分化、形态、肿瘤转移、微生物感染等 . 糖组学的内容主要涉及单个个体的全部糖蛋白结构分析,确定编码糖蛋白的基因和蛋白质糖基化的机制 . 综述了糖组学的分离和结构鉴定技术及其最新进展 .     

Dynamic Stabilization in the PU1-GATA1 Circuit Using a Model with Time-Dependent Kinetic Change

The PU.1 and GATA1 genes play an important role in the differentiation of blood stem cells. The protein levels expressed by these genes are thought to be regulated by a self-excitatory feedback loop for each gene and a cross-inhibitory feedback loop between the two genes. A mathematical model that captures the dynamical interaction between these two genes reveals that constant levels of self-excitation and cross-inhibition allow the most self-exciting or cross-inhibiting gene to dominate the system. However, since biological systems rarely exist in an unchanging equilibrium, we modeled this gene circuit using discrete time-dependent changes in the parameters in lieu of steady state parameters. These time-dependent parameters lead to new phenomena, including the development of new limit cycles and basins of attraction. These phenomena are not present in models using constant parameter values. Our findings suggest that even small perturbations in the PU.1 and GATA1 feedback loops may substantially alter the gene expression and therefore the cell phenotype. These time-dependent parameter models may also have implications for other gene systems and provide new ways to understand the mechanisms of cellular differentiation.