三维基因组学研究进展

三维基因组学是一门研究基因组三维空间结构与功能的新兴学科,主要研究基因组序列在细胞核内的三维空间构象,及其对DNA复制、DNA重组、基因表达调控等生物过程的生物学效应。自染色质构象捕获技术(3C)出现后,三维基因组学相关研究领域飞速发展。借助于3C及其衍生技术、Hi-C和ChIA-PET等技术,科学家能对各类物种的三维基因组进行更为深入的研究,从而揭示微生物、植物和动物基因组的空间构象、染色质的相互作用模式、转录调控以及不同生物学性状的形成机制;挖掘与生命活动和疾病相关的关键基因和信号通路;推动农业科学、生命科学和医学等领域的快速发展。文中就三维基因组学研究进展作一综述,主要阐述三维基因组学的概念和研究技术的发展及其在农业科学、生命科学和医学等领域的应用,尤其是肿瘤领域所取得的阶段性研究成果。     

Predicting protein three-dimensional structure

The current state of the art in modeling protein structure has been assessed, based on the results of the CASP (Critical Assessment of protein Structure Prediction) experiments. In comparative modeling, improvements have been made in sequence alignment, sidechain orientation and loop building. Refinement of the models remains a serious challenge. Improved sequence profile methods have had a large impact in fold recognition. Although there has been some progress in alignment quality, this factor still limits model usefulness. In ab initio structure prediction, there has been notable progress in building approximately correct structures of 40-60 residue-long protein fragments. There is still a long way to go before the general ab initio prediction problem is solved. Overall, the field is maturing into a practical technology, able to deliver useful models for a large number of sequences.     

Vision in our three-dimensional world

Many aspects of our perceptual experience are dominated by the fact that our two eyes point forward. Whilst the location of our eyes leaves the environment behind our head inaccessible to vision, co-ordinated use of our two eyes gives us direct access to the three-dimensional structure of the scene in front of us, through the mechanism of stereoscopic vision. Scientific understanding of the different brain regions involved in stereoscopic vision and three-dimensional spatial cognition is changing rapidly, with consequent influences on fields as diverse as clinical practice in ophthalmology and the technology of virtual reality devices.This article is part of the themed issue ‘Vision in our three-dimensional world’.     

High-throughput three-dimensional protein structure determination

In the wake of finished genomic sequencing projects, high-throughput analysis techniques are being developed in various fields of functional genomics. Of special interest in this regard is the three-dimensional structure analysis of proteins by X-ray crystallography and NMR spectroscopy, which has been characterized by distinctly low-throughput in the past. A number of recent advances in instrumentation and software are promising to radically change this situation, leaving the production of suitable protein samples as the sole rate-limiting step in structural analyses.     

Modern three-dimensional conformal craniospinal radiotherapy

The main problem of craniospinal irradiation (CSI) is the matching of the fields. The use of a suitable technique is very important because matching of the fields is necessary to use for the optimal cancer irradiation of the long planning target volume (PTV). Since 2007, 8 patients have received CT-based, 3D-planned conformal CSI in our Institute. Patient immobilization was made in prone position in a vacuum bed, using skull and pelvis masks. Organ-at-risk (OAR) contours were made by radiographers. PTV was contoured by radiation oncologists. The prescribed dose to the PTV was 36 Gy with 1.8 Gy dose per fraction. In the planning process the following aspects were taken under consideration: all points of the PTV had to receive at least 95% of the prescribed dose (according to ICRU 50, 62); at junction field edges the overlapping parts were eliminated using a multisegmental technique, where the adjacent segment ends of the neighbouring fields were shifted two times 2 cm, so that the three equally weighted segments used in one field had 2-2 cm distance from each other. In the CSI planning the shape of the patient and so the length of the PTV has made a big emphasis on determining the number of field matching. Thus in some cases instead of two, only one field matching was sufficient - this could be achieved by increasing the source-to-skin distance (SSD) of the fields. The verification made with a solid-water phantom justified the precision of the field matching. The offset used at junction field edges in between one treatment facilitates the verification of field matching - and so the patient positioning. Thus the possibility of having overdosed regions could be reduced, which was very important from a radiation biological point of view.     

Bioreactor cultivation of three-dimensional cartilage-carrier-constructs

A flow-chamber bioreactor was designed for generation of three-dimensional cartilage-carrier-constructs. A specific attribute of the flow-chamber is a very thin medium layer for improved oxygen supply and a counter current flow of medium and gas. Three-dimensional cartilage-carrier-constructs were produced according to a standard protocol from chondrocytes of an adult mini-pig. The final step of this protocol was performed either in the bioreactor or in 12-well plates. The bioreactor experiments showed a significantly higher matrix thickness but a lower ratio of glycosaminoglycan to DNA. For both culture methods the constructs contained a high amount of collagen II. Appearance of the cartilage obtained in the bioreactor seemed to be closer to native cartilage with respect to distribution of the cells within the matrix, smoothness of the surface etc. All results considered the flow-chamber bioreactor is a very useful tool for generation of three dimensional cartilage-carrier constructs.     

Cell interactions with three-dimensional matrices

Signaling and other cellular functions differ in three-dimensional compared with two-dimensional systems. Cell adhesion structures can evolve in vitro towards in-vivo-like adhesions with distinct biological activities. In this review, we examine recent advances in studies of interactions of fibroblasts with collagen gels and fibronectin-containing matrices that mimic in vivo three-dimensional microenvironments. These three-dimensional systems are illuminating mechanisms of cell-matrix interactions in living organisms.     

Vinculin regulates directionality and cell polarity in two- and three-dimensional matrix and three-dimensional microtrack migration

During metastasis, cells can use proteolytic activity to form tube-like “microtracks” within the extracellular matrix (ECM). Using these microtracks, cells can migrate unimpeded through the stroma. To investigate the molecular mechanisms of microtrack migration, we developed an in vitro three-dimensional (3D) micromolded collagen platform. When in microtracks, cells tend to migrate unidirectionally. Because focal adhesions are the primary mechanism by which cells interact with the ECM, we examined the roles of several focal adhesion molecules in driving unidirectional motion. Vinculin knockdown results in the repeated reversal of migration direction compared with control cells. Tracking the position of the Golgi centroid relative to the position of the nucleus centroid reveals that vinculin knockdown disrupts cell polarity in microtracks. Vinculin also directs migration on two-dimensional (2D) substrates and in 3D uniform collagen matrices, as indicated by reduced speed, shorter net displacement, and decreased directionality in vinculin-deficient cells. In addition, vinculin is necessary for focal adhesion kinase (FAK) activation in three dimensions, as vinculin knockdown results in reduced FAK activation in both 3D uniform collagen matrices and microtracks but not on 2D substrates, and, accordingly, FAK inhibition halts cell migration in 3D microtracks. Together these data indicate that vinculin plays a key role in polarization during migration.     

Modelling three-dimensional flow over spur-and-groove morphology

Spur-and-groove (SAG) morphology characterizes the fore reef of many coral reefs worldwide. Although the existence and geometrical properties of SAG have been well documented, an understanding of the hydrodynamics over them is limited. Here, the three-dimensional flow patterns over SAG formations, and a sensitivity of those patterns to waves, currents, and SAG geometry were characterized using the physics-based Delft3D-FLOW and SWAN models. Shore-normal shoaling waves over SAG formations were shown to drive two circulation cells: a cell on the lower fore reef with offshore flow over the spurs and onshore flow over the grooves, except near the seabed where velocities were always onshore, and a cell on the upper fore reef with offshore surface velocities and onshore bottom currents, which result in depth-averaged onshore and offshore flow over the spurs and grooves, respectively. The mechanism driving this flow results from the net of the radiation stress gradients and pressure gradient, which is balanced by the Reynolds stress gradients and bottom friction that differ over the spur and over the groove. Waves were the primary driver of variations in modelled flow over SAG, with the flow strength increasing for increasing wave heights and periods. Spur height, SAG wavelength, and the water depth at peak spur height were the dominant influences on the hydrodynamics, with spur heights directly proportional to the strength of SAG circulation cells. SAG formations with shorter SAG wavelengths only presented one circulation cell on the shallower portion of the reef, as opposed to the two circulation cells for longer SAG wavelengths. SAG formations with peak spur heights occurring in shallower water had stronger circulation than those with peak spur heights occurring in deeper water. These hydrodynamic patterns also likely affect coral and reef development through sediment and nutrient fluxes.

     

Regulating tension in three-dimensional culture environments

The processes of development, repair, and remodeling of virtually all tissues and organs, are dependent upon mechanical signals including external loading, cell-generated tension, and tissue stiffness. Over the past few decades, much has been learned about mechanotransduction pathways in specialized two-dimensional culture systems; however, it has also become clear that cells behave very differently in two- and three-dimensional (3D) environments. Three-dimensional in vitro models bring the ability to simulate the in vivo matrix environment and the complexity of cell–matrix interactions together. In this review, we describe the role of tension in regulating cell behavior in three-dimensional collagen and fibrin matrices with a focus on the effective use of global boundary conditions to modulate the tension generated by populations of cells acting in concert. The ability to control and measure the tension in these 3D culture systems has the potential to increase our understanding of mechanobiology and facilitate development of new ways to treat diseased tissues and to direct cell fate in regenerative medicine and tissue engineering applications.     

The three-dimensional structures of two beta-agarases

Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two beta-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 A for beta-agarases A and B, respectively. The structure of beta-agarase A was solved by the multiple anomalous diffraction method, whereas beta-agarase B was solved with molecular replacement using beta-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the beta-agarases.     

High-resolution confocal imaging and three-dimensional rendering

Intrinsic opacity and inhomeogeniety of most biological tissues have prevented the efficient light penetration and signal detection for high-resolution confocal imaging of thick tissues. Here, we summarize recent technical advances in high-resolution confocal imaging for visualization of cellular structures and gene expression within intact whole-mount thick tissues. First, we introduce features of the FocusClear technology that render biological tissue transparent and thus improve the light penetration and signal detection. Next, a universal fluorescence staining method that labels all nuclei and membranes is described. We then demonstrate the postrecording image processing techniques for 3D visualization. From these images, regions of interest in the whole-mount brain can be segmented and volume rendered. Together, these technical advances in confocal microscopy allow visualization of structures within whole-mount tissues up to 1mm thick at a resolution similar to that of the observation of single cells in culture. Practical uses and limitations of these techniques are discussed.