SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis

MOTIVATION: A comprehensive gene expression database is essential for computer modeling and simulation of biological phenomena, including development. Development is a four-dimensional (4D; 3D structure and time course) phenomenon. We are constructing a 4D database of gene expression for the early embryogenesis of the nematode Caenorhabditis elegans. As a framework of the 4D database, we have constructed computer graphics (CG), into which we will incorporate the expression data of a number of genes at the subcellular level. However, the assignment of 3D distribution of gene products (protein, mRNA), of embryos at various developmental stages, is both difficult and tedious. We need to automate this process. For this purpose, we developed a new system, named SPI after superimposing fluorescent confocal microscopic data onto a CG framework. RESULTS: The scheme of this system comprises the following: (1) acquirement of serial sections (40 slices) of fluorescent confocal images of three colors (4',6'-diamino-2-phenylindole (DAPI) for nuclei, indodicarbocyanine (Cy-3) for the internal marker, which is a germline-specific protein POS-1 and indocarbocyanine (Cy-5) for the gene product to be examined); (2) identification of several features of the stained embryos, such as contour, developmental stage and position of the internal marker; (3) selection of CG images of the corresponding stage for template matching; (4) superimposition of serial sections onto the CG; (5) assignment of the position of superimposed gene products. The Snakes algorithm identified the embryo contour. The detection accuracy of embryo contours was 92.1% when applied to 2- to 28-cell-stage embryos. The accuracy of the developmental stage prediction method was 81.2% for 2- to 8-cell-stage embryos. We manually judged only the later stage embryos because the accuracy for embryos at the later stages was unsatisfactory due to experimental noise effects. Finally, our system chose the optimal CG and performed the superposition and assignment of gene product distribution. We established an initial 4D gene expression database with 56 maternal gene products. AVAILABILITY: This system is available at http://anti.lab.nig.ac.jp/spi/ and http://anti.lab.nig.ac.jp/4ddb/     

Chromatin Immunoprecipitation Assay for Tissue-specific Genes using Early-stage Mouse Embryos

Chromatin immunoprecipitation (ChIP) is a powerful tool to identify protein:chromatin interactions that occur in the context of living cells ^1-3. This technique has been widely exploited in tissue culture cells, and to a lesser extent, in primary tissue. The application of ChIP to rodent embryonic tissue, especially at early times of development, is complicated by the limited amount of tissue and the heterogeneity of cell and tissue types in the embryo. Here we present a method to perform ChIP using a dissociated embryonic day 8.5 (E8.5) embryo. Sheared chromatin from a single E8.5 embryo can be divided into up to five aliquots, which allows the investigator sufficient material for controls and for investigation of specific protein:chromatin interactions.We have utilized this technique to begin to document protein:chromatin interactions during the specification of tissue-specific gene expression programs. The heterogeneity of cell types in an embryo necessarily restricts the application of this technique because the result is the detection of protein:chromatin interactions without distinguishing whether the interactions occur in all, a subset of, or a single cell type(s). However, examination of tissue-specific genes during or following the onset of tissue-specific gene expression is feasible for two reasons. First, immunoprecipitation of tissue specific factors necessarily isolates chromatin from the cell type where the factor is expressed. Second, immunoprecipitation of coactivators and histones containing post-translational modifications that are associated with gene activation should only be found at genes and gene regulatory sequences in the cell type where the gene is being or has been activated. The technique should be applicable to the study of most tissue-specific gene activation events.In the example described below, we utilized E8.5 and E9.5 mouse embryos to examine factor binding at a skeletal muscle specific gene promoter. Somites, which are the precursor tissues from which the skeletal muscles of the trunk and limbs will form, are present at E8.5-9.5^4,5. Myogenin is a regulatory factor required for skeletal muscle differentiation ^6-9. The data demonstrate that myogenin is associated with its own promoter in E8.5 and E9.5 embryos. Because myogenin is only expressed in somites at this stage of development ^6,10, the data indicate that myogenin interactions with its own promoter have already occurred in skeletal muscle precursor cells in E8.5 embryos.     

Integrating technologies for comparing 3D gene expression domains in the developing chick limb

Chick embryos are good models for vertebrate development due to their accessibility and manipulability. Recent large increases in available genomic data from both whole genome sequencing and EST projects provide opportunities for identifying many new developmentally important chicken genes. Traditional methods of documenting when and where specific genes are expressed in embryos using wholemount and section in-situ hybridisation do not readily allow appreciation of 3-dimensional (3D) patterns of expression, but this can be accomplished by the recently developed microscopy technique, Optical Projection Tomography (OPT). Here we show that OPT data on the developing chick wing from different labs can be reliably integrated into a common database, that OPT is efficient in capturing 3D gene expression domains and that such domains can be meaningfully compared. Novel protocols are used to compare 3D expression domains of 7 genes known to be involved in chick wing development. This reveals previously unappreciated relationships and demonstrates the potential, using modern genomic resources, for building a large scale 3D atlas of gene expression. Such an atlas could be extended to include other types of data, such as fate maps, and the approach is also more generally applicable to embryos, organs and tissues.     

A topographical map of spatiotemporal patterns of gene expression

A recent study by Folkes et al. in Cell generated a 3D atlas of gene expression for the Drosophila blastoderm embryo using a new approach for image registration. This virtual embryo allows in silico multiplexing of in situ hybridizations and lays the groundwork for new insights into gene regulatory networks.     

Visualizing plant development and gene expression in three dimensions using optical projection tomography

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, flowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as beta-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantified and visualized interactively in different ways.     

Production of mouse chimeras by injection of embryonic stem cells into the perivitelline space of one-cell stage embryos

Generation of mouse chimeras is useful for the elucidation of gene function. In the present report, we describe a new technique for the production of chimeras by injection of R1 embryonic stem (ES) cells into the perivitelline space of one-cell stage mouse embryos. One-cell embryos are injected with 2–6 ES cells into the perivitelline space under the zona pellucida without laser-assistance. Our embryo culture experiments reveal that ES cells injected at the one-cell stage embryo start to be incorporated into the blastomeres beginning at the 8-cell stage and form a chimeric blastocyst after 4 days. We have used this approach to successfully produce a high rate of mouse chimeras in two different mouse genetic backgrounds permitting the establishment of germ line transmitters. This method allows for the earlier introduction of ES cells into mouse embryos, and should free up the possibility of using frozen one-cell embryos for this purpose.     

斑马鱼整体原位杂交的技术改良

斑马鱼整体原位杂交技术广泛应用于基因表达谱、基因间相互关系和突变体筛选等方面,是研究斑马鱼发育相关基因功能的重要技术。本文从杂交探针的制备、浓度的选择和洗脱以及胚胎的脱色、蛋白酶K消化、底物显色等方面进行了摸索、改进及简化,获得了背景低、着色清晰、特异性高的实验结果,预示了简单实用、成本低廉的斑马鱼整胚原位杂交技术平台的成功建立。     

A new triple staining method for double in situ hybridization in combination with cell lineage tracing in whole-mount Xenopus embryos

To analyze cell to cell interaction effects on cell differentiation, we developed a new triple staining method for double in situ hybridization with cell lineage tracing in whole-mount Xenopus embryos. The method provides high color contrast views, and also enabled us to examine inside the embryos. Wild-type embryos whose blastomere(s) had been injected with a cell lineage tracer were cultured, fixed, hemisectioned when necessary, and first served for the double in situ hybridization, with two sequential chromogenic reactions. They were postfixed, and the labeled cells were retraced immunohistochemically. Finally, the pigment of the embryos was bleached to obtain a clear view. We applied this method to a blastomere transplantation experiment to examine whether the spatial gene expression patterns along the anteroposterior axis can be induced by cell to cell interactions. The presumptive organizer of a 32-cell embryo was replaced by the labeled presumptive epidermis of another synchronous embryo. The resultant triple-stained late gastrula showed quite similar anteroposterior expression patterns of gsc and Xbra to those of a normal embryo in the axial mesoderm derived from the transplanted presumptive epidermis, indicating that cell to cell interactions had induced these patterns.     

Combined method of whole mount and block-face imaging: Acquisition of 3D data of gene expression pattern from conventional in situ hybridization

Visualization of spatiotemporal expression of a gene of interest is a fundamental technique for analyzing the involvements of genes in organ development. In situ hybridization (ISH) is one of the most popular methods for visualizing gene expression. When conventional ISH is performed on sections or whole-mount specimens, the gene expression pattern is represented in 2-dimensional (2D) microscopic images or in the surface view of the specimen. To obtain 3-dimensional (3D) data of gene expression from conventional ISH, the “serial section method” has traditionally been employed. However, this method requires an extensive amount of time and labor because it requires researchers to collect a tremendous number of sections, label all sections by ISH, and image them before 3D reconstruction. Here, we proposed a rapid and low-cost 3D imaging method that can create 3D gene expression patterns from conventional ISH-labeled specimens. Our method consists of a combination of whole-mount ISH and Correlative Microscopy and Blockface imaging (CoMBI). The whole-mount ISH-labeled specimens were sliced using a microtome or cryostat, and all block-faces were imaged and used to reconstruct 3D images by CoMBI. The 3D data acquired using our method showed sufficient quality to analyze the morphology and gene expression patterns in the developing mouse heart. In addition, 2D microscopic images of the sections can be obtained when needed. Correlating 2D microscopic images and 3D data can help annotate gene expression patterns and understand the anatomy of developing organs. These results indicated that our method can be useful in the field of developmental biology.     

逆转录病毒介导myostatin在鸡胚胎中的过表达与检测

鸡的胚胎已经成为发育生物学、免疫学和癌症等学科的重要实验模型之一。以鸡胚胎为实验模型,以鸡myostatin为靶基因,利用逆转录病毒介导和原位杂交技术相结合的方法来研究目的基因的鸡胚胎转导和检测分析。实验结果表明：逆转录病毒介导的目的基因myostatin能够有效整合到胚胎基因组中,且具有转录活性;胚胎原位杂交检测能够准确直观的反映病毒的整合部位和转入基因的表达水平。不但为进一步研究鸡myostatin基因在胚胎发育中的功能奠定基础,同时在方法上也进行了简单的优化尝试。     

Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns

MOTIVATION: In this paper we address the problem of the determination of developmental age of an embryo from its segmentation gene expression patterns in Drosophila. RESULTS: By applying support vector regression we have developed a fast method for automated staging of an embryo on the basis of its gene expression pattern. Support vector regression is a statistical method for creating regression functions of arbitrary type from a set of training data. The training set is composed of embryos for which the precise developmental age was determined by measuring the degree of membrane invagination. Testing the quality of regression on the training set showed good prediction accuracy. The optimal regression function was then used for the prediction of the gene expression based age of embryos in which the precise age has not been measured by membrane morphology. Moreover, we show that the same accuracy of prediction can be achieved when the dimensionality of the feature vector was reduced by applying factor analysis. The data reduction allowed us to avoid over-fitting and to increase the efficiency of the algorithm.     

Gene expression of bovine embryos developing at the air-liquid interface on oviductal epithelial cells (ALI-BOEC)

We recently developed an air-liquid interface long-term culture of differentiated bovine oviductal epithelial cells (ALI-BOEC). This ex vivo oviduct epithelium is capable of supporting embryo development in co-culture up to the blastocyst stage without addition of embryo culture medium. However, blastocyst rates in co-culture were markedly lower than in conventional in vitro embryo production procedures. In the present study, we assessed target gene expression of ALI-BOEC derived embryos to test their similarity to embryos from conventional in vitro embryo culture. We screened previously published data from developing bovine embryos and selected 41 genes which are either differentially expressed during embryo development, or reflect differences between various in vitro culture conditions or in vitro and in vivo embryos. Target gene expression was measured in 8-cell embryos and blastocysts using a 48.48 Dynamic Array? on a Biomark HD instrument. For comparison with the ALI-BOEC system, we generated embryos by two different standard IVP protocols. The culture conditions lead to differential gene expression in both 8-cell embryos and blastocysts. Across the expression of all target genes the embryos developing on ALI-BOEC did not depart from conventional IVP embryos. These first results prove that gene expression in ALI-BOEC embryos is not largely aberrant. However, there was no clear indication for a more in vivo-like target gene expression of these embryos. This calls for further optimization of the ALI-BOEC system to increase its efficiency both quantitatively and qualitatively.     

Allele‐specific expression of the MAOA gene and X chromosome inactivation in in vitro produced bovine embryos

During embryogenesis, one of the two X chromosomes is inactivated in embryos. The production of embryos in vitro may affect epigenetic mechanisms that could alter the expression of genes related to embryo development and X chromosome inactivation (XCI). The aim of this study was to understand XCI during in vitro, pre‐implantation bovine embryo development by characterizing the allele‐specific expression pattern of the X chromosome‐linked gene, monoamine oxidase A (MAOA). Two pools of ten embryos, comprised of the 4‐, 8‐ to 16‐cell, morula, blastocyst, and expanded blastocyst stages, were collected. Total RNA from embryos was isolated, and the RT‐PCR‐RFLP technique was used to observe expression of the MAOA gene. The DNA amplicons were also sequenced using the dideoxy sequencing method. MAOA mRNA was detected, and allele‐specific expression was identified in each pool of embryos. We showed the presence of both the maternal and paternal alleles in the 4‐, 8‐ to 16‐cell, blastocyst and expanded blastocyst embryos, but only the maternal allele was present in the morula stage. Therefore, we can affirm that the paternal X chromosome is totally inactivated at the morula stage and reactivated at the blastocyst stage. To our knowledge, this is the first report of allele‐specific expression of an X‐linked gene that is subject to XCI in in vitro bovine embryos from the 4‐cell to expanded blastocyst stages. We have established a pattern of XCI in our in vitro embryo production system that can be useful as a marker to assist the development of new protocols for in vitro embryo production. Mol. Reprod. Dev. 77: 615–621, 2010. © 2010 Wiley‐Liss, Inc.     

Mosaic incorporation and regulated expression of an exogenous gene in the sea urchin embryo

A fusion gene construct in which the bacterial chloramphenicol acetyltransferase (CAT) gene is controlled by CyIIIa actin gene cis-regulatory sequences was injected into unfertilized eggs of the sea urchin Strongylocentrotus purpuratus. The distribution of CAT DNA sequences was measured directly by in situ hybridization in squashed 24-hr blastula preparations derived from these eggs. Earlier studies had shown that stable mosaic incorporation of the exogenous DNA occurs during cleavage, after which the exogenous sequences replicate at approximately the pace of the host cell genomes. The fractions of embryonic cells observed in this study to include CAT DNA sequences imply that their stable incorporation into a replicating nuclear form occurs most often in a single cell at the 3rd or 4th cleavage stages, though it may occur as early as 2nd cleavage, or as late as 7th cleavage. Corroborative measurements were carried out by the same method on squashed preparations of embryos at earlier stages, and by in situ hybridizations of CAT mRNA, both in dissociated embryos and in cytological sections of 72-hr pluteus-stage embryos. Hybridizations to CAT mRNA and to CAT DNA were carried out on alternate sections of several embryos. The results confirm unequivocally that although CAT mRNA appears only in the aboral ectoderm in embryos derived from eggs injected with the CyIIIa.CAT fusion gene, the exogenous sequences are indeed present, though silent, in the various other cell types of the late embryo.     

对与小鼠胚胎发育相关的印记基因Mcts2的研究

目的：对与小鼠胚胎发育相关的印记基因Mcts2表达模式及生物学功能做初步的分析。方法：采用切片原位杂交,全胚胎原位杂交,Northern blot和real-time PCR对该基因进行了表达谱的分析。结果：切片原位杂交结果显示Mcts2基因在E13.5和E15.5胚胎中的脑、舌、心脏、肺脏、肝脏、肾脏等重要脏器中都有普遍表达。全胚胎原位杂交结果显示Mcts2基因在E10.5胚胎中的前脑、前肢、尾芽中出现较强的信号,其他部位信号较弱。Northern和Real-time PCR实验分析了Mcts2基因在E12.5,E15.5,E18.5胚胎和新生小鼠的脑、心脏、肺脏、肝脏和肾脏中的表达谱,发现Mcts2基因在这几个主要发育时期都有普遍表达,在E15.5胚胎中表达信号最为强烈。结论：Mcts2基因在小鼠胚胎的发育的各主要时期的重要脏器中都有普遍的表达,提示该基因在小鼠胚胎发育过程中起到了重要的作用。     

Application of cDNA arrays to monitor mRNA profiles in single preimplantation mouse embryos

Array technology is a widely used tool for gene expression profiling in various biological systems. However, the application of this method to mammalian preimplantation embryos is limited by the small amount of mRNA that can be extracted from a single embryo, which is not sufficient for array analysis. Here we report a protocolfor the rapid global amplification of embryonic mRNA that permits the generation of expression profiles from single murine blastocysts. The approach combines global PCR and 77 RNA polymerase amplification and allows the preparation of labeled, amplified RNA for array hybridization from single murine blastocysts containing approximately 1.5 pg mRNA in less than 12 h. We demonstrate that this amplification procedure is highly reproducible and does not bias original relative mRNA levels. Signal patterns from various embryonic stages of murine development revealed marked differences in mRNA expression that were in accordance with previously published data. We found genes known to be involved in embryonic apoptosis expressed at different levels in individual murine day 3.5 blastocysts. This technique can thus be used to assess embryonic viability and investigate molecular mechanisms of embryonic development.