Characterization of mRNA-protein complexes from mammalian cells.

In a previous report we described the use of oligo(dT)-cellulose for the isolation of mRNA-protein complexes from EDTA-dissociated polysomes extracted from normally growing or adenovirus infected KB-cells (I). Experiments presented here provide evidence that proteins involved in these complexes bind specifically to mRNA since: a) the proteins and mRNA cosediment through sucrose gradients, b) they adsorb and elute from oligo(dT)-cellulose together, and c) analysis of the products from ribonuclease digestion experiments show that the poly (A) end and a separate small fraction of the mRNA are resistant to the enzymes and attached to protein.     

Analyzing mRNA-protein complexes using a yeast three-hybrid system

RNA-protein interactions are essential for the proper execution and regulation of every step in the life of a eukaryotic mRNA. Here we describe a three-hybrid system in which RNA-protein interactions can be analyzed using simple phenotypic or enzymatic assays in Saccharomyces cerevisiae. The system can be used to detect or confirm an RNA-protein interaction, to analyze RNA-protein interactions genetically, and to discover new protein or RNA partners when only one is known. Multicomponent complexes containing more than one protein can be detected, identified, and analyzed. We describe the method and how to use it, and discuss applications that bear particularly on eukaryotic mRNAs.     

Eukaryotic elongation factor Tu is present in mRNA-protein complexes

By two-dimensional gel electrophoresis, partial peptide mapping, and antibody binding we have shown that eukaryotic elongation factor Tu is in close contact with mRNA in rabbit reticulocytes. It can be crosslinked to mRNA by irradiating both polysomes and 40-80 S mRNA-protein complexes with short-wave UV light. To our knowledge this is the first case in which a known translation factor has been shown to be associated with mRNA in native ribonucleoproteins.     

Immunoprecipitation of DNA-protein complexes cross-linked by cis-diamminedichloroplatinum

For the study of in vitro and in vivo DNA-protein interactions, cross-linking reactions driven by UV or formaldehyde have been frequently used, followed by standard protocols of immunoprecipitation and analysis of the DNA isolated from the complexes. Here we present a basically modified method to analyze the DNA-protein cross-linked complexes obtained by an alternative cross-linking reagent. The innovations presented here include cross-linking by cis-diamminedichloroplatinum II, a fast method to isolate DNA-protein complexes using gel-filtration chromatography, and a modified procedure to obtain specific immunocomplexes that can be analyzed either for DNA or for protein content. The application of this method to two nuclear proteins from chicken liver nuclei is described.     

Proteomic and functional analysis of Argonaute-containing mRNA-protein complexes in human cells

Members of the Argonaute (Ago) protein family associate with small RNAs and have important roles in RNA silencing. Here, we analysed Ago1- and Ago2-containing protein complexes in human cells. Separation of Ago-associated messenger ribonucleoproteins (mRNPs) showed that Ago1 and Ago2 reside in three complexes with distinct Dicer and RNA-induced silencing complex activities. A comprehensive proteomic analysis of Ago-containing mRNPs identified a large number of proteins involved in RNA metabolism. By using co-immunoprecipitation experiments followed by RNase treatment, we biochemically mapped interactions within Ago mRNPs. Using reporter assays and knockdown experiments, we showed that the putative RNA-binding protein RBM4 is required for microRNA-guided gene regulation.     

Methylated DNA Immunoprecipitation

The identification of DNA methylation patterns is a common procedure in the study of epigenetics, as methylation is known to have significant effects on gene expression, and is involved with normal development as well as disease ^1-4. Thus, the ability to discriminate between methylated DNA and non-methylated DNA is essential for generating methylation profiles for such studies. Methylated DNA immunoprecipitation (MeDIP) is an efficient technique for the extraction of methylated DNA from a sample of interest ^5-7. A sample of as little as 200 ng of DNA is sufficient for the antibody, or immunoprecipitation (IP), reaction. DNA is sonicated into fragments ranging in size from 300-1000 bp, and is divided into immunoprecipitated (IP) and input (IN) portions. IP DNA is subsequently heat denatured and then incubated with anti-5''mC, allowing the monoclonal antibody to bind methylated DNA. After this, magnetic beads containing a secondary antibody with affinity for the primary antibody are added, and incubated. These bead-linked antibodies will bind the monoclonal antibody used in the first step. DNA bound to the antibody complex (methylated DNA) is separated from the rest of the DNA by using a magnet to pull the complexes out of solution. Several washes using IP buffer are then performed to remove the unbound, non-methylated DNA. The methylated DNA/antibody complexes are then digested with Proteinase K to digest the antibodies leaving only the methylated DNA intact. The enriched DNA is purified by phenol:chloroform extraction to remove the protein matter and then precipitated and resuspended in water for later use. PCR techniques can be used to validate the efficiency of the MeDIP procedure by analyzing the amplification products of IP and IN DNA for regions known to lack and known to contain methylated sequences. The purified methylated DNA can then be used for locus-specific (PCR) or genome-wide (microarray and sequencing) methylation studies, and is particularly useful when applied in conjunction with other research tools such as gene expression profiling and array comparative genome hybridization (CGH) ⁸. Further investigation into DNA methylation will lead to the discovery of new epigenetic targets, which in turn, may be useful in developing new therapeutic or prognostic research tools for diseases such as cancer that are characterized by aberrantly methylated DNA ^{2, 4, 9-11}.     

免疫沉淀法纯化线粒体的研究

传统的线粒体分离技术,如差速离心和密度梯度离心不能有效应用于小规模高纯度的线粒体制备。为了提高线粒体纯化的速度和质量,我们尝试运用免疫沉淀法制备线粒体。通过用EGFP-4Flag融合蛋白来标记线粒体外膜,然后用单克隆Flag抗体和Protein G Agarose珠子做免疫沉淀,从培养的细胞中分离出高纯度的线粒体。这一简便高效的方法将有助于线粒体的生化研究。     

免疫沉淀技术的最新进展

免疫沉淀(Immunoprecipitation,IP)技术是以抗体和抗原之间的专一性作用为基础的用于研究蛋白质相互作用的经典方法.也是确定两种蛋白质在完整细胞内生理性相互作用的有效方法.免疫沉淀技术现已广泛应用于基因、蛋白质以及它们之间相互作用等领域的研究,并且其可与多种技术联合应用,也可合并一些实验方法进行多方面探索.本文将主要介绍染色质免疫沉淀技术、蛋白质免疫沉淀技术和放射免疫沉淀技术的原理和方法,并对它们相应的应用作简要的说明.     

染色质免疫共沉淀实验方法

染色质免疫共沉淀(ChIP)技术是一种检测蛋白质与DNA结合的实验技术。该方法可以先进行样品交联, 然后将蛋白质与DNA复合物进行随机DNA切断, 再借助免疫学方法特异性富集与目的蛋白相结合的DNA片段, 从而检测转录因子等目的蛋白质与DNA的结合情况, 鉴定基因启动子或其它DNA结合位点。该方法同时也可应用于研究基因组特定位点的组蛋白修饰情况。该文介绍了依赖交联固定的常规免疫共沉淀(X-ChIP), 以及适用于10³细胞级别微量实验材料的基于微球菌核酸酶非交联免疫共沉淀(ULI-NChIP)具体操作过程和注意事项。     

Immunoprecipitation of human H-Y antigen

Summary In the absence of beta-2-microglobulin and MHC-determined cell surface antigens, cultured cells of the Burkitt lymphoma, Daudi, secrete testis-inducing H-Y antigen into the surrounding medium. We have precipitated Daudi-secreted H-Y antigen by two methods, one using mouse H-Y antibody and goat anti-mouse Ig, and the other using mouse H-Y antibody and Sepharose beads coated with protein A. The estimated molecular weight of the specific immunoprecipitate was 15,000–18,000 Daltons.     

An mRNA-protein fusion at N-terminus for evolutionary protein engineering

A novel method to link a nascent protein (phenotype) to its mRNA (genotype) covalently through the N-terminus was developed. The mRNA harboring amber stop codon at just downstream of initiation site was hybridized with hydrazide-modified ssDNA at upstream of coding region and was ligated to the DNA. This construct was then modified with 4-acetyl-phenylalanyl amber suppressor tRNA. This modified construct was fused with the nascent protein via the phenylalanine derivative when the mRNA uses the amber suppressor tRNA to decode the amber stop codon. The obtained fusion molecule was used successfully in selective enrichment experiments. It will be applicable for high-through-put screening in evolutionary protein engineering. In contrast to fusion molecules generated by other methods in which the protein is linked to genotype molecule through the C- terminus, our fusion molecule will serve to select a protein for which the C-terminus is essential to be active.     

Immunoprecipitation of native chromatin: NChIP

Chromatin immunoprecipitation (ChIP) is widely used in many fields to analyze the distribution of specific proteins, or their modified isoforms, across defined DNA domains. ChIP procedures fall into two main categories, namely, those that use native chromatin prepared by nuclease digestion (designated NChIP), and those that use chromatin in which DNA and proteins are crosslinked, either chemically or with UV light (designated XChIP). Each procedure has its own advantages and drawbacks. Here, we outline the methods currently in use in our laboratory to isolate and immunoprecipitate native chromatin from cultured cells, and to isolate and analyze immunoprecipitated protein and DNA.     

Immunoprecipitation of human adrenal microsomal antigen

Human adrenal microsomes have been labelled with 125I and immunoprecipitated with sera from patients with Addison's disease. The immunoprecipitates were then analysed by SDS-PAGE and autoradiography. 13 of the 23 sera from the Addison patients studied contained antibodies which reacted with a 55 kDa adrenal microsomal protein. The same 13 sera were also positive for adrenal antibodies as judged by immunofluorescence. The 55 kDa protein was not immunoprecipitated from placenta or thyroid microsomes by Addison sera. Furthermore, patients with Graves' disease or rheumatoid arthritis did not immunoprecipitate the 55 kDa protein from adrenal microsomes. Our studies suggest therefore that Addison sera contain antibodies to a 55 kDa adrenal specific protein which may well be the antigen observed on immunofluorescence.     

一种简便的染色质免疫沉淀法的建立

染色质结构和基因表达调节是当前国际前沿研究的热点.染色质免疫沉淀法是研究染色质结构的首选方法,它不仅可用来研究体内反式因子与DNA的相互作用,也可以用来研究组蛋白修饰与基因表达的关系.综合国外相关文献,建立了一种简便的染色质免疫沉淀法,并通过对诱导前后的MEL细胞中β-珠蛋白基因簇组蛋白H3乙酰化的研究,证实了其可操作性.结果表明：高敏位点HS2和活跃基因βmaj的启动子区域存在较高的组蛋白乙酰化水平,且诱导前后变化显著,而不活跃基因Ey的启动子区域则几乎检测不到组蛋白的乙酰化,且诱导前后无明显变化.这一结果与以前的报道相吻合.