Showing papers in "Methods of Molecular Biology in 2008"

Protein structure modeling with MODELLER.

Abstract: Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. This chapter presents an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of similar protocols (correction of protcols) has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

LC3 and Autophagy.

Abstract: Microtubule-associated protein 1A/1B-light chain 3 (LC3) is a soluble protein with a molecular mass of approximately 17 kDa that is distributed ubiquitously in mammalian tissues and cultured cells. During autophagy, autophagosomes engulf cytoplasmic components, including cytosolic proteins and organelles. Concomitantly, a cytosolic form of LC3 (LC3-I) is conjugated to phosphatidylethanolamine to form LC3-phosphatidylethanolamine conjugate (LC3-II), which is recruited to autophagosomal membranes. Autophagosomes fuse with lysosomes to form autolysosomes, and intra-autophagosomal components are degraded by lysosomal hydrolases. At the same time, LC3-II in autolysosomal lumen is degraded. Thus, lysosomal turnover of the autophagosomal marker LC3-II reflects starvation-induced autophagic activity, and detecting LC3 by immunoblotting or immunofluorescence has become a reliable method for monitoring autophagy and autophagy-related processes, including autophagic cell death. Here we describe basic protocols to assay for endogenous LC3-II by immunoblotting, immunoprecipitation, and immunofluorescence.

UNAFold: software for nucleic acid folding and hybridization.

Abstract: The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. The name is derived from "Unified Nucleic Acid Folding." Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (C(p)), and mole fractions of different molecular species are computed as a function of temperature. The package installs and runs on all Unix and Linux platforms that we have looked at, including Mac OS X. Images of secondary structures, hybridizations, and dot plots may be computed using common formats. Similarly, a variety of melting profile plots is created when appropriate. These latter plots include experimental results if they are provided. The package is "command line" driven. Underlying compiled programs may be used individually, or in special combinations through the use of a variety of Perl scripts. Users are encouraged to create their own scripts to supplement what comes with the package. This evolving software is available for download at http://www.bioinfo.rpi.edu/applications/hybrid/download.php .

Pharmacological inhibition of endocytic pathways: is it specific enough to be useful?

Abstract: Eukaryotic cells constantly form and internalize plasma membrane vesicles in a process known as endocytosis. Endocytosis serves a variety of housekeeping and specialized cellular functions, and it can be mediated by distinct molecular pathways. Among them, internalization via clathrin-coated pits, lipid raft/caveolae-mediated endocytosis and macropinocytosis/phagocytosis are the most extensively characterized. The major endocytic pathways are usually distinguished on the basis of their differential sensitivity to pharmacological/chemical inhibitors, although the possibility of nonspecific effects of such inhibitors is frequently overlooked. This review provides a critical evaluation of the selectivity of the most widely used pharmacological inhibitors of clathrin-mediated, lipid raft/caveolae-mediated endocytosis and macropinocytosis/phagocytosis. The mechanisms of actions of these agents are described with special emphasis on their reported side effects on the alternative internalization modes and the actin cytoskeleton. The most and the least-selective inhibitors of each major endocytic pathway are highlighted.

Automated Structure Solution with the PHENIX Suite

Abstract: Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

Bayesian regularization of neural networks.

Abstract: Bayesian regularized artificial neural networks (BRANNs) are more robust than standard back-propagation nets and can reduce or eliminate the need for lengthy cross-validation. Bayesian regularization is a mathematical process that converts a nonlinear regression into a "well-posed" statistical problem in the manner of a ridge regression. The advantage of BRANNs is that the models are robust and the validation process, which scales as O(N2) in normal regression methods, such as back propagation, is unnecessary. These networks provide solutions to a number of problems that arise in QSAR modeling, such as choice of model, robustness of model, choice of validation set, size of validation effort, and optimization of network architecture. They are difficult to overtrain, since evidence procedures provide an objective Bayesian criterion for stopping training. They are also difficult to overfit, because the BRANN calculates and trains on a number of effective network parameters or weights, effectively turning off those that are not relevant. This effective number is usually considerably smaller than the number of weights in a standard fully connected back-propagation neural net. Automatic relevance determination (ARD) of the input variables can be used with BRANNs, and this allows the network to "estimate" the importance of each input. The ARD method ensures that irrelevant or highly correlated indices used in the modeling are neglected as well as showing which are the most important variables for modeling the activity data. This chapter outlines the equations that define the BRANN method plus a flowchart for producing a BRANN-QSAR model. Some results of the use of BRANNs on a number of data sets are illustrated and compared with other linear and nonlinear models.

Monte Carlo simulations.

Abstract: A description of Monte Carlo methods for simulation of proteins is given. Advantages and disadvantages of the Monte Carlo approach are presented. The theoretical basis for calculating equilibrium properties of biological molecules by the Monte Carlo method is presented. Some of the standard and some of the more recent ways of performing Monte Carlo on proteins are presented. A discussion of the estimation of errors in properties calculated by Monte Carlo is given.

In-line probing analysis of riboswitches.

Abstract: Riboswitches are intricate, metabolite-binding RNA structures found in the non-coding regions of mRNA. Allosteric changes in the riboswitch that are induced by metabolite binding are harnessed to control the genes of a variety of essential metabolic pathways in eubacteria and in some eukaryotes. In this chapter, we describe an RNA structure analysis technique called "in-line probing." This assay makes use of the natural instability of RNA to elucidate secondary structure characteristics and ligand-binding capabilities of riboswitches in an entirely protein-free manner. Although this method has most frequently been used to examine riboswitches, the structures of any RNAs can be examined using this technique.

Inhibition of glycogen synthase kinase-3.

Abstract: There are two homologous forms of glycogen synthase kinase (GSK)-3, GSK-3alpha and GSK-3beta, which play overlapping roles in the regulation of Wnt, Hedgehog, and insulin pathways, as well as the activation of nuclear factor (NF)-kappaB-mediated gene transcription. These signaling pathways regulate gene transcription, cell cycle, apoptosis, inflammation, glucose metabolism, stem-cell renewal, and differentiation. More than 50 GSK-3 inhibitors representing a wide range of chemical structures have already been identified, and their utility in the treatment of type II diabetes mellitus, Alzheimer's disease, bipolar diseases, cancer, and other human pathologies is currently being investigated. Here, we discuss two methods of GSK-3 inhibition, which can be used to determine the involvement of GSK-3 in a cellular process of interest.

Chaperone-mediated autophagy.

Abstract: Chaperone-mediated autophagy (CMA) is the only type of autophagy in mammalian cells able to selectively degrade cytosolic proteins in lysosomes. CMA is maximally activated in response to stressors such as prolonged starvation, exposure to toxic compounds, or oxidative stress. We have found that CMA activity decreases in aging and in some age-related disorders such as Parkinson's disease. Impaired CMA under these conditions may be responsible for the accumulation of damaged proteins inside cells and for their higher vulnerability to stressors. In contrast to other forms of autophagy, where substrates are engulfed or sequestered along with other cytosolic components, CMA substrates are translocated one-by-one across the lysosomal membrane. Changes in the levels/activity of the lysosomal components required for substrate translocation can be used to stimulate CMA activity. However, the most unequivocal method to measure CMA is by directly tracking the translocation of substrate proteins into isolated lysosomes.

Assembling DNA Barcodes

Abstract: The Barcode of Life initiative represents an ambitious effort to develop an identification system for eukaryotic life based on the analysis of sequence diversity in short, standardized gene regions. Work is furthest advanced for members of the animal kingdom. In this case, a target gene region has been selected (cytochrome c oxidase I) and pilot studies have validated its effectiveness in species discovery and identification. Based on these positive results, there is now a growing effort to both gather barcode records on a large-scale for members of this kingdom and to identify target barcode regions for the other kingdoms of eukaryotes. In this chapter, we detail the protocols involved in the assembly of DNA barcode records for members of the animal kingdom, but many of these approaches are of more general application.

Drug Delivery Systems - An Overview

Abstract: This is an overview of drug delivery systems (DDS), starting with various routes of drug administration. Various drug formulations, as well as devices used for drug delivery and targeted drug delivery, are then described. Delivery of proteins and peptides presents special challenges. Nanoparticles are considered to be important in refining drug delivery; they can be pharmaceuticals as well as diagnostics. Refinements in drug delivery will facilitate the development of personalized medicine, which includes pharmacogenomics, pharmacogenetics, and pharmacoproteomics. The ideal DDS, commercial aspects, current achievements, challenges, and future prospects are also discussed.

Adipose-Derived Stem Cells

Abstract: Human adipose tissue has been shown to contain a population of cells that possesses extensive proliferative capacity and the ability to differentiate into multiple cell lineages. These cells are referred to as adipose tissue-derived stem cells (ADSCs) and are generally similar, though not identical, to mesenchymal stem cells (also referred to as marrow stromal cells). ADSCs for research are most conveniently extracted from tissue removed during an elective cosmetic liposuction procedure but may also be obtained from resected adipose tissue. This chapter describes surgical procedures associated with improved ADSC recovery and the processes by which aspirated adipose tissue is washed and digested with collagenase to yield a heterogeneous population from which ADSCs can be expanded. The large volume of tissue obtained from a liposuction procedure (average approximately 2 L), combined with the relatively high frequency of ADSC within the digestate, yields substantially more stem cells than can be realized from marrow without extensive expansion in culture.

Overview of artificial neural networks.

Abstract: The artificial neural network (ANN), or simply neural network, is a machine learning method evolved from the idea of simulating the human brain. The data explosion in modem drug discovery research requires sophisticated analysis methods to uncover the hidden causal relationships between single or multiple responses and a large set of properties. The ANN is one of many versatile tools to meet the demand in drug discovery modeling. Compared to a traditional regression approach, the ANN is capable of modeling complex nonlinear relationships. The ANN also has excellent fault tolerance and is fast and highly scalable with parallel processing. This chapter introduces the background of ANN development and outlines the basic concepts crucially important for understanding more sophisticated ANN. Several commonly used learning methods and network setups are discussed briefly at the end of the chapter.

Comparison of protein force fields for molecular dynamics simulations.

Abstract: In the context of molecular dynamics simulations of proteins, the term "force field" refers to the combination of a mathematical formula and associated parameters that are used to describe the energy of the protein as a function of its atomic coordinates. In this review, we describe the functional forms and parameterization protocols of the widely used biomolecular force fields Amber, CHARMM, GROMOS, and OPLS-AA. We also summarize the ability of various readily available noncommercial molecular dynamics packages to perform simulations using these force fields, as well as to use modern methods for the generation of constant-temperature, constant-pressure ensembles and to treat long-range interactions. Finally, we finish with a discussion of the ability of these force fields to support the modeling of proteins in conjunction with nucleic acids, lipids, carbohydrates, and/or small molecules.

Mesenchymal stem cells from adult bone marrow.

Abstract: Mesenchymal stem cells (MSCs), sometimes referred to as marrow stromal cells or multipotential stromal cells, represent a class of adult progenitor cells capable of differentiation to several mesenchymal lineages. They can be isolated from many tissues although bone marrow has been used most often. The MSCs may prove useful for repair and regeneration of a variety of mesenchymal tissues such as bone, cartilage, muscle, marrow stroma, and the cells produce useful growth factors and cytokines that may help repair additional tissues. There is also evidence for their differentiation to nonmesenchymal lineages, but that work will not be considered here. This chapter will provide the researcher with some background, and then provide details on MSC isolation, expansion and multilineage differentiation. These are the beginning steps toward formulating tissue repair strategies. The methods provided here have been used in many laboratories around the world and the reader can begin by following the methods presented here, and then test other methods if these prove unsatisfactory for your intended purpose.

Overview of adipose tissue and its role in obesity and metabolic disorders.

Abstract: As the result of its apparent structural and histological simplicity, adipose tissue (AT) functions initially were limited to energy storage, insulation, and thermoregulation. Only decades later was the extraordinarily dynamic role of AT recognized, revealing its participation in a broad range of physiological processes, including reproduction, apoptosis, inflammation, angiogenesis, blood pressure, atherogenesis, coagulation, fibrinolysis, immunity and vascular homeostasis with either direct or indirect implications in the regulation of proliferation. The functional pleiotropism of AT relies on its ability to synthesize and, in some cases,secrete a large number of enzymes, hormones, growth factors, cytokines, complement factors, and matrix and membrane proteins, collectively termed adipokines. At the same time, white AT expresses receptors for most of these factors, warranting a wide cross-talk at both local and systemic levels in response to metabolic changes or other external stimuli. In this chapter, mounting evidence on the specific characteristics of AT from different depots is outlined in relation to fat distribution and comorbidity development. The current knowledge in this field is reviewed with a broad perspective ranging from classification, structure, and distribution to the key functional roles of AT with a particular focus on the role of adipokines and their involvement in the metabolic disorders accompanying obesity.

Multiple Sequence Alignment

Abstract: The increasing importance of Next Generation Sequencing (NGS) techniques has highlighted the key role of multiple sequence alignment (MSA) in comparative structure and function analysis of biological sequences. MSA often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families. Significant advances have been achieved in this field, and many useful tools have been developed for constructing alignments, although many biological and methodological issues are still open. This chapter first provides some background information and considerations associated with MSA techniques, concentrating on the alignment of protein sequences. Then, a practical overview of currently available methods and a description of their specific advantages and limitations are given, to serve as a helpful guide or starting point for researchers who aim to construct a reliable MSA.

FlyBase : a database for the Drosophila research community.

Abstract: FlyBase ( http://flybase.org ) is the primary database of integrated genetic and genomic data about the Drosophilidae, of which Drosophila melanogaster is the most extensively studied species. Information in FlyBase originates from a variety of sources ranging from large-scale genome projects to the primary research literature. Data-types include sequence-level gene models, molecular classification of gene product functions, mutant phenotypes, mutant lesions and chromosome aberrations, gene expression patterns, transgene insertions, and anatomical images. Query tools allow interrogation of FlyBase through DNA or protein sequence, by gene or mutant name, or through terms from the several ontologies used to capture functional, phenotypic, and anatomical data. Links between FlyBase and external databases provide extensive opportunity for extending exploration into other model organism databases and resources of biological and molecular information. This review will introduce the FlyBase web server and query tools.

Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes.

Abstract: Fluorescence in situ hybridization (FISH) of specific DNA probes has become a widely used technique mostly for chromosome analysis and for studies of the chromosomal location of specific DNA segments in metaphase preparations as well as in interphase nuclei. FISH on 3D-preserved nuclei (3D-FISH) in combination with 3D-microscopy and image reconstruction is an efficient tool to analyze the spatial arrangement of targeted DNA sequences in the nucleus. Recent developments of a "new generation" of confocal microscopes that allow the distinct visualization of at least five different fluorochromes within one experiment opened the way for multicolor 3D-FISH experiments. Thus, numerous differently labeled nuclear targets can be delineated simultaneously and their spatial interrelationships can be analyzed on the level of individual nuclei.In this chapter, we provide protocols for the preparation of complex DNA-probe sets suitable for 3D-FISH with up to six different fluorochromes, for 3D-FISH on cultured mammalian cells (growing in suspension or adherently) as well as on tissue sections, and for 3D immuno-FISH.In comparison with FISH on metaphase chromosomes and conventional interphase cytogenetics, FISH on 3D-preserved nuclei requires special demands with regard to probe quality, fixation, and pretreatment steps of cells in order to achieve the two goals, namely the best possible preservation of the nuclear structure and at the same time an efficient probe accessibility.

Methods for Assessing Autophagy and Autophagic Cell Death

Abstract: Autophagic (or type 2) cell death is characterized by the massive accumulation of autophagic vacuoles (autophagosomes) in the cytoplasm of cells that lack signs of apoptosis (type 1 cell death). Here we detail and critically assess a series of methods to promote and inhibit autophagy via pharmacological and genetic manipulations. We also review the techniques currently available to detect autophagy, including transmission electron microscopy, half-life assessments of long-lived proteins, detection of LC3 maturation/aggregation, fluorescence microscopy, and colocalization of mitochondrion- or endoplasmic reticulum-specific markers with lysosomal proteins. Massive autophagic vacuolization may cause cellular stress and represent a frustrated attempt of adaptation. In this case, cell death occurs with (or in spite of) autophagy. When cell death occurs through autophagy, on the contrary, the inhibition of the autophagic process should prevent cellular demise. Accordingly, we describe a strategy for discriminating cell death with autophagy from cell death through autophagy.

The canonical Wnt/beta-catenin signalling pathway.

Abstract: Embryonic development of multicellular organisms is an incredibly complex process that relies heavily on evolutionarily conserved signalling pathways to provide crucial cell-cell communication. Typically, secreted signalling proteins such as Wnts, BMPs, and Hedgehogs released by one cell population will trigger concentration-dependent responses in other cells located some distance away. In adults, the same signalling pathways orchestrate tissue renewal in organs such as the intestine and skin, and direct tissue regeneration in many organs following injury. Strict regulation of these signalling pathways is critical, with insufficient or excess activity having catastrophic consequences including severe developmental defects or, later in life, cancer. This chapter deals with the beta-catenin-dependent branch of Wnt signalling (also referred to the canonical pathway).

Quantitative analysis of protein-RNA interactions by gel mobility shift

Abstract: The gel mobility shift assay is routinely used to visualize protein-RNA interactions. Its power resides in the ability to resolve free from bound RNA with high resolution in a gel matrix. In this chapter, we review the quantitative application of this approach to elucidate thermodynamic properties of protein-RNA complexes. Assay designs for titration, competition, and stoichiometry experiments are presented for two unrelated model complexes.

Models of Caenorhabditis elegans infection by bacterial and fungal pathogens.

Abstract: The nematode Caenorhabditis elegans is a simple model host for studying the relationship between the animal innate immune system and a variety of bacterial and fungal pathogens. Extensive genetic and molecular tools are available in C. elegans, facilitating an in-depth analysis of host defense factors and pathogen virulence factors. Many of these factors are conserved in insects and mammals, indicating the relevance of the nematode model to the vertebrate innate immune response. Here, we describe pathogen assays for a selection of the most commonly studied bacterial and fungal pathogens using the C. elegans model system.

Stable isotope labeling by amino acids in cell culture (SILAC)

Abstract: Quantitative proteomics has become a pivotal tool that has been applied to the investigation of many different biological processes such diverse as the detection of biomarkers in tissue samples, the regulation of cell signaling, and the characterization of protein interactions. Stable isotope labeling techniques have facilitated the precise quantitation of changes in protein abundance by mass spectrometry. Among different choices, Stable Isotope Labeling by Amino acids in Cell culture (SILAC) is an easy and reliable method for unbiased comparative proteomic experiments, which has been employed to study post-translational modifications such as protein phosphorylation and methylation, to characterize signaling pathways and to determine specific protein interactions. Here we describe detailed procedures for SILAC experiments in mammalian and yeast cells.

Isolation of human adipose-derived stem cells from biopsies and liposuction specimens.

Abstract: Adipose tissue has proven to serve as an abundant, accessible, and rich source of adult stem cells with multipotent properties suitable for tissue engineering and regenerative medical applications Here, we describe a detailed method for the isolation and expansion of adipose-derived stem cells (ASCs) We present a large scale procedure suitable for processing >100 mL volumes of lipoaspirate tissue specimens and a small scale procedure suitable for processing adipose tissue biopsy specimens of < 05 g Although we have focused on the isolation of ASCs from human adipose tissue, the procedure can be applied to adipose tissues from other species with minimal modifications

The GAL4 system : a versatile system for the expression of genes.

Abstract: Over the past decade the adoption and refinement of the GAL4 system by the Drosophila field has resulted in a wide array of tools with which the researcher can drive transgene expression in a precise spatiotemporal pattern. The GAL4 system relies on two components: (1) GAL4, a transcriptional activator from yeast, which is expressed in a tissue-specific manner and (2) a transgene under the control of the upstream activation sequence that is bound by GAL4 (UASG). The two components are brought together in a simple genetic cross. In the progeny of the cross, the transgene is only transcribed in those cells or tissues expressing the GAL4 protein. Recent modifications of the GAL4 system have improved the control of both the initiation and the spatial restriction of transgene expression. Here we describe the GAL4 system highlighting the properties that make it a powerful tool for the analysis of gene function in Drosophila and higher organisms.

Hemagglutination-inhibition test for avian influenza virus subtype identification and the detection and quantitation of serum antibodies to the avian influenza virus.

Abstract: The hemagglutination-inhibition (HI) assay is a classical laboratory procedure for the classification or subtyping of hemagglutinating viruses. For the avian influenza (AI) virus, the HI assay is used to identify the hemagglutinin (H) subtype of an unknown AI virus isolate or the HA subtype specificity of antibodies to AI virus. Since the HI assay is quantitative, it is frequently applied to evaluate the antigenic relationships between different AI virus isolates of the same subtype. The basis of the HI test is inhibition of hemagglutination with subtype-specific antibodies. The HI assay is a relatively inexpensive procedure utilizing standard laboratory equipment, is less technical than molecular tests, and is easily completed within several hours. However, when working with uncharacterized viruses or antibody subtypes, the library of reference reagents required for identifying antigentically distinct AI viruses and/or antibody specificities from multiple lineages of a single hemagglutinin subtype requires extensive laboratory support for the production and optimization of reagents.

Evolution of the Wnt pathways.

Abstract: Wnt proteins mediate the transduction of at least three major signaling pathways that play central roles in many early and late developmental decisions. They control diverse cellular behaviors, such as cell fate decisions, proliferation, and migration, and are involved in many important embryological events, including axis specification, gastrulation, and limb, heart, or neural development. The three major Wnt pathways are activated by ligands, the Wnts, which clearly belong to the same gene family. However, their signal is then mediated by three separate sets of extracellular, cytoplasmic, and nuclear components that are pathway-specific and that distinguish each of them. Homologs of the Wnt genes and of the Wnt pathways components have been discovered in many eukaryotic model systems and functional investigations have been carried out for most of them. This review extracts available data on the Wnt pathways, from the protist Dictyostelium discoideum to humans, and provides from an evolutionary prospective the overall molecular and functional conservation of the three Wnt pathways and their activators throughout the eukaryotic superkingdom.

CLIP: Crosslinking and ImmunoPrecipitation of In Vivo RNA Targets of RNA-Binding Proteins

Abstract: We present a newly developed method for fixing RNA-protein complexes in situ in living cells and the subsequent purification of the RNA targets. Using this approach, complex tissue such as mouse brain can be ultraviolet (UV) irradiated to covalently crosslink RNA-protein complexes. Once covalently bound, RNA-protein complexes can be purified under stringent conditions, allowing a highly specific purification scheme to be employed. After UV irradiation, the tissue is solubilized and the RNA partially digested, allowing a small fragment to remain attached to protein. RNA-protein complexes of interest are partially purified by immunoprecipitation and noncovalently associated RNA removed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). These purified RNA-protein complexes are isolated and treated with proteinase K, which removes protein but leaves intact RNA. This RNA is abundant enough, and competent for, RNA linker ligation, reverse transcriptase polymerase chain reaction (RT-PCR) amplification, and sequencing. Database matching of these short 70- to 100-nt RNA CLIP (crosslinking and immunoprecipitation of RNA-protein complexes) "tags," which mark the native binding sites of RNA binding proteins, potentially allows the entire target repertoire of an RNA binding protein to be determined.