About this book
Genomic sequences, now emerging at a rapid rate, are greatly expediting certain aspects of molecular biology. However, in more complex organisms, predicting mRNA structure from genomic sequences can often be difficult. Alternative splicing, the use of alternative promoters, and orphan genes without known analogues can call present difficulties in the predictions of the structure of mRNAs or even in gene detection. Both computational and experimental methods remain useful for recognizing genes and transcript templates, even in sequenced DNA. Methods for producing full-length cDNAs are important for determining the structures of the proteins the mRNA encodes, the positions of promoters, and the considerable regulatory information for translation that may be encoded in the 5' untranslated regions of the mRNA. Methods for studying levels of mRNA and their changes in different physiological circumstances are rapidly evolving, and the information from this area will rival the superabundance of information derived from genomic sequences. In particular, cDNAs can be prepared even from single cells, and this approach has already yielded valuable information in several areas. To the extent that reliable and reproducible information, both quantitative and qualitative, can be generated from very small numbers of cells, there are rather remarkable possibilities for complementing functional and genetic analysis of developmental patterns with descriptions of changes in mRNAs. Dense array analysis promises to be particularly valuable for the rapid expression pattern of known genes, while other methods such as gel display approaches offer the opportunity of discovering unidentified genes or for investigating species whose cDNAs or genomes have not been studied intensively. Knowledge of mRNA structure, genomic location, and patterns of expression must be converted into information of the function of the encoded proteins. Each gene can be the subject of years of intensive study. Nevertheless, a number of methods are being developed that use cDNA to predict properties or permit the selective isolation of cDNAs encoding proteins with certain general properties such as selective isolation of cDNAs encoding proteins with certain general properties such as subcellular location. This volume presents an update of a number of approaches relevant to the areas referred to above. The technology in this field is rapidly evolving and these contributions represent a snapshot in time of the number of currently available and useful approaches to the problems referred to above. The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the series contains much material still relevant today--truly an essential publication for researchers in all fields of life sciences.
Contents
cDNA Preparation: J. Estee, P. Crino, and J. Eberwine, Preparation of cDNA from Single Cells and Subcellular Regions. P. Carninci and Y. Hayashizaki, High-Efficiency Full-length cDNA Cloning. M. Liu, Y.V.B.K. Subramanyam, and N. Baskaran, Preparation and Analysis of cDNA from a Small Number of Hematopoietic Cells. C. Aston, C. Hiort and D.C. Schwartz, Optical Mapping: An Approach for Fine Mapping. Gene Identification: R.J. Mural, Current Status of Computational Gene Finding: A Perspective. D.M. Church and A.J. Buckler, Gene Identification by Exon Amplification. J.T. den Dunnen, Cosmid-Based Exon Trapping. A.D. Simmons and M. Lovett, Direct cDNA Selection Using Large Genomic DNA Targets. S. Parimoo and S.M. Weissman, cDNA Selection: An Approach for Isolation of Chromosome Specific cDNAs. K. Gardiner, Saturation Identification of Coding Sequences in Genomic DNA. Patterns of mRNA Expression: R. Drmanac and S. Drmanac, cDNA Screening by Array Hybridization. M.B. Eisen and P.O. Brown, DNA Arrays for Analysis of Gene Expression. M.D. Clark, G.D. Panopoulou, D.J. Cahill, K. Bussow, and H. Lehrach, Construction and Analysis of Arrayed cDNA Libraries. K.J. Martin and A.B. Pardee, Principles of Differential Display. Y. Prashar and S.M. Weissman, A Method for Display of 3'-End Fragments of Restriction Enzyme Digested cDNAs for Analysis of Differential Gene Expression. Y.V.B.K. Subrahmkanyam, N. Baskaran, P.E. Newburger, and S.M. Weissman, A Modified Method for the Display of 3'-End Restriction Fragments of cDNAs: Molecular Profiling of Gene Expression in Neutrophils. T. Ito and Y. Sakaki, Fluorescent Differential Display (FDD): A Fast and Reliable Method for Message Display PCR. F. Mathieu-Daude, T. Trenkle, J. Welsh, B. Jung, T. Vogt, and M. McClelland, Identification of Differentially Expressed Genes Using RNA Fingerprinting by Arbitrarily Primed PCR. M. Hubank and D.G. Schatz, cDNA RDA: A Sensitive and Flexible Method for the Identification of Differentially Expressed Genes. L. Diatchenko, S. Lukyanov, Y.-F.C. Lau and P.D. Siebert, Suppression Subtractive Hybridization: A Versatile Method for Identifying Differentially Expressed Genes. T. Trenkle, F. Mathieu-Daude, J. Welsh and M. McClelland, Reduced Complexity Probes for DNA Arrays. Alastair J.H. Brown, Catherine Hutchings, J.F. Burke and L.V. Mayne, Targeted Display, A New Technique for the Analysis of Differential Gene Expression. Functional Relationship Among cDNA Translation Productions: M.-C. Marsolier and A. Sentenac, Pol III-Based Two-Hybrid System. F.J. Germino and N.K. Moskowitz, Screening for Protein-Protein Interactions. N.L. Sticker and M. Li, Using the Lac Repressor System to Identify Interacting Proteins. K.A. Jacobs, L.A. Collins-Racie, M. Colbert, M. Duckett, C. Evans, M. Golden-Fleet, K. Kelleher, R. Kriz, E.R. LaVallie, D. Merberg, V. Spaulding, J. Stover, M.J. Williamson and J.M. McCoy, A Genetic Selection for Isolating cDNA Clones That Encode Signal Peptides. K. Tashiro, T. Nakamura and T. Honjo, The Signal Sequence Trap Method. S. Stahl, J. Odeberg, M. Larsson, O. Rosok, A.H. Ree, and J. Lundeberg, Solid-Phase Differential Display and Bacterial Expression Systems in Selection and Functional Analysis of cDNAs. P. Ross-Macdonald, A. Sheehan, C. Friddle, G.S. Roeder, and M. Snyder, Transposon Mutagenesis for the Analysis of Protein Production, Function, and Localization. Author Index. Subject Index.
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