Gene Mapping, Discovery, and Expression: Methods and Protocols

ISBN-13: 9781617376511 / Angielski / Miękka / 2010 / 334 str.

Minou Bina

Opis

Completion of the sequence of the human genome represents an unpar- leled achievement in the history of biology. The project has produced nearly complete, highly accurate, and comprehensive sequences of genomes of s- eral organisms including human, mouse, drosophila, and yeast. Furthermore, the development of high-throughput technologies has led to an explosion of projects to sequence the genomes of additional organisms including rat, chimp, dog, bee, chicken, and the list is expanding. The nearly completed draft of genomic sequences from numerous species has opened a new era of research in biology and in biomedical sciences. In keeping with the interdisciplinary nature of the new scientific era, the chapters in Gene Mapping, Discovery, and Expression: Methods and Protocols recapitulate the necessity of integration of experimental and computational tools for solving - portant research problems. The general underlying theme of this volume is DNA sequence-based technologies. At one level, the book highlights the importance of databases, genome-browsers, and web-based tools for data access and ana- sis. More specifically, sequencing projects routinely deposit their data in p- licly available databases including GenBank, at the National Center of Biotechnology (NCBI) in the United States; EMBL, maintained by the European Bioinformatics Institute; and DDBJ, the DNA Data Bank of Japan. Currently, several browsers offer facile access to numerous genomic DNA sequences for gene mapping and data retrieval.

Spis treści

Use of Genome Browsers to Locate Your Favorite Genes Minou Bina Methods for Identifying and Mapping Recent Segmental and Gene Duplications in Eukaryotic Genomes Razi Khaja, Jeffrey R. MacDonald, Junjun Zhang, and Stephen W. Scherer Identification and Mapping of Paralogous Genes on a Known Genomic DNA Sequence Minou Bina Quantitative DNA Fiber Mapping in Genome Research and Construction of Physical Maps Heinz-Ulrich G. Weier and Lisa W. Chu PRINS for Mapping Single-Copy Genes Avirachan T. Tharapel and Stephen S. Wachtel VISTA Family of Computational Tools for Comparative Analysis of DNA Sequences and Whole Genomes Inna Dubchak and Dmitriy V. Ryaboy Computational Prediction of cis-Regulatory Modules from Multispecies Alignments Using Galaxy, Table Browser, and GALA Laura Elnitski, David King, and Ross C. Hardison Comparative Promoter Analysis in Vertebrate Genomes with the CORG Workbench Christoph Dieterich and Martin Vingron cis-Regulatory Region Analysis Using BEARR Vinsensius Berlian Vega A Database of 9-Mers from Promoter Regions of Human Protein-Coding Genes Minou Bina, Phillip Wyss, and Syed Rehan Shah A Program Toolkit for the Analysis of Regulatory Regions of Genes Phillip Wyss, Sheryl A. Lazarus, and Minou Bina Analysis of Allele-Specific Gene Expression Julian C. Knight Construction of microRNA-Containing Vectors for Expression in Mammalian Cells Yoko Fukuda, Hiroaki Kawasaki, and Kazunari Taira Mining Microarray Data at NCBI's Gene Expression Omnibus (GEO) Tanya Barrett and Ron Edgar The Stanford Microarray Database: A User's Guide Jeremy Gollub, Catherine A. Ball, and Gavin Sherlock Detecting Nucleosome Ladders on Unique DNA Sequences in Mouse Liver Nuclei Tomara J. Fleury, Alfred Cioffi, and Arnold Stein DNA Methyltransferase Probing of DNA-Protein Interactions Scott A. Hoose and Michael P. Kladde Protein Binding Microarrays (PBMs) for Rapid, High-Throughput Characterization of the Sequence Specificities of DNA Binding Proteins Michael F. Berger and Martha L. Bulyk Quantitative Profiling of Protein-DNA Binding on Microarrays Jiannis Ragoussis, Simon Field, and Irina A. Udalova Analysis of Protein-DNA Binding by Streptavidin-Agarose Pulldown Kenneth K. Wu Isolation and Mass Spectrometry of Specific DNA Binding Proteins Mariana Yaneva and Paul Tempst Isolation of Transcription Factor Complexes by In Vivo Biotinylation Tagging and Direct Binding to Streptavidin Beads Patrick Rodriguez, Harald Braun, Katarzyna E. Kolodziej, Ernie de Boer, Jennifer Campbell, Edgar Bonte, Frank Grosveld, Sjaak Philipsen, and John Strouboulis Index

Blurb

Completion of the sequence of the human genome and the development of high-throughput technologies have opened a new era of research in biology and medicine. In Gene Mapping, Discovery, and Expression: Methods and Protocols, a panel of researchers from around the world and from a variety of disciplines offer a unique blend of computational tools and experimental techniques for gene mapping, comparative genomics, and studies of the control of gene expression. On the computational side, for beginners in the field, the book describes web-based technologies to localize and map genes, to access and retrieve data from microarray databases, to conduct comparative genomics, and to discover the potential "codes" in genomic DNA that may control the expression of protein-coding genes. Detailed experimental techniques described include methods for studying chromatin structure and allele-specific gene expression, methods for high-throughput analysis and characterization of transcription factor binding elements, and methods for isolation and identification of proteins that interact with DNA. The protocols in the book follow the successful Methods in Molecular Biology™ series format, offering step-by-step instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding pitfalls.
Cutting-edge and interdisciplinary, Gene Mapping, Discovery, and Expression: Methods and Protocols offers a collection of DNA-sequence-based technologies for gene discovery, retrieval of gene expression data, discovery of regulatory elements, and discovery of transcription factors that interact with DNA.