Chromosome Structural Analysis — A Practical Guide

. W. A. Bickmore (ed.). Oxford University Press, Oxford. 1999. Pp. 209. Price £29.95, paperback. ISBN 0 19 963698 2.

As we enter the postgenomics age, finding the answers to questions about the packaging, physical organization (and perhaps indexing), behaviour and accessibility of all of that sequenced DNA become more and more important. This volume, in the Practical Approach Series now consisting of more than 150 volumes, covers some of the key techniques used over the last 5 years to study the complex and hierarchical packaging of DNA and associated proteins. Advances in methods to study the functioning of the nucleus have been rapid and the volume presents a useful selection of these.

About half the chapters describe in situ hybridization to chromosomal targets of one form or another: Karl Ekwall and Janet Partridge discuss key techniques used for fission yeast chromosome analysis by the laboratories of Robin Allshire and M. Yanagida, and Jeff Craig introduces the purposes and techniques for in situ hybridization to vertebrate metaphase chromosomes. The following chapters, by Beth Sullivan and Peter Warburton, and Joanna Bridger and Peter Lichter, add dynamics to this view by showing in situ methods applied to looking at chromosomes at all stages of the vertebrate cell cycle. Abby Dernburg takes us up a level to show the use of in situ hybridization to study the organization of whole mounts of tissue — Drosophila, Caenorhabditis and yeast.

Outside the in situ hybridization chapters, Dean Jackson details a range of extraction methods that enable nuclear substructure and contents to be analysed — or not, as evidenced by the rightly generous peppering of the chapter with ‘attempted’, ‘presumed’, ‘thought’, ‘believed’ and similar words! Electron imaging is out of fashion at the moment, but for ‘chromosome structural analysis’ the light microscope is just too limited in its resolution, whatever one might learn from ingenious probes and stains, so ultimately, visualization of what is there in the electron microscope will show chromosome structure, notwithstanding the formidable problems of artefact-free fixation, preparation and examination. Jason Swedlow describes the impressive methods pioneered by T. Hirano and Timothy Mitchison for in vitro assembly of Xenopus mitotic chromosomes. Two chapters concentrate on advanced molecular techniques to study protein–DNA interactions: Donald Macleod describes the ingenious ligation-mediated polymerase chain reaction method pioneered by Pfeifer and colleagues, while Giacomo Cavalli, Valerio Orlando and Renato Paro show how formaldehyde fixation can be used to investigate chromatin–protein interactions. The final chapter, by Christine Farr, is somewhat different from others in describing methods to generate human mini-chromosomes by seeding de novo telomere formation.

In the main, chapters in this volume give extensive details and tips on using techniques which are perforce described only briefly in the Materials and methods section of primary papers. The standard presentation of protocols with Equipment and Reagents, Methods and footnotes is easy to follow. It is interesting to note chapter authors’ personal comments about aspects of the technique that they consider critically important. Three of the in situ hybridization chapters discuss the feature of probe length (including impressive comparative pictures by Dernburg), when perhaps 3 years ago little mention would be made of this. But some factors I would have considered equally important — stringency and probe concentration, for example, are hardly mentioned, and methods of adjustment and calculation are not described.

None of the chapters covers work on plants, but more generally I felt authors could have tried to make techniques more accessible outside the specific system they are working with: the supposition being that future researchers will want to use the techniques in a heterologous system or in a different way. There is only one figure showing meiosis (too small to really see), and, given the impressive progress in plants, yeast and mammals with understanding of pairing and recombination using in situ hybridization and immunostaining in the last 5 years, I think that meiosis deserved a specialized chapter.

In a book like this, which includes only brief reviews of the science, I am always annoyed to find that titles of articles are not given in the citations. This adds a completely unnecessary step to one’s search for the most relevant primary paper describing the work. As all but the two DNA-protein chapters require microscopy, I was happy to see the inclusion of numerous colour illustrations, but unfortunately, some chapters are entirely devoid of illustrations which will not help the reader with the assessment of their data. Both indexes and lists of suppliers are notoriously difficult to get right: these are about average and could certainly have done with checks for names and consistency.

Reading my review after a month’s break, I am surprised that it comes over as rather negative, although my feeling about both the individual chapters and the compilation as a whole was positive. Would I buy this book? It gives specialized chromosome and chromatin protocols, so does not cover material repeated in a plethora of free catalogues and kit instructions: there is little (perhaps no) reason to buy most molecular biology technique books except for the remarkable, decade old Sambrook et al. (1989). But Chromosome Structural Analysis? I would buy it only if I saw a cross-reference in the primary literature to the exact technique I wanted to replicate. In more general terms, and without any implied criticism of the excellent job done by the editor in selecting a up-to-date and useful set of protocols, what is to be gained by publishing compilations like this, rather than making reference to the day-to-day protocols of individual laboratories on their own web-sites?