The May issue of CSH Protocols is now live, and in it you’ll find featured articles on classic techniques for the analysis of chromosomes. With the leaps and bounds being made in epigenetics these days, knowing your way around chromatin becomes even more valuable. This month’s freely accessible articles give you methods for chromosome analysis in Drosophila and in Mouse.

Mapping Protein Distributions on Polytene Chromosomes by Immunostaining takes advantage of the formidable size and structure of the large polytene chromosomes found in Drosophila salivary glands. These easily dissected chromosomes allow mapping of chromosomal protein distributions at very high resolution. May’s issue also contains a protocol for the Dissection of Larval Salivary Glands and Polytene Chromosome Preparation.

The second featured method for May, Karyotyping Mouse Cells, is drawn from the widely used laboratory manual Manipulating the Mouse Embryo. A karyotype is a visual presentation of a cell’s chromosomes, and can be used as a test for quickly identifying chromosomal abnormalities.

This month’s issue of CSH Protocols features an article by Andrew Salinger and Monica Justice, detailing a technique for Mouse Mutagenesis Using N-Ethyl-N-Nitrosourea (ENU) (article is freely available as one of our featured protocols). Back in the ancient days of my graduate school work, the idea of doing large scale forward genetics in mouse was unthinkable. Who had the space, let alone the funding and personnel to keep and track all of those cages? It was always one of those reasons we grumbled about the Drosophila labs, and the incredibly cool tools they had at their disposal. Over the years, the techniques were refined, and now, according to Justice, screens like this are an “established as part of a mouse geneticist’s toolkit,” and can be effective even in labs with very limited amounts of mouse space. So it’s nice to see this incredibly productive method readily available for use in mouse. Now if we can just do something about that pesky internal development that’s so limiting to imaging experiments…..

The March issue of CSH Protocols has two featured (freely available) protocols on high-throughput methods for studying gene regulation.

The first method approaches regulatory analysis through epigenetic mechanisms. Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation, developed by Marcos Estecio and Jean-Pierre Issa of the MD Anderson Cancer Center, and Pearlly Yan and Tim Huang of the Ohio State University Comprehensive Cancer Center is a rapid, genome-wide method for identifying regions where methylation is occurring. This protocol has proven successful for proven successful for use in comparing normal tissues and tumors, helping researchers better understand the factors responsible for cancer.

The second protocol looks at the binding of regulatory proteins to DNA and their role in transcriptional regulation. The method, DNA Immunoprecipitation (DIP) for the Determination of DNA-binding Specificity, allows researchers to determine the specific DNA sequence that a regulatory protein binds. The technique allows for rapid screening of the entire genome for these binding sites, which gives insight into which genes these protein factors control.

Tandem repeats are short stretches of DNA that are repeated head-to-tail. These are increasingly used as markers in forensic and genotyping research. But not all tandem repeats are created equal, as they display varying rates of stability. A repeat must exhibit enough instability to generate enough heterozygosity in a population to be of use in discriminating between individuals in a population. Too much instability though makes it difficult to look over large evolutionary distances, as it becomes difficult to see relatedness between samples. To determine which repeats are useful as markers, Kevin Verstrepen’s lab at Harvard has created the SERV (”Sequence-Based Estimation of Repeats Variability”) applet, which enables finding repeats in DNA sequences and estimating their variability. First introduced in this Genome Access paper, Sequence-based estimation of minisatellite and microsatellite repeat variability, Verstrepen and colleagues have now written a guide to using the SERV Applet, available in this month’s issue of CSH Protocols.

Legendre, M., Pochet, N., Pak, T., Verstrepen, K.J. (2007). Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Research, 17(12), 1787-1796. DOI: 10.1101/gr.6554007
Legendre, M., Verstrepen, K.J. (2008). Using the SERV Applet to Detect Tandem Repeats in DNA Sequences and to Predict Their Variability. Cold Spring Harbor Protocols, 2008(2), pdb.ip50-pdb.ip50. DOI: 10.1101/pdb.ip50

Over the last few months (and in coming months), we’ve presented a series of protocols for genotyping and DNA isolation in a variety of model organisms. Much of this material was adapted in advance from Genetic Variation: A Laboratory Manual, which is now available from CSHL Press. It’s a difficult subject for a laboratory manual, as it’s such a rapidly advancing field, and the question when it was proposed was, is it possible to put together a manual that isn’t obsolete the moment it’s published? Read the rest of this entry »

September’s issue of CSH Protocols is upon us (my, that was a quick summer–Kurt Weill sure knew what he was talking about). We’re featuring two protocols this month, both available freely to non-subscribers (as are all of our sample protocols). The first is for generating mouse models for squamous cell carcinoma and the second is for the Oligonucleotide Ligation Assay (OLA), used for finding Single-Nucleotide Polymorphisms (SNP’s). Read the rest of this entry »

The July issue of CSH Protocols is available and features a set of articles detailing the basics for common Bioinformatics techniques (and just in time for the 4th of July, allowing me to make a “blast” pun). Read the rest of this entry »

With the explosive growth in Epigenetics research in recent years, new techniques have come along that help clarify the relationships between proteins (or protein complexes) and chromosomal DNA. Chromatin Immunoprecipitation (ChIP) technology allows the dynamic visualization of chromosomal proteins in their natural context. Read the rest of this entry »

With the rapid growth of siRNA techniques in so many experimental systems, it’s important to know your options for getting those RNAs into your cells or organism of choice. This month CSH Protocols presents four different methods for delivering siRNAs and shRNAs into various organisms. Read the rest of this entry »

Rochelle Easton Esposito, working with the Genetics Society of America, has put together a spectacular set of video interviews with the founders of modern genetics. The series, “Conversations In Genetics“, provides an oral history of the last century of biology, and also serves as a larger commentary on how ideas evolve. What sets these interviews apart is that they’re each conducted by a prominent colleague, someone with a great depth of knowledge of the discoveries of the person being interviewed. These DVDs make wonderful teaching tools and are fascinating viewing for anyone interested in the process of science. Read the rest of this entry »