Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line

SQUAT: A web tool to mine human, murine and avian SAGE data

Background

There is an increasing need in transcriptome research for gene expression data and pattern warehouses. It is of importance to integrate in these warehouses both raw transcriptomic data, as well as some properties encoded in these data, like local patterns.

Description

We have developed an application called SQUAT (SAGE Querying and Analysis Tools) which is available at: . This database gives access to both raw SAGE data and patterns mined from these data, for three species (human, mouse and chicken). This database allows to make simple queries like "In which biological situations is my favorite gene expressed?" as well as much more complex queries like: ≪what are the genes that are frequently co-over-expressed with my gene of interest in given biological situations?≫. Connections with external web databases enrich biological interpretations, and enable sophisticated queries. To illustrate the power of SQUAT, we show and analyze the results of three different queries, one of which led to a biological hypothesis that was experimentally validated.

Conclusion

SQUAT is a user-friendly information retrieval platform, which aims at bringing some of the state-of-the-art mining tools to biologists.

LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs

BACKGROUND

Obese and lean pig breeds show obvious differences in muscle growth; however, the molecular mechanism underlying phenotype variation remains unknown. Prenatal muscle development programs postnatal performance. Here, we describe a genome-wide analysis of differences in prenatal skeletal muscle between Tongcheng (a typical indigenous Chinese breed) and Landrace (a leaner Western breed) pigs.

RESULTS

We generated transcriptome profiles of skeletal muscle from Tongcheng and Landrace pigs at 33, 65 and 90 days post coitus (dpc), using long serial analysis of gene expression (LongSAGE). We sequenced 317,115 LongSAGE tags and identified 1,400 and 1,201 differentially expressed transcripts during myogenesis in Tongcheng and Landrace pigs, respectively. From these, the Gene Ontology processes and expression patterns of these differentially expressed genes were constructed. Most of the genes showed different expression patterns in the two breeds. We also identified 532, 653 and 459 transcripts at 33, 65 and 90 dpc, respectively, that were differentially expressed between the two breeds. Growth factors, anti-apoptotic factors and genes involved in the regulation of protein synthesis were up-regulated in Landrace pigs. Finally, 12 differentially expressed genes were validated by quantitative PCR.

CONCLUSION

Our data show that gene expression phenotypes differ significantly between the two breeds. In particular, a slower muscle growth rate and more complicated molecular changes were found in Tongcheng pigs, while genes responsible for increased cellular growth and myoblast survival were up-regulated in Landrace pigs. Our analyses will assist in the identification of candidate genes for meat production traits and elucidation of the development of prenatal skeletal muscle in mammals.

Serial analysis of gene expression

Serial analysis of gene expression (SAGE) is a method used to obtain comprehensive, unbiased and quantitative gene-expression profiles. Its major advantage over arrays is that it does not require a priori knowledge of the genes to be analyzed and reflects absolute mRNA levels. Since the original SAGE protocol was developed in a short-tag (10-bp) format, several modifications have been made to produce longer SAGE tags for more precise gene identification and to decrease the amount of starting material necessary. Several SAGE-like methods have also been developed for the genome-wide analysis of DNA copy-number changes and methylation patterns, chromatin structure and transcription factor targets. In this protocol, we describe the 17-bp longSAGE method for transcriptome profiling optimized for a small amount of starting material. The generation of such libraries can be completed in 7-10 d, whereas sequencing and data analysis require an additional 2-3 wk.

Avian model for B-cell immunology--new genomes and phylotranscriptomics

The purpose of this review is to discuss the use of chicken and other model organisms in the study of B-cell development and function as well as to highlight the opportunities afforded by the expanded genome-sequencing efforts. A brief introduction on chicken B-cell biology is followed by discussion of somatic cell reverse genetic approaches using the DT40 cell line. The unique advantages of the DT40 system are emphasized with discussion on B-cell receptor signalling research as well as on DNA repair and mechanisms of immunoglobulin diversification. An attempt is made to compare and contrast the results from chicken with mouse knockouts on the one hand and RNAi with human cell lines on the other. Chicken is also emerging strongly as a platform for gene expression analysis, and avian studies are compared with mammalian studies. Multi-species gene co-expression analysis, which could also be termed phylotranscriptomics, aims to use the evolutionary distance between organisms to its advantage. This approach, still in its infancy, is also reviewed and its applicability to the chicken is discussed.

Manipulation of small RNAs to modify the chicken transcriptome and enhance productivity traits

In recent years there has been a revolution in our understanding of genes and how they come to control the physical outcomes of development. Central to this has been the understanding of the cellular processes of RNA interference (RNAi), for which the Nobel Prize for Physiology or Medicine was awarded in 2006. Coupled with this has been the recognition that microRNAs are key mediators of this process within cells. RNAi whether mediated exogenously by synthetic oligonucleotides or vector-delivered double stranded RNA or endogenously by microRNAs can have a profound and specific effect on gene expression. Elucidating and understanding these processes in the chicken will provide critical information to enable more precise control over breeding strategies for improvement of traits in production poultry, either by direct or indirect means. It will also provide alternative strategies for the control and prevention of important avian diseases.

Gene function analysis using the chicken B-cell line DT40

Quidquid agis, prudenter agas et respice finem!-Whatever you do, do it wisely and consider the goal. In consideration of that sage advice, the chicken B-cell line DT40 is an excellent model cell system to study the function of vertebrate genes. In addition to being highly amenable to gene manipulations, the recent influx of genome and gene/protein resources allows for the straightforward selection, design, and targeting of candidate genes for knockout analysis. This chapter will give a step by step standardized protocol to creating a gene knockout mutant in DT40. With careful consideration, the methods and protocols described herein can be easily modified to allow for further gene manipulations such as creating a knockin or a conditional mutant.

Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis

This article reports a cDNA collection representing more than 2000 new, full-length transcripts from a high-quality cDNA library.

A large number of cDNA inserts were sequenced from a high-quality library of chicken bursal lymphocyte cDNAs. Comparisons to public gene databases indicate that the cDNA collection represents more than 2,000 new, full-length transcripts. This resource defines the structure and the coding potential of a large fraction of B-cell specific and housekeeping genes whose function can be analyzed by disruption in the chicken DT40 B-cell line.