A Large Database of Chicken Bursal ESTs as a Resource for the Analysis of Vertebrate Gene Function

Abstract

Chicken B cells create their immunoglobulin repertoire within the Bursa of Fabricius by gene conversion. The high homologous recombination activity is shared by the bursal B-cell-derived DT40 cell line, which integrates transfected DNA constructs at high rates into its endogenous loci. Targeted integration in DT40 is used frequently to analyze the function of genes by gene disruption. In this paper, we describe a large database of >7000 expressed sequence tags (ESTs) from bursal lymphocytes that should be a valuable resource for the identification of gene disruption targets in DT40. ESTs of interest can be recognized easily by online BLAST or keyword searches. Because the database reflects the gene expression profile of bursal lymphocytes, it provides valuable hints as to which genes might be involved in B-cell-specific processes related to immunoglobulin repertoire formation, signal transduction, transcription, and apoptosis. This large collection of chicken ESTs will also be useful for gene expression studies and comparative gene mapping within the chicken genome project. Details of the bursal EST sequencing project and access to database search forms can be found on the DT40 web site

Analysis of gene expression during myc oncogene-induced lymphomagenesis in the bursa of Fabricius

“…Finally, 50 selected nonoverlapping expressed sequence tagged clones from a normal 2-week posthatching bursal library, DKFZ426, previously sequenced and gene-identified by J.-M. Buerstedde (21), were supplied by the Resource Center of the German Human Genome Project and added to the array. The completed array contained 3,011 chicken lymphocyte cDNA spots representing about 2,200 different genes.…”

A gene-based radiation hybrid map of chicken microchromosome 14: Comparison to human and alignment to the assembled chicken sequence

“…All publicly available chicken EST (>420 000) from Genbank and other sources [1,4,37] were collected in a local database, after which EST selection and primer design were performed after comparison to the human genome sequence using the Iccare web server [26]. EST markers corresponding to the COQ7 and DREV1 genes had been previously developed in our laboratory and were found to be linked to the GGA14 RH linkage group.…”

“…Thus, a large genomic toolset was developed including a detailed consensus linkage map of the genome including over two thousand markers [15,16]. Large collections of chicken expressed sequence tags (EST) were released [1,4,37] and bacterial artificial chromosome (BAC) libraries [9,21] were constituted and used to assemble both local and genomewide chicken BAC contig maps [11,29]. BAC contigs are usually used as a platform on which full genome sequences are assembled.…”

ChickRH6: a chicken whole-genome radiation hybrid panel

“…Two BAC libraries were constructed in the chicken [5,20] and a large amount of chicken ESTs were produced [1,34], (see also: http://chick.umist.ac.uk, http://www.chickest.udel.edu).…”