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A correction to the article "Benchmarking Tools for the Alignment of Functional Noncoding DNA," by D. A. Pollard, C. M. Bergman, J. Stoye, S. E. Celniker and M. B. Eisen that was published in the 2004 issue of the periodical "BMC Bioinformatics" is presented.

Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are “off” and survival/growth pathways “on.” Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal disc-derived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common “cell line“ gene expression pattern., Organismic and Evolutionary Biology

The past year has been a spectacular one for Drosophila research. The sequencing and annotation of the Drosophila melanogaster genome has allowed a comprehensive analysis of the first three eukaryotes to be sequenced-yeast, worm and fly-including an analysis of the fly's influences as a model for the study of human disease. This year has also seen the initiation of a full-length cDNA sequencing project and the first analysis of Drosophila development using high-density DNA microarrays containing several thousand Drosophila genes. For the first time homologous recombination has been demonstrated in flies and targeted gene disruptions may not be far off.

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

We constructed a bacterial artificial chromosome (BAC)-based physical map of chromosomes 2 and 3 of Drosophila melanogaster, which constitute 81% of the genome. Sequence tagged site (STS) content, restriction fingerprinting, and polytene chromosome in situ hybridization approaches were integrated to produce a map spanning the euchromatin. Three of five remaining gaps are in repeat-rich regions near the centromeres. A tiling path of clones spanning this map and STS maps of chromosomes X and 4 was sequenced to low coverage; the maps and tiling path sequence were used to support and verify the whole-genome sequence assembly, and tiling path BACs were used as templates in sequence finishing.

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

Using markers that are expressed at muscle attachment sites, we have examined the early pupal development (first 36 hr) of Indirect Flight Muscle (IFM) attachments in the fruit fly Drosophila melanogaster. Expression of the Drosophila homologs of vertebrate integrins, the Position-Specific (PS) antigens, is known to differentially mark epidermal (PS1alpha) and muscle (PS2alpha) components of the developing IFM attachment sites. During myogenesis, PS2alpha is detected transiently in imaginal myoblasts that fuse with persistent larval muscles to give rise to the Dorsal Longitudinal Muscles (DLMs), but not in myoblasts that fuse de novo to give rise to the Dorso Ventral Muscles. The integrins are not expressed at attachment sites when the muscle fibers first make their appearance (12-20 hr). Following muscle-epidermal contact, PS1 and PS2 are detected at muscle attachment sites. PS1 expression is at the muscle ends and also in the long epidermal processes that connect the developing muscle fibers to their sites of attachment in the epidermis, while PS2 expression is restricted to the muscle ends. Epidermal cells that will contribute to the adult attachment sites are defined as early as the third larval instar. Both anterior and posterior sites of attachment of the IFMs are marked by the expression of reporter beta-galactosidase activity in a P-element line B14.0, which is an insertion at the stripe locus. B14.0 (stripe) is seen in distinct domains in the wing and leg imaginal discs which give rise to the thoracic cuticle. The expression is maintained during pupal development. The B14.0 (stripe) expressing epidermal cells contact the developing muscle fibers, leading to the formation of the myotendon junction. We show that the dorsal and ventral attachment sites of one group of IFMs, the DVMs arise from two different imaginal discs (wing and leg, respectively), which may explain the differential effect of mutations such as bendless on these muscles. Attachment sites for the other group of IFMs, the DLMs, on the other hand, arise from one imaginal disc (wing). B14.0 (stripe) expression defines epidermal cells of the adult attachment sites and is likely to function during early events leading to the formation of muscle-epithelial contacts. The PS integrins are detected at later stages, suggesting a role in the stabilization and maturation of the muscle-epidermal contacts into myotendon junctions.

Background: In the fruitfly Drosophila melanogaster, segment identity is specified by the homoeotic selector genes of the bithorax and Antennapedia complexes. The functions of these genes in the segmental specification of the Drosophila ectoderm have been well studied, but their roles in muscle development have been relatively poorly investigated. Recent experiments have strongly suggested that homeotic selector genes are directly involved in one aspect of mesodermal patterning during Drosophila embryogenesis. But muscle development is a complex process, requiring for its completion the correct positioning of the epidermis, the nervous system and the developing muscles in a segment-specific manner. Many aspects of homeotic selector gene function in this process remain to be understood., Results: In flies that are homozygous for three mutant alleles (anterobithorax, bithorax3, postbithorax) of the Ultrabithorax gene, the third thoracic segment (T3) is transformed towards the second (T2). The adults have two pairs of wings, but the homeotically transformed T3 (HT3) has only rudimentary indirect flight muscles. We used the 'four-winged' fly to study the role of homeotic selector genes in the development of the indirect flight muscles, which we classify into four 'events'. First, the determination of the segment-specific pattern of myoblasts in the larval thorax; second, the specific pattern of migration of myoblasts during metamorphosis; third, the fusion of myoblasts to form adult indirect flight muscles and fourth, the development of the branching pattern of adult motor innervation. Our study shows that the segmental identity of the epidermis determines the segment-specific pattern and number of myoblasts on the larval discs, and the pattern of their migration during metamorphosis. The segmental identity of the mesoderm, however, is crucial for the fusion of myoblasts to form indirect flight muscles, and also influences the branching pattern of innervation of indirect flight muscles., Conclusions: Segmental information expressed in the ectoderm, and the autonomous function of homeotic selector genes in the mesoderm, are both required for the complete development of indirect flight muscles.

An enzyme system prepared from Saccharomyces cerevisiae carries out the replication of exogenous yeast plasmid DNA. Replication in vitro mimics that in vivo in that DNA synthesis in extracts of strain cdc8, a temperature-sensitive DNA replication mutant, is thermolabile relative to the wild-type, and in that aphidicolin inhibits replication in vitro. Furthermore, only plasmids containing a functional yeast replicator, ARS, initiate replication at a specific site in vitro. Analysis of replicative intermediates shows that plasmid YRp7, which contains the chromosomal replicator ARS1, initiates bidirectional replication in a 100 bp region within the sequence required for autonomous replication in vivo. Plasmids containing ARS2, another chromosomal replicator, and the ARS region of the endogenous yeast plasmid 2 microns circle give similar results, suggesting that ARS sequences are specific origins of chromosomal replication. Used in conjunction with deletion mapping, the in vitro system allows definition of the minimal sequences required for the initiation of replication.