Introns in sequence tags

Computational methods for exon detection

Computer methods for the complete and accurate detection of genes in vertebrate genomic sequences are still a long way to perfection. The intermediate task of identifying the coding moiety of genes (coding exons) is now reasonably well achieved using a combination of methods. After reviewing the intrinsic difficulties in interpreting vertebrate genomic sequences, this article presents the state-of-the-art, with an emphasis on similarity search methods and the resources available through Internet.

Osteoclast molecular phenotyping by random cDNA sequencing

The osteoclast is a cell type that is highly specialized for its bone resorption function. In order to decipher the numerous biochemical functions of osteoclasts, a description of the gene expression profile of osteoclasts would be beneficial. We have sought to identify genes that are highly expressed in osteoclasts by partially sequencing 194 randomly chosen cDNA clones from a representative rabbit osteoclast cDNA library. Comparison to nucleic acid and protein sequence databases indicates that 135 of these cDNAs are identical to or homologous to known mammalian genes. Reverse transcription-polymerase chain reaction (RT-PCR) assays with microisolated osteoclasts were used to verify the osteoclast expression of some of these genes. Fifty-nine cDNAs, including two abundantly expressed species, have no significant similarity to the sequence databases and likely represent novel genes. The most abundant of the osteoclast expressed genes encode cofilin and the vacuolar H(+)-ATPase 16 kd subunit. Each were represented at a frequency of 4.1% of the clones in the library (95% confidence interval = 2.4-6.6%). The high expression of these gene products is consistent with the high motility of osteoclasts and their very active hydrogen ion secretion. Other abundantly expressed sequences include beta-actin (95% C.I. = 2.0-6.0%), creatine kinase B (95% C.I. = 1.2-4.9%), c-fms and ribosomal protein L18 (95% C.I. = 0.8-4.3%), and cathepsin-OC2, cyclophilin, delta-aminolevulinate synthetase, 16S mitochondrial rRNA, and two novel gene sequences (95% C.I. = 0.5-3.6%).

A quality control algorithm for DNA sequencing projects

Heterologous DNA sequences from rearrangements with the genomes of host cells, genomic fragments from hybrid cells, or impure tissue sources can threaten the purity of libraries that are derived from RNA or DNA. Hybridization methods can only detect contaminants from known or suspected heterologous sources, and whole library screening is technically very difficult. Detection of contaminating heterologous clones by sequence alignment is only possible when related sequences are present in a known database. We have developed a statistical test to identify heterologous sequences that is based on the differences in hexamer composition of DNA from different organisms. This test does not require that sequences similar to potential heterologous contaminants are present in the database, and can in principle detect contamination by previously unknown organisms. We have applied this test to the major public expressed sequence tag (EST) data sets to evaluate its utility as a quality control measure and a peer evaluation tool. There is detectable heterogeneity in most human and C.elegans EST data sets but it is not apparently associated with cross-species contamination. However, there is direct evidence for both yeast and bacterial sequence contamination in some public database sequences annotated as human. Results obtained with the hexamer test have been confirmed with similarity searches using sequences from the relevant data sets.

cDNA cloning, structural features, and eucaryotic expression of human TAG-1/axonin-1

Axonal surface glycoproteins, composed of repeated immunoglobulin-like and fibronectin-type-III(FNIII)-like domains, mediate adhesion between axons or between axons and non-neuronal cells or extracellular matrix proteins. Several representatives of this group promote neurite outgrowth, when presented as substratum to neurons in culture, and have been implicated in axonal guidance mechanisms. TAG-1 and axonin-1 are presumptive species homologues of the rat and the chick, respectively; together with F11/F3, they form a subgroup of Ig/FNIII-like molecules containing a glycosyl-PtdIns membrane anchor. Recent reports on tumor suppressor genes encoding Ig-like and FNIII-like sequences prompted us to isolate the human homologue to TAG-1 and axonin-1. Polymerase chain reaction (PCR) primers were designed to regions conserved in both TAG-1 and axonin-1 using deoxyinosine at ambiguous positions. An expected 1000-bp fragment was obtained from cDNA derived from adult human cerebellum. Using this PCR fragment as a probe, several clones were isolated from a human fetal brain cDNA library. Nucleotide sequence analysis of a full-length clone, as expected, revealed a high degree of similarity to rat TAG-1 (91% identity) and chicken axonin-1 (75% identity) at the amino acid level. The encoded protein was then transiently expressed in monkey COS1 cells, and a stable mouse myeloma cell line was established expressing human TAG-1/axonin-1. The transfected COS1 and myeloma cells showed immunoreactivity on the cell surface with polyclonal anti-(chicken axonin-1) serum. On Western blots, the same antibodies recognized the recombinant protein migrating slightly slower on SDS/PAGE than chicken axonin-1. A comparison of chicken and human brain-tissue proteins by Western-blot analysis revealed a similar apparent molecular mass difference between the two species, which might be due to three additional N-glycosylation sites present on human TAG-1/axonin-1. Immunostaining of cryostat sections of embryonic retinas with polyclonal anti-(axonin-1) serum showed similar expression patterns in chicken and human samples at corresponding developmental stages. An additional shared feature of human TAG-1/axonin-1, rat TAG-1 and chick axonin-1 is their attachment to the cell membrane with a glycosyl-PtdIns anchor.