Conversion events in gene clusters

<p>Abstract</p> <p>Background</p> <p>Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are difficult to analyze due to their structural complexity and their complicated evolutionary histories, reflecting a variety of large-scale mutational events. In particular, conversion events can mislead inferences about the relationships among these regions, as traced by traditional methods such as construction of phylogenetic trees or multi-species alignments.</p> <p>Results</p> <p>To correct the distorted information generated by such methods, we have developed an automated pipeline called CHAP (Cluster History Analysis Package) for detecting conversion events. We used this pipeline to analyze the conversion events that affected two well-studied gene clusters (α-globin and β-globin) and three gene clusters for which comparative sequence data were generated from seven primate species: CCL (chemokine ligand), IFN (interferon), and CYP2abf (part of cytochrome P450 family 2). CHAP is freely available at <url>http://www.bx.psu.edu/miller_lab</url>.</p> <p>Conclusions</p> <p>These studies reveal the value of characterizing conversion events in the context of studying gene clusters in complex genomes.</p

Structure and expression of Ri T-DNA from Agrobacterium rhizogenes in: Nicotiana tabacum

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Further characterization of the 5'-flanking DNA of the gene encoding human plasminogen activator inhibitor-1

Previous nucleotide (nt) sequence analysis of the 5'-flanking DNA of the gene (PAI-1) encoding plasminogen activator inhibitor-1 revealed an extensive region of shared nt sequence identity with the 5'-flanking region of the gene (t-PA) encoding tissue-type plasminogen activator [Bosma et al., J. Biol. Chem. 263 (1988) 9129-9141]. Additional sequence (1642 bp) from the PAI-1 gene 5'-flanking region reveals that these 'PAI-1/t-PA' sequence elements share an alignment that contains a total of 575 positions. This additional PAI-1 5'-flanking sequence also contains two Alu elements that form inverted repeats. Southern-blot analysis using the PAI-1/t-PA element as a probe indicates that this element is repeated in the human genome. which supports the classification of this element as a medium reiteration frequency sequence [Jurka, Nucleic Acids Res. 18 (1990) 137-141

Nucleotide sequence analysis of the TL-DNA of an Agrobacterium rhizogenes agropine type plasmid: identification of open-reading frames

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