Two jobs for the origin replication complex

Functional analysis of an Orc6 mutant in Drosophila

The origin recognition complex (ORC) is a 6-subunit complex required for the initiation of DNA replication in eukaryotic organisms. ORC is also involved in other cell functions. The smallest Drosophila ORC subunit, Orc6, is important for both DNA replication and cytokinesis. To study the role of Orc6 in vivo, the orc6 gene was deleted by imprecise excision of P element. Lethal alleles of orc6 are defective in DNA replication and also show abnormal chromosome condensation and segregation. The analysis of cells containing the orc6 deletion revealed that they arrest in both the G(1) and mitotic stages of the cell cycle. Orc6 deletion can be rescued to viability by a full-length Orc6 transgene. The expression of mutant transgenes of Orc6 with deleted or mutated C-terminal domain results in a release of mutant cells from G(1) arrest and restoration of DNA replication, indicating that the DNA replication function of Orc6 is associated with its N-terminal domain. However, these mutant cells accumulate at mitosis, suggesting that the C-terminal domain of Orc6 is important for the passage through the M phase. In a cross-species complementation experiment, the expression of human Orc6 in Drosophila Orc6 mutant cells rescued DNA replication, suggesting that this function of the protein is conserved among metazoans.

Minimal interval defined on 7q in uterine leiomyoma

Uterine leiomyomata are benign, smooth-muscle tumors. The tumors are very common, affecting approximately 10-15 million women in the United States annually. Uterine leiomyomata are often asymptomatic, but may cause symptoms that range in severity from mild abdominal discomfort to uterine prolapse. Several different chromosomal aberrations have been found in the tumor tissue. Because of the common occurrence of this tumor and the potential severity of associated sequelae, research delineating the different molecular subtypes is needed. Deletions on the long arm of chromosome 7 are believed to be the most common genetic anomaly in uterine leiomyoma. The size of the deletion varies, which makes it difficult to identify the genes that, upon deletion, contribute to tumor growth. The smallest previously defined interval was >12,000 kb. We have narrowed a minimal region to an interval of <500 kb.

Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation

The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation ( approximately 2 bits) at a minor groove that faces RepA. However, B-form DNA can support only 1 bit of sequence conservation via contacts into the minor groove. The high conservation in RepA sites therefore implies a distorted DNA helix with direct or indirect contacts to the protein. Here I show that a high minor groove conservation signature also appears in sequence logos of sites for other replication origin binding proteins (Rts1, DnaA, P4 alpha, EBNA1, ORC) and promoter binding proteins (sigma(70), sigma(D) factors). This finding implies that DNA binding proteins generally use non-B-form DNA distortion such as base flipping to initiate replication and transcription.

Repression and activation by multiprotein complexes that alter chromatin structure

Recent studies have provided strong evidence that macromolecular complexes are used in the cell to remodel chromatin structure during activation and to create an inaccessible structure during repression, Although there is not yet any rigorous demonstration that modification of chromatin structure plays a direct, causal role in either activation or repression, there is sufficient smoke to indicate the presence of a blazing inferno nearby. It is clear that complexes that remodel chromatin are tractable in vitro; hopefully this will allow the establishment of systems that provide a direct analysis of the role that remodeling might play in activation. These studies indicate that establishment of functional systems to corroborate the elegant genetic studies on repression might also be tractable. As the mechanistic effects of these complexes are sorted out, it will become important to understand how the complexes are regulated. In many of the instances discussed above, the genes whose products make up these complexes were identified in genetic screens for effects on developmental processes. This implies a regulation of the activity of these complexes in response to developmental cues and further implies that the work to fully understand these complexes will occupy a generation of scientists.

Common structural features of replication origins in all life forms

Origins of replication (ORIs) among prokaryotes, viruses, and multicellular organisms appear to possess simple tri-, tetra-, or higher dispersed repetitions of nucleotides, AT tracts, inverted repeats, one to four binding sites of an initiator protein, intrinsically curved DNA, DNase I-hypersensitive sites, a distinct pattern of DNA methylation, and binding sites for transcription factors. Eukaryotic ORIs are sequestered on the nuclear matrix; this attachment is supposed to facilitate execution of their activation/deactivation programs during development. Furthermore, ORIs fall into various classes with respect to their sequence complexity: those enriched in AT tracts, those with GA- and CT-rich tracts, a smaller class of GC-rich ORIs, and a major class composed of mixed motifs yet containing distinct AT and polypurine or GC stretches. Multimers of an initiator protein in prokaryotes and viruses that might have evolved into a multiprotein replication initiation complex in multicellular organisms bind to the core ORI, causing a structural distortion to the DNA which is transferred to the AT tract flanking the initiator protein site; single-stranded DNA-binding proteins then interact with the melted AT tract as well as with the DNA polymerase alpha-primase complex in animal viruses and mammalian cells, causing initiation in DNA replication. ORIs in mammalian cells seem to colocalize with matrix-attached regions and are proposed to become DNase I-hypersensitive during their activation.

Sequencing and promoter analysis of the genomic region between the rat neuronal nicotinic acetylcholine receptor beta 4 and alpha 3 genes

Nicotinic acetylcholine receptors (nAChRs) found on neurons are composed of ligand binding (alpha) and structural (beta) subunits. Different combinations of alpha and beta subunits produce nAChR subtypes with different pharmacological and ion-conducting properties. Transcriptional regulation may be an important determinant of receptor subtype in a neuronal population and thus influence transmission through a ganglion or group of neurons in the CNS by controlling the nAChR subtype(s) present. In order to understand the transcriptional regulation of neuronal nAChRs by cell contact and electrical activity, it will be first necessary to identify DNA elements that control the expression of members of this family and to identify factors required for the expression of these genes. In this report we have begun to examine the 5'-flanking region of one member of the nAChR family of genes, alpha 3. We have sequenced the region between the beta 4 and alpha 3 genes and have identified two promoter regions in the beta 4-alpha 3 intergenic region. One region is close to the beta 4 gene downstream of exon 6 and has strong promoter activity in both orientations; the other is close to the start of the alpha 3 gene coding region. A region with putative silencer activity is also found near the upstream promoter. This bidirectional promoter region could be involved in the control of alpha 3 and beta 4 gene expression.