Parent-dependent loss of gene silencing during interspecies hybridization

Speciation depends on the establishment of reproductive barriers that allow populations to diverge from each other. Such divergence may involve protein sequence, copy number, or expression changes that are predicted to result in dosage-dependent effects. In plants, such as Arabidopsis thaliana and A. arenosa, postzygotic species barriers often affect seed abortion, and hybrid failure resembles that of interploidy crosses where the paternal genome is in excess. We used this species pair to explore the relationship between hybrid incompatibility and gene silencing. In incompatible crosses, the normally silenced and heterochromatic element ATHILA was expressed from the paternal, but not maternal, chromosomes. Three Polycomb-regulated genes; PHERES1, MEIDOS, and MEDEA, were also induced. At PHERES1, maternal imprinting of the promoter was disrupted, and paternal imprinting of MEDEA appeared to be lost. The rate of hybrid seed lethality was sensitive to parental genome dosage, and gene activation was proportional to the dosage of parental genomes. A causal link was established between PHE1 and hybrid seed failure; a transposon-induced disruption of PHE1 significantly improved fertility. We propose that the dosage-dependent regulation of chromatin could be a universal phenomenon affecting lethality in interspecies hybrids.     

Fundamentals of DNA hybridization arrays for gene expression analysis

DNA hybridization arrays [also known as macroarrays, microarrays and/or high-density oligonucleotide arrays (Gene Chips)] bring gene expression analysis to a genomic scale by permitting investigators to simultaneously examine changes in the expression of literally thousands of genes. For hybridization arrays, the general approach is to immobilize gene-specific sequences (probes) on a solid state matrix (nylon membranes, glass microscope slides, silicon/ceramic chips). These sequences are then queried with labeled copies of nucleic acids from biological samples (targets). The underlying theory is that the greater the expression of a gene, the greater the amount of labeled target, and hence, the greater output signal. In spite of the simplicity of the experimental design, there are at least four different platforms and several different approaches to processing and labeling the biological samples. Moreover, investigators must also determine whether they will utilize commercially available arrays or generate their own. This review will cover the status of the hybridization array field with an eye toward underlying principles and available technologies. Future developments and technological trends will also be evaluated.     

A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus

The recent sequencing of a large number of Xenopus tropicalis expressed sequences has allowed development of a high-throughput approach to study Xenopus global RNA gene expression. We examined the global gene expression similarities and differences between the historically significant Xenopus laevis model system and the increasingly used X.tropicalis model system and assessed whether an X.tropicalis microarray platform can be used for X.laevis. These closely related species were also used to investigate a more general question: is there an association between mRNA sequence divergence and differences in gene expression levels? We carried out a comprehensive comparison of global gene expression profiles using microarrays of different tissues and developmental stages of X.laevis and X.tropicalis. We (i) show that the X.tropicalis probes provide an efficacious microarray platform for X.laevis, (ii) describe methods to compare interspecies mRNA profiles that correct differences in hybridization efficiency and (iii) show independently of hybridization bias that as mRNA sequence divergence increases between X.laevis and X.tropicalis differences in mRNA expression levels also increase.     

Intra- and interspecies relatedness ofYersinia pestis by DNA hybridization and its relationship toYersinia pseudotuberculosis

The biochemical characteristics ofYersinia pestis are presented and compared with those ofY. pseudotuberculosis. Motility at 28°C, urease, fermentation of rhamnose, and growth rate on nutrient agar are the best means of separating these organisms. DNA hybridization studies demonstrated thatY. pestis strains are 90% or more interrelated and thatY. pestis andY. pseudotuberculosis are indistinguishable by DNA relatedness. On the basis of DNA data and biochemical and antigenic similarity, these organisms should be treated as two separate subspecies of the same species.Y. pseudotuberculosis was described beforeY. pestis and therefore has priority.Y. pseudotuberculosis subsp.pseudotuberculosis andY. pseudotuberculosis subsp.pestis are recommended as new designations forY. pseudotuberculosis andY. pestis. For medical purposes,Y. pestis andY. pseudotuberculosis can and should continue to be used.     

Split-dose recovery is due to the repair of DNA double-strand breaks

DNA double-strand breaks are the molecular lesions the repair of which leads to the reappearance of the shoulder observed in split-dose experiments. This conclusion is based on results obtained with the help of a diploid yeast mutant rad 54-3 which is temperature-conditional for the repair of DNA double-strand breaks. Two repair steps must be met to yield the reappearance of the shoulder on a split-dose survival curve: the repair of double-strand breaks during the interval between two doses and on the nutrient agar plate after the second dose. In yeast lethality may be attributable to either an unrepaired double-strand break (i.e. a double-strand break is a potentially lethal lesion) or to the interaction of two double-strand breaks (misrepair of double-strand breaks). Evidence is presented that the two cellular phenomena of liquid holding recovery (repair of potentially lethal damage) and of split-dose recovery (repair of sublethal damage) are based on the repair of the same molecular lesion, the DNA double-strand break.     

The application of DNA repair vectors to gene therapy

The nature of DNA, the sequence of the human genome and our increased understanding of the genetic basis of many inherited and acquired disorders have made the possibility of curing diseases a reality. The modulation of a host's genome is now the ultimate goal in the treatment of genetic diseases. Historically, gene therapy recognized two very different approaches: gene replacement or augmentation and gene repair. Gene repair precisely targets and corrects the chromosomal mutation responsible for a genetic and/or acquired disorder. Many recent advances have been made in this area of research.     

Germline susceptibility to colorectal cancer due to base-excision repair gene defects

DNA repair is a key process in the maintenance of genome integrity. Here, we present a large, systematically collected population-based association study (2,239 cases; 1,845 controls) that explores the contribution to colorectal cancer incidence of inherited defects in base-excision repair (BER) genes. We show that biallelic MUTYH defects impart a 93-fold (95% CI 42-213) excess risk of colorectal cancer, which accounts for 0.8% of cases aged <55 years and 0.54% of the entire cohort. Penetrance for homozygous carriers was almost complete by age 60 years. Significantly more biallelic carriers had coexisting adenomatous polyps. However, notably, 36% of biallelic carriers had no polyps. Three patients with heterozygous MUTYH defects carried monoallelic mutations in other BER genes (OGG1 and MTH1). Recessive inheritance accounted for the elevated risk for those aged <55 years. However, there was also a 1.68-fold (95% CI 1.07-2.95) excess risk for heterozygous carriers aged >55 years, with a population attributable risk in this age group of 0.93% (95% CI 0%-2.0%). These data provide the strongest evidence to date for a causative role of BER defects in colorectal cancer etiology and show, to our knowledge for the first time, that heterozygous MUTYH mutations predispose to colorectal cancer later in life. These findings have clinical relevance for BER gene testing for patients with colorectal cancer and for genetic counseling of their relatives.     

Terminally differentiated human neurons repair transcribed genes but display attenuated global DNA repair and modulation of repair gene expression

Repair of UV-induced DNA lesions in terminally differentiated human hNT neurons was compared to that in their repair-proficient precursor NT2 cells. Global genome repair of (6-4)pyrimidine-pyrimidone photoproducts was significantly slower in hNT neurons than in the precursor cells, and repair of cyclobutane pyrimidine dimers (CPDs) was not detected in the hNT neurons. This deficiency in global genome repair did not appear to be due to denser chromatin structure in hNT neurons. By contrast, CPDs were removed efficiently from both strands of transcribed genes in hNT neurons, with the nontranscribed strand being repaired unexpectedly well. Correlated with these changes in repair during neuronal differentiation were modifications in the expression of several repair genes, in particular an up-regulation of the two structure-specific nucleases XPG and XPF/ERCC1. These results have implications for neuronal dysfunction and aging.     

Structure and expression of the alkB gene of Escherichia coli related to the repair of alkylated DNA

When the alkB gene of Escherichia coli that controls sensitivity of bacteria to methyl methanesulfonate was placed under the control of the lac regulatory region on a multicopy plasmid, the gene product, AlkB protein, was overproduced. By monitoring the band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the protein was purified to near physical homogeneity. An amino-terminal sequence and total amino acid composition of the purified AlkB protein were in accord with the amino acid sequence deduced from the nucleotide sequence of the alkB gene, determined by the phage M13 dideoxy method. It was concluded that the AlkB protein is comprised of 216 amino acids and has a molecular weight of 23,900. The nucleotide sequence analysis also revealed that the ada and alkB genes are adjacent on the E. coli chromosome and that the first initiation codon for AlkB protein overlaps with the termination codon for Ada protein. We constructed hybrid plasmids carrying an alkB'-lacZ' fusion, with or without the ada control region, and investigated expression of the alkB gene in response to the alkylating agent. We obtained evidence that the ada and alkB genes constitute an operon.     

Alterations in expression and structure of the DNA repair gene XRCC1.

The repair-associated gene XRCC1 was previously cloned by complementing the hamster mutant EM9, which has a high rate of spontaneous SCE and hypersensitivity to DNA damaging agents. In analyzing XRCC1 gene expression, similar levels of steady-state mRNA were found in normal cells, Bloom's syndrome cells with altered SCE, and in squamous carcinoma cells with differential X-ray sensitivity. An EcoRI restriction fragment-length polymorphism previously identified in XRCC1 did not correlate with the repair phenotypes of these cells. The mRNA of XRCC1 decreased to 20-40% after treatment of cells with a DNA damaging agent. XRCC1 also showed tissue specific expression in rats. The mRNA levels were high in testis (7-8 fold), ovary (3-4 fold) and brain (4-5 fold), when compared with those in intestine, liver and spleen (1-2 fold). These data and the high levels of XRCC1 protein detected in testis indicate that XRCC1 may play an important role in DNA processing during meiogenesis and recombination in germ cells.     

The ancient and evolving roles of cohesin in gene expression and DNA repair

The cohesin complex, named for its key role in sister chromatid cohesion, also plays critical roles in gene regulation and DNA repair. It performs all three functions in single cell eukaryotes such as yeasts, and in higher organisms such as man. Minor disruption of cohesin function has significant consequences for human development, even in the absence of measurable effects on chromatid cohesion or chromosome segregation. Here we survey the roles of cohesin in gene regulation and DNA repair, and how these functions vary from yeast to man.