Molecular cytotaxonomy of primates by chromosomal in situ suppression hybridization

A new strategy for analyzing chromosomal evolution in primates is presented using chromosomal in situ suppression (CISS) hybridization. Biotin-labeled DNA libraries from flow-sorted human chromosomes are hybridized to chromosome preparations of catarrhines, platyrrhines, and prosimians. By this approach rearrangements of chromosomes that occurred during hominoid evolution are visualized directly at the level of DNA sequences, even in primate species with pronounced chromosomal shuffles

Determination of plasmid copy number in yeast transformants by means of agarose plugs

The determination of plasmid copy number in Saccharomyces cerevisiaetransformants containing circular or linear plasmids is currently performed with total yeast DNA extracts obtained from cultures grown under selection. The determination is based essentially on quantitative Southern hybridization of an appropirate probe to a sequence present both on plasmid and chromosomal DNA in digested or undigested samples run out on conventional agarose gels. The DNA extraction procedure calls for treatment of cell lysates with organic solvents that could entail systemic losses of eithr plasmid or chromosomal DNA thus producing artifactual results. We propose here a method based on the assumption that quantitative analysis of plasmid and chromosomal DNA extracted from yeast cells embedded in agarose plugs will furnish more reliable results. With this procedure the cells are lysed in situ, thus avoiding possible losses of material, and the chromosomes and plasmid DNAs, trapped within the agarose matrix, can be separated by pulse field electrophoresis

APLF (C2orf13) is a novel component of poly(ADP-ribose) signaling in mammalian cells

APLF is a novel protein of unknown function that accumulates at sites of chromosomal DNA strand breakage via forkhead-associated (FHA) domain-mediated interactions with XRCC1 and XRCC4. APLF can also accumulate at sites of chromosomal DNA strand breaks independently of the FHA domain via an unidentified mechanism that requires a highly conserved C-terminal tandem zinc finger domain. Here, we show that the zinc finger domain binds tightly to poly(ADP-ribose), a polymeric posttranslational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Protein poly(ADP-ribosyl)ation is tightly regulated and defects in either its synthesis or degradation slow global rates of chromosomal single-strand break repair. Interestingly, APLF negatively affects poly(ADP-ribosyl)ation in vitro, and this activity is dependent on its capacity to bind the polymer. In addition, transient overexpression in human A549 cells of full-length APLF or a C-terminal fragment encoding the tandem zinc finger domain greatly suppresses the appearance of poly(ADP-ribose), in a zinc finger-dependent manner. We conclude that APLF can accumulate at sites of chromosomal damage via zinc finger-mediated binding to poly(ADP-ribose) and is a novel component of poly(ADP-ribose) signaling in mammalian cells

PARP-3 and APLF function together to accelerate nonhomologous end joining

PARP-3 is a member of the ADP-ribosyl transferase superfamily of unknown function. We show that PARP-3 is stimulated by DNA double-strand breaks (DSBs) in vitro and functions in the same pathway as the poly (ADP-ribose)-binding protein APLF to accelerate chromosomal DNA DSB repair. We implicate PARP-3 in the accumulation of APLF at DSBs and demonstrate that APLF promotes the retention of XRCC4/DNA ligase IV complex in chromatin, suggesting that PARP-3 and APLF accelerate DNA ligation during nonhomologous end-joining (NHEJ). Consistent with this, we show that class switch recombination in Aplf−/− B cells is biased toward microhomology-mediated end-joining, a pathway that operates in the absence of XRCC4/DNA ligase IV, and that the requirement for PARP-3 and APLF for NHEJ is circumvented by overexpression of XRCC4/DNA ligase IV. These data identify molecular roles for PARP-3 and APLF in chromosomal DNA double-strand break repair reactions

Genetic Requirements for Intra-Chromosomal Deletions

Chromosomal deletions are one of the most dangerous types of DNA damage and often arise as a result of inappropriately repaired DNA double strand breaks (DSB). These breaks are usually formed either in an induced manner from exogenous damage such as radiation, or more commonly caused from spontaneous replication errors. If there is a single strand break during replication and it is not repaired properly, as the replication fork progresses it can lead to the formation of a DSB. When there is a DSB present, there is the opportunity for a chromosomal deletion to occur. If the break is in between non-tandem direct repeats, the DNA repair machinery will degrade what is between the direct repeats through a process called Single Strand Annealing (SSA). This massive loss of DNA is what is known as a chromosomal deletion. Using an assay that in Schizosaccharomyces pombe, we can detect DSBs and determine DNA repair pathways through a selection screen of yeast cells with inactivated DNA repair genes. We generated an in vivo assay that reports exclusively SSA. We validated the assay by showing its dependence on rad52+ and independence rad51+. However, we show that earlier events epistatic to rad52+ and rad51+ have differential requirements for deletions vs. other forms of repair. Here, we delineate a more detailed epistatic pathway for intrachromosomal deletions.No embargoAcademic Major: Biolog

Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries

A method of in situ hybridization for visualizing individual human chromosomes from pter to qter, both in metaphase spreads and interphase nuclei, is reported. DNA inserts from a single chromosomal library are labeled with biotin and partially preannealed with a titrated amount of total human genomic DNA prior to hybridization with cellular or chromosomal preparations. The cross-hybridization of repetitive sequences to nontargeted chromosomes can be markedly suppressed under appropriate preannealing conditions. The remaining single-stranded DNA is hybridized to specimens of interest and detected with fluorescent or enzymelabeled avidin conjugates following post-hybridization washes. DNA inserts from recombinant libraries for chromosomes 1, 4, 7, 8, 13, 14, 18, 20, 21, 22, and X were assessed for their ability to decorate specifically their cognate chromosome; most libraries proved to be highly specific. Quantitative densitometric analyses indicated that the ratio of specific to nonspecific hybridization signal under optimal preannealing conditions was at least 8:1. Interphase nuclei showed a cohesive territorial organization of chromosomal domains, and laserscanning confocal fluorescence microscopy was used to aid the 3-D visualization of these domains. This method should be useful for both karyotypic studies and for the analysis of chromosome topography in interphase cells

Absence of BLM leads to accumulation of chromosomal DNA breaks during both unperturbed and disrupted S phases

Bloom's syndrome (BS), a disorder associated with genomic instability and cancer predisposition, results from defects in the Bloom's helicase (BLM) protein. In BS cells, chromosomal abnormalities such as sister chromatid exchanges occur at highly elevated rates. Using Xenopus egg extracts, we have studied Xenopus BLM (Xblm) during both unperturbed and disrupted DNA replication cycles. Xblm binds to replicating chromatin and becomes highly phosphorylated in the presence of DNA replication blocks. This phosphorylation depends on Xenopus ATR (Xatr) and Xenopus Rad17 (Xrad17), but not Claspin. Xblm and Xenopus topoisomerase III{alpha} (Xtop3{alpha}) interact in a regulated manner and associate with replicating chromatin interdependently. Immunodepletion of Xblm from egg extracts results in accumulation of chromosomal DNA breaks during both normal and perturbed DNA replication cycles. Disruption of the interaction between Xblm and Xtop3{alpha} has similar effects. The occurrence of DNA damage in the absence of Xblm, even without any exogenous insult to the DNA, may help to explain the genesis of chromosomal defects in BS cells