Direct selection of cDNAs using whole chromosomes

Chromatin dynamics is correlated with replication timing

Discrete chromatin domains (ChrD), containing an average of approximately 1 Mbp DNA, represent the basic structural units for the regulation of DNA organization and replication in situ. In this study, a bio-computational approach is employed to simultaneously measure the translational motion of large populations of ChrD in the cell nucleus of living cells. Both movement and configurational changes are strikingly higher in early S-phase replicating ChrD compared to those that replicate in mid and late S-phase. The chromatin dynamics was not sensitive to transcription inhibition by alpha-amanitin but was significantly reduced by actinomycin D treatment. Since a majority of active genes replicate in early S-phase, our results suggest a correlation between levels of chromatin dynamics and chromatin poised for active transcription. Analysis of ChrD colocalization with transcription sites and cDNA with ChrD and transcription sites further supports this proposal.

MMASS: an optimized array-based method for assessing CpG island methylation

We describe an optimized microarray method for identifying genome-wide CpG island methylation called microarray-based methylation assessment of single samples (MMASS) which directly compares methylated to unmethylated sequences within a single sample. To improve previous methods we used bioinformatic analysis to predict an optimized combination of methylation-sensitive enzymes that had the highest utility for CpG-island probes and different methods to produce unmethylated representations of test DNA for more sensitive detection of differential methylation by hybridization. Subtraction or methylation-dependent digestion with McrBC was used with optimized (MMASS-v2) or previously described (MMASS-v1, MMASS-sub) methylation-sensitive enzyme combinations and compared with a published McrBC method. Comparison was performed using DNA from the cell line HCT116. We show that the distribution of methylation microarray data is inherently skewed and requires exogenous spiked controls for normalization and that analysis of digestion of methylated and unmethylated control sequences together with linear fit models of replicate data showed superior statistical power for the MMASS-v2 method. Comparison with previous methylation data for HCT116 and validation of CpG islands from PXMP4, SFRP2, DCC, RARB and TSEN2 confirmed the accuracy of MMASS-v2 results. The MMASS-v2 method offers improved sensitivity and statistical power for high-throughput microarray identification of differential methylation.

Polyelectrolyte functionalized magnetic emulsion for specific isolation of nucleic acids

A magnetic oil in water (o/w) emulsion was cationized by adsorption of poly(ethyleneimine) (PEI). In a subsequent step, the cationic particles were derivatized with partially hydrolyzed poly(maleic anhydride-alt-methyl vinyl ether) copolymer (PMAMVE) to lead negatively charged colloids. The experimental conditions for the covalent grafting of the PMAMVE were selected on the basis of colloidal stability, charge inversion and absence of inhibition of the enzymatic DNA/RNA amplification reactions. Once the experimental conditions were selected, oligonucleotides (ODN) bearing particles were obtained according to the sequential process: (i) grafting of single stranded ODNs onto PMAMVE; (ii) grafting of the PMAMVE-ODN conjugates onto the cationic particles according to the conditions defined above. In this strategy, both steps could be independently controlled. The ODN-PMAMVE-particles conjugates were very stable with time, did not inhibit RT-PCR and were capable of hybridizing specifically with the complementary target.

Magnetic colloids for the generic capture of viruses

In molecular biology or in the diagnostic field, a strong interest has been devoted to the use of magnetic nanoparticles as an efficient tool for a fast and easy biomolecule extraction. Various methods allow the synthesis of numerous types of magnetic particles, but very few of them can be adapted to biological protocols. For biological tests based on the final detection of nucleic acids, the major difficulties in the choice of these magnetic beads are their fast magnetic separation, requiring a high magnetic oxide content and overall a good compatibility with enzymes used for nucleic acid amplification. In this study, magnetic colloids were obtained from oil in water (o/w) magnetic emulsion by a two-step polymer immobilization procedure. First, a polycation, poly(ethyleneimine), was adsorbed to ensure charge inversion of the emulsion droplets. Then poly(maleic anhydride-co-methyl vinyl ether) was either chemically grafted or adsorbed if under its hydrolyzed form. The obtained colloids were characterized in terms of colloidal stability, surface charge density, and morphology and were evaluated in a reverse transcription-PCR (RT-PCR) inhibition test. Selected colloids were used for the nonspecific capture of viruses, with RT-PCR being used as a means of detection. Particle size and charge studies allowed us to follow each step of their synthesis, showing the relevance of these methods. The prepared magnetic particles exhibit a good RT-PCR compatibility when used in the range of 5-40 microg in the 50 microl amplification mix. Finally, virus capture tests revealed a capture efficiency of 90% with an average detection sensitivity of 10(3)pfu/ml.

Comparative expressed sequence hybridization to chromosomes for tumor classification and identification of genomic regions of differential gene expression

Altered expression of genes can have phenotypic consequences in cancer development and treatment, developmental abnormalities, and differentiation processes. Here we describe a rapid approach, termed comparative expressed sequence hybridization (CESH), which gives a genome-wide view of relative expression patterns within tissues according to chromosomal location. No prior knowledge of genes or cloning is required, and minimal amounts of tissue can be used. Expression profiles are achieved in a manner similar to the identification of chromosomal imbalances by comparative genomic hybridization analysis. The approach is demonstrated to indicate a chromosomal region that harbors overexpressed genes that may be associated with a drug-resistant phenotype. In addition, known and new regions of differential gene expression in both normal tissues and tumor samples from the soft tissue sarcoma group of rhabdomyosarcoma (RMS) are indicated. These regions included 2p24; overexpression of MYCN at 2p24 was confirmed by quantitative reverse transcription-PCR for all of the alveolar RMS cases and did not necessarily correspond to genomic amplification. Evidence including region specific microarray analysis indicated that overexpression of several genes from a region may be required for detection by CESH. This evidence is consistent with clusters of functionally related genes and mechanisms that affect the expression of a number of genes at a particular genomic location. The distinctive CESH profiles demonstrated in different subtypes of RMS show potential for tumor classification.

Quantitative microscopy after fluorescence in situ hybridization - a comparison between repeat-depleted and non-depleted DNA probes

Complex probes used in fluorescence in situ hybridization (FISH) usually contain repetitive DNA sequences. For chromosome painting, in situ suppression of these repetitive DNA sequences has been well established. Standard painting protocols require large amounts of an unlabeled 'blocking agent', for instance Cot-1 DNA. Recently, it has become possible to remove repetitive DNA sequences from library probes by means of magnetic purification and affinity PCR. Such a 'repeat depleted library probe' was hybridized to the q-arm of chromosome 15 of human metaphase spreads and interphase cell nuclei without any preannealing by Cot-1 DNA. Apart from this, 'standard' FISH conditions were used. After in situ hybridization, microscope images were obtained comparable to those achieved with the #15q library probe prior to depletion. The images were recorded by a true color CCD camera. By digital image analysis using 'line scan' and 'area scan' procedures, the painting efficiency expressed in terms of relative fluorescence signal intensity was quantitatively evaluated. The painting efficiency using the repeat depleted probe of chromosome 15q was compared to the painting efficiency after standard FISH. The results indicate that both types of probes are compatible to a high FISH efficiency. Using equivalent probe concentrations, no significant differences were found for FISH with standard painting probes and repeat depleted painting probes.

Distribution of olfactory receptor genes in the human genome

We demonstrate that members of the olfactory receptor (OR) gene family are distributed on all but a few human chromosomes. Through FISH analysis, we show that OR sequences reside at more than 25 locations in the human genome. Their distribution is biased for terminal bands. Flow-sorted chromosomes were used to isolate 87 OR sequences derived from 16 chromosomes. Their sequence-relationships are indicative of the inter- and intrachromosomal duplications responsible for OR family expansion. The human genome has accumulated a striking number of dysfunctional copies: 72% of the sequences are pseudogenes. ORF-containing sequences predominate on chromosomes 7, 16 and 17.

A rapid RT-PCR based method to isolate complementary DNA fragments flanking retrovirus integration sites

Proto-oncogenes in retrovirally induced myeloid mouse leukemias are frequently activated following retroviral insertion. The identification of common virus integration sites (VISs) and isolation of the transforming oncogene is laborious and time consuming. We established a rapid and simple PCR based procedure which facilitates the identification of VISs and novel proto-oncogenes. Complementary DNA fragments adjacent to retrovirus integration sites were selectively isolated by applying a reverse transcriptase (RT) reaction using an oligo(dT)-adaptor primer, followed by PCR using the adaptor sequence and a retrovirus long terminal repeat (LTR) specific primer. Multiple chimeric cDNA fragments suitable for Southern and northern blot analysis were isolated.