High resolution southern analysis of genomic DNA using heat denatured acrylamide gels

The promoter and transcribed regions of the Leishmania tarentolae spliced leader RNA gene array are devoid of nucleosomes

BACKGROUND

The spliced leader (SL) RNA provides the 5' m7G cap and first 39 nt for all nuclear mRNAs in kinetoplastids. This small nuclear RNA is transcribed by RNA polymerase II from individual promoters. In Leishmania tarentolae the SL RNA genes reside in two multi-copy tandem arrays designated MINA and MINB. The transcript accumulation from the SL promoter on the drug-selected, episomal SL RNA gene cassette pX-tSL is ~10% that of the genomic array in uncloned L. tarentolae transfectants. This disparity is neither sequence- nor copy-number related, and thus may be due to interference of SL promoter function by epigenetic factors. To explore these possibilities we examined the nucleoplasmic localization of the SL RNA genes as well as their nucleosomal architecture.

RESULTS

The genomic SL RNA genes and the episome did not co-localize within the nucleus. Each genomic repeat contains one nucleosome regularly positioned within the non-transcribed intergenic region. The 363-bp MINA array was resistant to micrococcal nuclease digestion between the -258 and -72 positions relative to the transcription start point due to nucleosome association, leaving the promoter elements and the entire transcribed region exposed for protein interactions. A pattern of ~164-bp protected segments was observed, corresponding to the amount of DNA typically bound by a nucleosome. By contrast, nucleosomes on the pX-tSL episome were randomly distributed over the episomal SL cassette, reducing transcription factor access to the episomal promoter by approximately 74%. Cloning of the episome transfectants revealed a range of transcriptional activities, implicating a mechanism of epigenetic heredity.

CONCLUSION

The disorganized nucleosomes on the pX episome are in a permissive conformation for transcription of the SL RNA cassette approximately 25% of the time within a given parasite. Nucleosome interference is likely the major factor in the apparent transcriptional repression of the SL RNA gene cassette. Coupled with the requirement for run-around transcription that drives expression of the selectable drug marker, transcription of the episomal SL may be reduced even further due to sub-optimal nucleoplasmic localization and initiation complex disruption.

Southern and northern analysis

This review on Southern and Northern analysis, rather than providing step-by-step protocols, focuses on a critical evaluation of the existing experimental methods and modifications thereof. Principal parameters influencing electrophoresis of DNA/RNA in agarose gels are outlined and at the same time alterations in these parameters for optimal resolution of DNA of varying length are discussed. Further, methods for evaluating the quality of DNA/RNA size separation in agarose gels are described. Since efficient transfer of DNA/RNA from the gel onto a membrane support is critical in both methods, several experimental approaches for transfer are compared. Also discussed in this review are alternative methods for radioactive and non-radioactive labeling of DNA probes. Finally, detailed protocols are provided for an effective hybridization of Southern and Northern blots.

Tissue-specific methylation of a CpG island in transgenic mice

Clustering of CpG dinucleotides in CpG-rich islands is a characteristic feature of mammalian genomes. Such CpG islands are frequently associated with genes and usually hypomethylated, regardless of the gene activity. This is the case for the CpG island of the murine Thy-1 gene. A transgenic line containing multiple copies of a truncated, concatemeric CpG island from the Thy-1.1 allele (Thy-1.2 background) showed that a stable fraction (approx. 0.20) became fully methylated in somatic tissues of homozygous mice with respect to testable restriction sites, while the remaining copies were methylation-free, i.e., this methylation appears to be an 'all-or-none' phenomenon. DNA from extraembryonic tissues (placenta and yolk sac) and epididymal sperm showed, however, an even higher degree of methylation in two distinct patterns. In the extraembryonic tissue, partial methylation of each copy was seen, whereas in sperm a high degree of 'all-or-none' methylation (greater than 0.35) was observed.

A putative serine/threonine protein kinase encoded by the segment-polarity fused gene of Drosophila

The segmented pattern of the Drosophila embryo depends on a regulatory cascade involving three main classes of genes. An early regulatory programme, set up before cellularization, involves direct transcriptional regulation mediated by gap and pair-rule genes. In a second phase occurring after cellularization, interactions between segment-polarity genes are involved in cell communication. Segment-polarity genes are required for pattern formation in different domains of each metamere and act to define and maintain positional information in each segment. The segment-polarity gene fused is maternally required for correct patterning in the posterior part of each embryonic metamere. It is also necessary later in development, as fused mutations lead to anomalies of adult cuticular structures and tumorous ovaries. Here we provide molecular evidence that this gene encodes a putative serine/threonine protein kinase, a new function for the product of a segmentation gene. This result provides further insight into segment-polarity interactions and their role in pattern formation.