Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.

Ribosomal DNA: molecular evolution and phylogenetic inference.

TELOMERES DEFINED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579 TELOMERE FUNCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 580 SEQUENCE AND STRUCTURE OF TELOMERES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 581 SOLUTIONS FOR REPLICATION OF DNA TERMINI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 586 STRUCTURE OF SUBTELOMERIC REGIONS.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 589 FORMA TION OF TELOMERES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ... . . . . . .. 591 PROTEINS THAT INTERACT WITH TELOMERES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 594 ARE TELOMERES REALLY ESSENTIAL? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 597 FUTURE PROSPECTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 598

Structure and function of telomeres

A process is provided of introducing an RNA into a living cell to inhibit gene expression of a target gene in that cell. The process may be practiced ex vivo or in vivo. The RNA has a region with double-stranded structure. Inhibition is sequence-specific in that the nucleotide sequences of the duplex region of the RNA and of a portion of the target gene are identical. The present invention is distinguished from prior art interference in gene expression by antisense or triple-strand methods.

Genetic Inhibition by Double-Stranded RNA

Many examples of extreme virus resistance and posttranscriptional gene silencing of endogenous or reporter genes have been described in transgenic plants containing sense or antisense transgenes. In these cases of either cosuppression or antisense suppression, there appears to be induction of a surveillance system within the plant that specifically degrades both the transgene and target RNAs. We show that transforming plants with virus or reporter gene constructs that produce RNAs capable of duplex formation confer virus immunity or gene silencing on the plants. This was accomplished by using transcripts from one sense gene and one antisense gene colocated in the plant genome, a single transcript that has self-complementarity, or sense and antisense transcripts from genes brought together by crossing. A model is presented that is consistent with our data and those of other workers, describing the processes of induction and execution of posttranscriptional gene silencing.

/pdf/virus-resistance-and-gene-silencing-in-plants-can-be-induced-dwautat2u4.pdf

Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA

Arabidopsis SGS2 and SGS3 Genes Are Required for Posttranscriptional Gene Silencing and Natural Virus Resistance

A molecular description of telomeric heterochromatin in Secale species.

https://www.cell.com/cell/pdf/S0092-8674(00)81930-3.pdf

RNA-Mediated RNA Degradation and Chalcone Synthase A Silencing in Petunia

The wheat variety Chinese Spring has four pairs of nucleolus organisers of known rDNA content. The genetic control of these has been investigated in root tip cells by cytologically scoring the number of nucleoli per cell in (a) aneuploid derivatives each having a different dosage of a particular chromosome or chromosome arm and (b) in substitution lines where nucleolus organiser chromosomes have been replaced by homologues possessing different amounts of rDNA. It has been assumed that nucleolus organiser activity is correlated with nucleolus size and thus with the presence of a cytologically visible nucleolus. Those nucleolus organisers on chromosomes 1A and 5D, which together possess only 10% of the rDNA form a visible nucleolus only infrequently in the presence of the larger nucleolus organisers on chromosomes 1B and 6B. When a major pair of organisers on chromosomes 1B or 6B is deleted, the smaller nucleolus organisers form a visible nucleolus more frequently. Similarly, when the major nucleolus organisers are replaced by organisers with less rDNA, the smaller nucleolus organisers form visible nucleoli more frequently. When a small nucleolus organiser is replaced by one with much more rDNA, a larger nucleolus is formed. These and other findings lead to the general conclusions that there is a frequently, but not invariably, seen correlation between rRNA gene number and nucleolus size. However the relative size of the nucleolus formed depends principally upon the proportion of the total active rRNA genes in the cell which are localised at the nucleolus organiser in question. Varying the dosage of at least 13 non nucleolus organiser chromosomes also resulted in changes in the number of visible nucleoli per cell. This implies the genetic control of individual nucleolus organisers is complex. Inclusion in the wheat genome of the nucleolus organiser chromosome from Aegilops umbellulata, causes suppression of the wheat nucleolus organisers, the Aegilops umbellulata organiser remaining active. This suppression is similar to that observed in many interspecific plant and animal hybrids.

The genetic control of nucleolus formation in wheat

The families of repeated sequences in the genomes of a range of Triticum and Aegilops species have been compared. All the genomes are very similar. However, using a DNA probe from Aegilops speltoides that contains the most highly repeated sequences, diploid Aegilops species could be distinguished from diploid Triticum species. Different Aegilops species' DNAs also hybridise to differing extents with this probe. The results are consistent with the hypothesis that speciation is accompanied by quantitative changes in the repeated sequence complements of genomes. Most if not all of the families of repeated sequences in hexaploid wheat can be detected in Aegilops speltoides (related to the B genome) and in Aegilops squarrosa (related to the D genome). However, some families of repeated sequences of hexaploid wheat were not found in Triticum monococcum (related to the A genome). Some of the most highly repeated sequences of hexaploid wheat are preferentially concentrated in the B genome. These sequences are useful as probes for distinguishing the three diploid genomes of hexaploid wheat.

/pdf/repeated-sequence-dna-comparisons-between-triticum-and-1nw4epbahw.pdf

Repeated sequence DNA comparisons between Triticum and Aegilops species

Petunia plants that exhibit a white-flowering phenotype as a consequence of chalcone synthase transgene-induced silencing occasionally give rise to revertant branches that produce flowers with wild-type pigmentation. Transcription run-on assays confirmed that the production of white flowers is caused by post-transcriptional gene silencing (PTGS), and indicated that transgene transcription is repressed in the revertant plants, providing evidence that induction of PTGS depends on the transcription rate. Transcriptional repression of the transgene was associated with cytosine methylation at CpG, CpNpG and CpNpN sites, and the expression was restored by treatment with either 5-azacytidine or trichostatin A. These results demonstrate that epigenetic changes occurred in the PTGS line, and these changes interfere with the initiation of transgene transcription, leading to a reversion of the PTGS phenotype.

Epigenetic Inactivation of Chalcone Synthase-A Transgene Transcription in Petunia Leads to a Reversion of the Post-Transcriptional Gene Silencing Phenotype

Michael O'Dell

Papers

A molecular description of telomeric heterochromatin in Secale species.

RNA-Mediated RNA Degradation and Chalcone Synthase A Silencing in Petunia

The genetic control of nucleolus formation in wheat

Repeated sequence DNA comparisons between Triticum and Aegilops species

Epigenetic Inactivation of Chalcone Synthase-A Transgene Transcription in Petunia Leads to a Reversion of the Post-Transcriptional Gene Silencing Phenotype