The ends and the middle: putting chromosomes together

Reverse transcriptase activity in bovine bone marrow: purification of a 66-kDa enzyme

The presence of reverse transcriptase (RT) activity in a DNA-binding protein complex of the goat bone marrow has been reported earlier from our laboratory. Here we report a procedure for the purification of the enzyme with RT activity from bovine bone marrow and show that the basic function is associated with a approximately 66-kDa protein. This enzyme can use RT specific homopolymers as template and short oligonucleotides as primers, while displaying a Mg(2+)-ion requirement. Eukaryotic RTs have been shown to have endogenous RNAs associated with the enzymes. Evidence is presented here to show that some endogenous RNAs are associated with the RT activity in bovine bone marrow. Even though the enzyme activity appears to be associated with a approximately 66-kDa protein, the results indicate that for a full expression of its activity, the enzyme needs to interact with a 55-kDa protein that co-purifies with the enzyme during ion-exchange chromatography.

Molecular cloning of bovine telomerase RNA

Telomerase is a ribonucleoprotein reverse transcriptase essential for the maintenance of telomere length. However, the available information concerning the biochemical and structural aspects of mammalian telomerases is scarce, primarily due to the low abundance of these enzymes and the difficulty and expense involved in its purification. To overcome these problems, we started to purify and characterize telomerase from bovine testis. Bovine telomerase was purified over columns of hydroxyapatite, DEAE-Sepharose, heparin-agarose, phenyl-agarose and spermine-agarose. In a sedimentation study performed using a 15-40% glycerol gradient, partially purified bovine telomerase exhibited an apparent molecular weight of more than 1000 kDa. One 435-bp RNA, bTR, was cloned from the most purified telomerase fraction and shown to be co-purified with telomerase activity in a glycerol gradient. bTR shares 83% similarity to the human telomerase RNA and 65% to the mouse telomerase RNA. A putative template region encompassing 10 nucleotides (5'-CUAACCCUAA-3') complementary to the mammalian telomere sequence (TTAGGG)n is located between nucleotides 38-47 of bTR. Besides, the bTR 5'-flanking region shares only three regulatory elements with that of hTR: a TATA-like sequence, a CCAAT box and an E1A-F box. Furthermore, the addition of in-vitro transcribed bTR reconstituted telomerase activity after removal of the endogenous bTR by micrococcal nuclease digestion. Northern blot analysis identified a single RNA of about 430-440 nucleotides expressed in the bovine testis and an immortalized bovine cell line. Taken together, these data strongly suggest that bTR is the RNA component of bovine telomerase.

In vitro reconstitution of Artemia satellite chromatin

We report the characterization of an in vitro chromatin assembly system derived from Artemia embryos and its application to the study of AluI-113 satellite DNA organization in nucleosomes. The system efficiently reconstitutes chromatin templates by associating DNA, core histones, and H1. The polynucleosomal complexes show physiological spacing of repeat length 190 +/- 5 base pairs, and the internucleosomal distances are modulated by energy-using activities that contribute to the dynamics of chromatin conformation. The assembly extract was used to reconstitute tandemly repeated AluI-113 sequences. The establishment of preferred histone octamer/satellite DNA interactions was observed. In vitro, AluI-113 elements dictated the same nucleosome translational localizations as found in vivo. Specific rotational constraints seem to be the central structural requirement for nucleosome association. Satellite dinucleosomes showed decreased translational mobility compared with mononucleosomes. This could be the consequence of interactions between rotationally positioned nucleosomes separated by linker DNA of uniform length. AluI-113 DNA led to weak cooperativity of nucleosome association in the proximal flanking regions, which decreased with distance. Moreover, the structural properties of satellite chromatin can spread, thus leading to a specific organization of adjacent nucleosomes.

Junk DNA and sectorial gene repression

Transcriptional repression in eukaryotes often involves tens or hundreds of kilobase pairs, two to three orders of magnitude more than the bacterial operator/repressor model does. Classical repression, represented by this model, was maintained over the whole span of evolution under different guises, and consists of repressor factors interacting primarily with promoters and, in later evolution, also with enhancers. The use of much larger amounts of DNA in the other mode of repression, here called the sectorial mode ('superrepression'), results in the conceptual transfer of so-called junk DNA to the domain of functional DNA. This contribution to the solution of the c-value paradox involves perhaps 15% of genomic 'junk,' and encompasses the bulk of the introns, thought to fill a stabilizing role in sectorially repressed chromatin structures. In the case of developmental genes, such structures appear to be heterochromatoid in character. However, solid clues regarding general structural features of superrepressed terminal differentiation genes remain elusive. The competition among superrepressible DNA sectors for sectorially binding factors offers, in principle, a molecular mechanism for developmental switches. Position effect variegation may be considered an abnormal manifestation of normal processes that underly development and involve heterochromatoid sectorial repression, which is apparently required for local elimination or modulation of morphological features (morpholysis). Sectorial repression of genes participating either in development or in terminal differentiation is considered instrumental in establishing stable cell types, and provides a basis for the distinction between determination and cell type specification. The gamut of possible stable cell types may have been broadened by the appearance in evolution of heavy isochores. Additional types of relatively frequent GC-rich cis-acting DNA motifs may offer reiterated binding sites to factors endowed with a selective (though not individually strong) affinity for these motifs. The majority of sequence motifs thought to be used in superrepression need not be individually maintained by natural selection. It is re-emphasized that the dispensability of sequences is not an indicator of their nonfunctionality and that in many cases, along noncoding sequences, nucleotides tend to fill functions collectively, rather than individually.

A fluorescent method for detection of telomerase activity

The telomere repeat amplification protocol (TRAP) was recently developed to detect telomerase activity in cellular protein extracts. Teleomerase synthesizes a specific repeating nucleotide sequence onto the ends of telomeres, which stabilize eukaryotic chromosomes. Telomeric repeats are identified in the TRAP method by polymerase chain reaction amplification and incorporation of radionucleotides detected by autoradiography. Several drawbacks to this method have been recognized, including the time required to complete the assay, the resolution of the results, and the hazards of radioactive material. We have developed a new fluorescent method of detecting telomerase to alleviate these problems. Telomeric repeats are identified in the fluorescent TRAP (F-TRAP) assay by incorporation of fluorescein-labeled primers during amplification and subsequent detection with an automated DNA sequencer. This new method appears to be as sensitive as the standard TRAP assay and offers advantages in speed, resolution, cost, and safety.

Evolutionary links between telomeres and transposable elements

Transposable elements are abundant in the genomes of higher organisms but are usually thought to affect cells only incidentally, by transposing in or near a gene and influencing its expression. Telomeres of Drosophila chromosomes are maintained by two non-LTR retrotransposons, HeT-A and TART. These are the first transposable elements with identified roles in chromosome structure. We suggest that these elements may be evolutionarily related to telomerase; in both cases an enzyme extends the end of a chromosome by adding DNA copied from an RNA template. The evolution of transposable elements from chromosomal replication mechanisms may have occurred multiple times, although in other organisms the new products have not replaced the endogenous telomerase, as they have in Drosophila. This is somewhat reminiscent of the oncogenes that have arisen from cellular genes. Perhaps the viruses that carry oncogenes have also arisen from cellular genetic systems.

Drosophila telomeres: new views on chromosome evolution

In Drosophila, chromosome ends (telomeres) are composed of telomere-specific transposable elements (the retroposons HeT-A and TART). These elements are a bona fide part of the cellular machinery yet have many of the hallmarks of retrotransposable elements and retroviruses, raising the possibility that parasitic transposable elements and viruses might have evolved from mechanisms that the cell uses to maintain its chromosomes. It is striking that Drosophila, the model organism for many discoveries in genetics, development and molecular biology (including the classical concept of telomeres), should prove to have chromosome ends different from the generally accepted model. Studies of these telomere-specific retrotransposable elements raise questions about conventional wisdom concerning not only telomeres, but also transposable elements and heterochromatin.

The chromosome ends of Saccharomyces cerevisiae

Yeast chromosome ends are similar in structure and function to chromosome ends in most, if not all, eukaryotic organisms. There is a G-rich terminal repeat at the ends which is maintained by telomerase. In addition to the classical functions of protecting the end from degradation and end-to-end fusions, and completing replication, yeast telomeres have several interesting properties including: non-nucleosomal chromatin structure; transcriptional position effect variegation for genes with adjacent telomeres; nuclear peripheral localization; apparent physical clustering; non-random recombinational interactions. A number of genes have been identified that are involved in modifying one or more of these properties. These include genes involved in general DNA metabolism, chromatin structure and telomere maintenance. Adjacent to the terminal repeat is a mosaic of middle repetitive elements that exhibit a great deal of polymorphism both between individual strains and among different chromosome ends. Much of the sequence redundancy in the yeast genome is found in the sub-telomeric regions (within the last 25 kb of each end). The sub-telomeric regions are generally low in gene density, low in transcription, low in recombination, and they are late replicating. The only element which appears to be shared by all chromosome ends is part of the previously defined X element containing an ARS consensus. Most of the 'core' X elements also contain an Abf1p binding site and a URS1-like element, which may have consequences for the chromatin structure, nuclear architecture and transcription of native telomeres. Possible functions of sub-telomeric repeats include: fillers for increasing chromosome size to some minimum threshold level necessary for chromosome stability; barrier against transcriptional silencing; a suitable region for adaptive amplification of genes; secondary mechanism of telomere maintenance via recombination when telomerase activity is absent.

Isolation of a Chlamydomonas reinhardtii telomere by functional complementation in yeast

We attempted to determine whether Chlamydomonas reinhardtii telomeres, which do not form G-quartet structures readily in vitro, are able to nucleate telomere addition in Saccharomyces cerevisiae. Restricted C. reinhardtii genomic DNA was ligated to a linear S. cerevisiae vector lacking a telomere. A C. reinhardtii telomere ligated to this unprotected end allowed vector replication as a linear DNA molecule in S. cerevisiae. DNA sequencing revealed common [T4AG3]n and variant T6AG3 and T5AG3 C. reinhardtii telomere repeats capped by S. cerevisiae telomere repeat units. The recognition of a C. reinhardtii telomere by the telomere maintenance machinery of S. cerevisiae is consistent with a common theme for telomere structure in organisms with divergent telomere repeats.

Runaway telomere elongation caused by telomerase RNA gene mutations

The ribonucleoprotein enzyme telomerase adds telomeric DNA onto chromosome ends and is normally regulated so that telomeric DNA lengths are kept within defined bounds. In the telomerase RNA gene from the yeast Kluyveromyces lactis, specific mutations that alter telomeric DNA sequences result in telomeres elongating to up to 100 times their normal length and impair cell growth. Some mutations cause immediate elongation whereas others behave like genetic time bombs, causing elongation only after a latent period of hundreds of generations.