Transcriptional control: rheostat converted to on/off switch.

Individual cells translate concentration gradients of extracellular factors into all-or-none threshold responses leading to discrete patterns of gene expression. Signaling cascades account for some but not all such threshold responses, suggesting the existence of additional mechanisms. Here we show that all-or-none responses can be generated at a transcriptional level. A graded rheostat mechanism obtained when either transactivators or transrepressors are present is converted to an on/off switch when these factors compete for the same DNA regulatory element. Hill coefficients of dose-response curves confirm that the synergistic responses generated by each factor alone are additive, obviating the need for feedback loops. We postulate that regulatory networks of competing transcription factors prevalent in cells and organisms are crucial for establishing true molecular on/off switches.

Tetracycline-regulatable factors with distinct dimerization domains allow reversible growth inhibition by p16.

Continuous regulation is required to maintain a given cell state or to allow it to change in response to the environment. Studies of the mechanisms underlying such regulation have often been hindered by the inability to control gene expression at will. Among the inducible systems available for regulating gene expression in eukaryotes, the tetracycline (tet) regulatable system has distinct advantages. It is highly specific, non-toxic and non-eukaryotic, and consequently does not have pleiotropic effects on host cell genes. Previously this system also had drawbacks, as it did not extinguish gene expression completely, precluding the study of toxic or growth-inhibitory gene products. We report here the development of a facile reversible tetracycline-inducible retroviral system (designated RetroTet-ART) in which activators and repressors together are expressed in cells. Gene expression can now be actively repressed in the absence of tet and induced in the presence of tet, as we have engineered distinct dimerization domains that allow co-expression of homodimeric tet-regulated transactivators and transrepressors in the same cells, without the formation of non-functional heterodimers. Using this system, we show that growth arrest by the cell cycle inhibitor p16 is reversible and dependent on its continuous expression.

Highly conserved RNA sequences that are sensors of environmental stress.

The putative function of highly conserved regions (HCRs) within 3' untranslated regions (3'UTRs) as regulatory RNA sequences was efficiently and quantitatively assessed by using modular retroviral vectors. This strategy led to the identification of HCRs that alter gene expression in response to oxidative or mitogenic stress. Databases were screened for UTR sequences of >100 nucleotides that had retained 70% identity over more than 300 million years of evolution. The effects of 10 such HCRs on a standard reporter mRNA or protein were studied. To this end, we developed a modular retroviral vector that can allow for a direct comparison of the effects of different HCRs on gene expression independent of their gene-intrinsic 5'UTR, promoter, protein coding region, or poly(A) sequence. Five of the HCRs tested decreased mRNA steady-state levels 2- to 10-fold relative to controls, presumably by altering mRNA stability. One HCR increased translation, and one decreased translation. Elevated mitogen levels caused four HCRs to increase protein levels twofold. One HCR increased protein levels fourfold in response to hypoxia. Although nonconserved UTR sequences may also have a role, these results provide evidence that sequences that are highly conserved during evolution are good candidates for RNA motifs with posttranscriptional regulatory functions in gene expression.

Extremely stable transcripts may compensate for the elimination of the gene fert-1 from all Ascaris lumbricoides somatic cells.

The single-copy gene fert-1 becomes eliminated from all somatic cells during the process of chromatin diminution in Ascaris lumbricoides var. suum. By using Northern blot and in situ hybridization techniques, we have analyzed its rather unusual expression pattern. Different splicing and 3' end formation events generate in a developmentally regulated manner various poly(A)+ and poly(A)- fert-1 RNA species. The lack of any significant open reading frame in most of its RNA products indicates that fert-1 may function as structural RNA rather than encoding a protein. Fert-1 transcripts are produced in the precursors of the gametes, but degraded at the time of meiosis and not passed on to the zygote. Embryonic transcription of fert-1 sets in as soon as the female nucleus has completed its meiosis. Our data thus demonstrate that the Ascaris transcription apparatus is active prior to the general onset of zygotic transcription, which we think takes place in the four- to six-cell-stage embryos. Upon elimination of fert-1 gene from the somatic cells, most of its transcripts disappear. Two short fert-1 RNA products, however, are stably maintained throughout development until the second larval stage, which is more than 1 month after the elimination of their coding sequences. Possible functions of fert-1 are discussed.

New telomere formation after developmentally regulated chromosomal breakage during the process of chromatin diminution in Ascaris lumbricoides.

During the process of chromatin diminution, which takes place in all presomatic cells of the early Ascaris embryo, the heterochromatic termini of the chromosomes are lost. Here we show that the newly formed ends of the reduced somatic chromosomes carry tandem repeats of the telomeric sequence TTAGGC. Comparison of a cloned somatic telomere with the corresponding germline chromosomal region revealed that these telomeric repeats are not present at or near the chromosomal breakage site. They are most likely added by a telomerase-mediated event. Chromosomal breakage, which precedes the telomere addition process, takes place within a short, specific chromosomal region (CBR); however, it does not occur at a single locus, but rather at many different sites. Altogether, our data show that chromatin diminution in Ascaris is a complex molecular process that includes site-specific chromosomal breakage, new telomere formation, and DNA degradation.

Cloning and expression in vitro of a gene encoding tRNAArgACG from the nematode Caenorhabditis elegans.

A gene (rtr-1) coding for the tRNAArgACG has been isolated and characterized from the nematode, Caenorhabditis elegans. The coding portion is not interrupted by an intron and is followed by a track of four thymidines associated with termination by RNA polymerase III. The predicted mature product is 76 nucleotides (nt) long including the CCA tail, and is specific for the most used Arg codon in C. elegans. The gene can be transcribed and processed in a homologous in vitro system. The 82-nt primary transcript begins at the first purine upstream from the mature tRNA 5' end and terminates after the first thymidine of the terminator signal.

Cloning and analysis of three new homeobox genes from the nematode Caenorhabditis elegans.

Three homeobox-containing genes from the nematode Caenorhabditis elegans are described. Two of them (ceh-11 and ceh-12) were isolated from a genomic library by hybridization at low stringency with the Ascaris lumbricoides homeobox AHB-1. The first clone contains a homeobox defining a new class of homeoboxes (ceh-11). This gene maps on the third chromosome of C. elegans, at the same locus as egl-5, a gene already known to be essential for the determination of specific neurons. In the second clone, sequence analysis revealed the existence of the third helix of a putative homeobox (ceh-12) which is interrupted by an intron located upstream of the codon for the amino acid 45 of the homeodomain. Using the ceh-11 homeobox as a probe, a third homeobox (ceh-13) was isolated from a cDNA library. As ceh-13 belongs to the labial class of homeoboxes, we conclude that, at the time when the nematode lineage diverged from the myriapod-insect and the vertebrate lineages, the duplication which led to the Antp and the labial families of homeoboxes had already taken place.

Structure and genomic organization of proretrovirus-like elements partially eliminated from the somatic genome of Ascaris lumbricoides.

A clone containing a middle repetitive element next to satellite DNA has been isolated from a germ line genomic library of the chromatin eliminating nematode Ascaris lumbricoides var. suum. The structure of this element has been elucidated by comparison of several clones containing the element in different environments. It is flanked by 256-bp-long terminal repeats (LTRs) and has an internal region of approximately 7 kb. The nucleotide sequences of both the 5' and the 3' LTRs have been determined. The element has a strong structural similarity with retroviral proviruses and related mobile elements. It was therefore named 'Tas', for transposon-like element of Ascaris. Approximately 50 Tas copies are dispersed over approximately 20 different chromosomal sites. Their genomic distribution varies between individuals, indicating that Tas elements are mobile in the Ascaris genome. Two variant forms, Tas-1 and Tas-2, present in a ratio of approximately 2 to 1 in the germ line genome, have been characterized. They differ not only in their restriction pattern, but also in their elimination behaviour. While only about one-fourth of the Tas-1 elements are expelled from the somatic cell lineage, all Tas-2 copies are specifically eliminated and are thus confined to the germ line cells. We have demonstrated that a cloned representative of Tas-1 elements is expelled concomitantly with its flanking DNA sequences during the chromatin elimination process.