Premature termination of tubulin gene transcription in Xenopus oocytes is due to promoter-dependent disruption of elongation

Intron 1 rather than 5' flanking sequence mediates cell type-specific expression of c-myb at level of transcription elongation

Previous studies have shown that expression of steady-state c-myb mRNA was regulated primarily by a block in intron 1 during transcription elongation. This study shows that the block site maps approximately 1700 bp from the start of the intron. Studies based on a reporter construct containing c-myb flanking region and intron 1 suggest that the flanking region is not important in the regulation of the cell type-specific expression of c-myb. RNA splicing of intron 1 may enhance the expression in a non-cell type-specific manner. A conserved intron domain comprising the block site is required for defining this site, but this function of the domain is independent of cell type. The cell type-specific regulation of c-myb transcription elongation is mediated by a 5' intron sequence. A mechanism for down regulation of c-myb gene expression by the block to transcription elongation has been proposed.

Evolution, organization, and expression of alpha-tubulin genes in the antarctic fish Notothenia coriiceps. Adaptive expansion of a gene family by recent gene duplication, inversion, and divergence

To assess the organization and expression of tubulin genes in ectothermic vertebrates, we have chosen the Antarctic yellowbelly rockcod, Notothenia coriiceps, as a model system. The genome of N. coriiceps contains approximately 15 distinct DNA fragments complementary to alpha-tubulin cDNA probes, which suggests that the alpha-tubulins of this cold-adapted fish are encoded by a substantial multigene family. From an N. coriiceps testicular DNA library, we isolated a 13.8-kilobase pair genomic clone that contains a tightly linked cluster of three alpha-tubulin genes, designated NcGTbalphaa, NcGTbalphab, and NcGTbalphac. Two of these genes, NcGTbalphaa and NcGTbalphab, are linked in head-to-head (5' to 5') orientation with approximately 500 bp separating their start codons, whereas NcGTbalphaa and NcGTbalphac are linked tail-to-tail (3' to 3') with approximately 2.5 kilobase pairs between their stop codons. The exons, introns, and untranslated regions of the three alpha-tubulin genes are strikingly similar in sequence, and the intergenic region between the alphaa and alphab genes is significantly palindromic. Thus, this cluster probably evolved by duplication, inversion, and divergence of a common ancestral alpha-tubulin gene. Expression of the NcGTbalphac gene is cosmopolitan, with its mRNA most abundant in hematopoietic, neural, and testicular tissues, whereas NcGTbalphaa and NcGTbalphab transcripts accumulate primarily in brain. The differential expression of the three genes is consistent with distinct suites of putative promoter and enhancer elements. We propose that cold adaptation of the microtubule system of Antarctic fishes is based in part on expansion of the alpha- and beta-tubulin gene families to ensure efficient synthesis of tubulin polypeptides.

Stimulation of RNA 3' processing by flanking DNA in Xenopus oocytes

We have previously shown that the second poly(A) signal of the Xenopus laevis alpha-tubulin gene X alpha T14, which contains the rare hexanucleotide CAUAAA, requires a surprisingly large amount of 3' flanking DNA to be used efficiently in Xenopus oocytes. To investigate the nature of the interaction between the X alpha T14 3' flank and upstream 3' processing sites, we have developed a modified oocyte assay based on the stimulation of processing at a single poly(A) signal. We mutated both the hexanucleotide and GU/U-rich components of a strong synthetic poly(A) signal (SPA) in order to weaken it severely. We found that efficient use of the mutant signal could be fully restored by the addition of 1.2 kb of X alpha T14 3' flank, but only in its natural orientation. Functional dissection of the X alpha T14 3' flank defined two separate regions that were each capable of partially restoring processing efficiency, presumably because they contain multiple, relatively weak processing enhancers. We discuss how the stimulation of 3' processing by flanking regions in oocytes could be explained by mechanisms that operate on the processing machinery directly or by indirect effects mediated by transcriptional pausing.

Basic mechanisms of transcript elongation and its regulation

Ternary complexes of DNA-dependent RNA polymerase with its DNA template and nascent transcript are central intermediates in transcription. In recent years, several unusual biochemical reactions have been discovered that affect the progression of RNA polymerase in ternary complexes through various transcription units. These reactions can be signaled intrinsically, by nucleic acid sequences and the RNA polymerase, or extrinsically, by protein or other regulatory factors. These factors can affect any of these processes, including promoter proximal and promoter distal pausing in both prokaryotes and eukaryotes, and therefore play a central role in regulation of gene expression. In eukaryotic systems, at least two of these factors appear to be related to cellular transformation and human cancers. New models for the structure of ternary complexes, and for the mechanism by which they move along DNA, provide plausible explanations for novel biochemical reactions that have been observed. These models predict that RNA polymerase moves along DNA without the constant possibility of dissociation and consequent termination. A further prediction of these models is that the polymerase can move in a discontinuous or inchworm-like manner. Many direct predictions of these models have been confirmed. However, one feature of RNA chain elongation not predicted by the model is that the DNA sequence can determine whether the enzyme moves discontinuously or monotonically. In at least two cases, the encounter between the RNA polymerase and a DNA block to elongation appears to specifically induce a discontinuous mode of synthesis. These findings provide important new insights into the RNA chain elongation process and offer the prospect of understanding many significant biological regulatory systems at the molecular level.

Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase

The entry of RNA polymerase II into a productive mode of elongation is controlled, in part, by the postinitiation activity of positive transcription elongation factor b (P-TEFb) (Marshall, N. F., and Price, D. H. (1995) J. Biol. Chem. 270, 12335-12338). We report here that removal of the carboxyl-terminal domain (CTD) of the large subunit of RNA polymerase II abolishes productive elongation. Correspondingly, we found that P-TEFb can phosphorylate the CTD of pure RNA polymerase II. Furthermore, P-TEFb can phosphorylate the CTD of RNA polymerase II when the polymerase is in an early elongation complex. Both the function and kinase activity of P-TEFb are blocked by the drugs 5, 6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) and H-8. P-TEFb is distinct from transcription factor IIH (TFIIH) because the two factors have no subunits in common, P-TEFb is more sensitive to DRB than is TFIIH, and most importantly, TFIIH cannot substitute functionally for P-TEFb. We propose that phosphorylation of the CTD by P-TEFb controls the transition from abortive into productive elongation mode.

Ovary-specific expression of a gene encoding a divergent alpha-tubulin isotype in Xenopus

We are investigating the structure and regulation of alpha-tubulin genes expressed in amphibian oocytes. We have characterised here a gene, X alpha T207, that produces a major alpha-tubulin mRNA of Xenopus laevis ovary. X alpha T207 mRNA was not detected in other frog tissues and its production may therefore be a key identifying feature of ovarian differentiation. In comparison to the tubulin isotypes so far described in mammals and Xenopus, the alpha-tubulin encoded by X alpha T207 is divergent in overall amino acid sequence, particularly in the N-terminal region between residues 39-50. This pattern of divergence is also displayed by the ovary-specific alpha-tubulin gene of Drosophila, D alpha 4, although the two genes do not appear to be orthologous. The development of specialised microtubular structures and activities in oocytes, eggs and early embryos may then be correlated with the expression of a divergent alpha-tubulin isotype in a wide range of organisms. To understand the basis of the ovary-specific expression of X alpha T207 we examined the transcriptional activity of wild type and mutant promoters after their microinjection in Xenopus oocytes. Only 65 bp upstream of the initiation site were required for full activity of the X alpha T207 promoter, and an element fitting the Y-box consensus was involved in controlling the efficiency of initiation. Previous oocyte injection experiments have implicated the Y-box in the oocyte-specific transcription of genes that are also expressed in other cell types, so its involvement in the oocyte-restricted expression of X alpha T207 further suggests that transcription factors recognising the Y-box normally regulate gene expression during oocyte development. Since a Y-box also occurs in the D alpha 4 promoter, our results suggest that in both organisms oocyte-specific expression of a divergent alpha-tubulin could be achieved by a common mechanism.

Transcriptional elongation by RNA polymerase II is stimulated by transactivators

We report that a variety of transactivators stimulate elongation by RNA polymerase II. Activated transcription complexes have high processivity and are able to read through pausing and termination sites efficiently. In contrast, nonactivated and "squelched" transcription mostly arrests prematurely. Activators differ in the extent to which they stimulate processivity; for example, GAL4-VP16 and GAL4-E1a are more effective than GAL4-AH. The stimulation of elongation can be as important as the stimulation of initiation in activating expression of a reporter gene. We suggest that setting the competence of polymerase II to elongate is an integral part of the initiation step that is controlled by activators cooperating with the general transcription factors.