Transcription termination at the chicken beta H-globin gene

The poly(A) signal, without the assistance of any downstream element, directs RNA polymerase II to pause in vivo and then to release stochastically from the template

Genes encoding polyadenylated mRNAs depend on their poly(A) signals for termination of transcription. Typically, transcription downstream of the poly(A) signal gradually declines to zero, but often there is a transient increase in polymerase density immediately preceding the decline. Special elements called pause sites are traditionally invoked to account for this increase. Using run-on transcription from the nuclei of transfected cells, we show that both the pause and the gradual decline that follow a poly(A) site are generated entirely by the poly(A) signal itself in a series of model constructs. We found no other elements to be involved and argue that the elements called pause sites do not function through pausing. Both the poly(A)-dependent pause and the subsequent decline occurred earlier for a stronger poly(A) signal than for a weaker one. Because the gradual decline resembles the abortive elongation that occurs downstream of many promoters, one model has proposed that the poly(A) signal flips the polymerase from the elongation mode to the abortive mode like a binary switch. We compared abortive elongators with poly(A) terminators and found a 4-fold difference in processivity. We conclude that poly(A) terminating polymerases do not merely revert to their prior state of low processivity but rather convert to a new termination-prone condition.

The 3'-untranslated region of membrane exon 2 from the gamma 2a immunoglobulin gene contributes to efficient transcription termination

Elements of the mouse Immunoglobulin gamma 2a gene, near the membrane-specific poly(A) addition site, were inserted into a heterologous location in either a synthetic mouse gamma 2b gene or a gpt/SV40 chimeric gene and then assayed for their ability to terminate RNA polymerase II transcription in isolated nuclei of transfected myeloma cells. The intact gamma 2a membrane-specific 3'-untranslated region, with its potential stem loop forming sequences and poly(A) site, is able to efficiently terminate transcription in the absence of the downstream region in which transcription normally terminates (term). Termination efficiency in the presence of the termination fragment decreases either when sequences specifying a potential stem/loop, upstream of the poly(A) region, are interrupted or when the stronger membrane poly(A) site is substituted with a weaker, secretory-specific poly(A) site. We therefore conclude that the gamma 2a membrane-specific untranslated region plays a major role in specifying downstream termination. We further conclude that the immunoglobulin gamma 2a, membrane-specific, 3'-untranslated region can function in the context of the gpt gene, driven by an SV40 promoter, to terminate transcription in a poly(A) site dependent fashion.

Nucleosome spacing is compressed in active chromatin domains of chick erythroid cells

We have cleaved the chromatin of embryonic and adult chicken erythroid cells using a novel nuclease that is capable of resolving clearly the nucleosomes of active chromatin. We found that in active chromatin, nucleosomes are spaced up to 40 base pairs closer together than in inactive chromatin. This was true for both "housekeeping" and "luxury" genes and was observed whether the digestion was carried out on isolated nuclei in vitro or by activating the endogenous nuclease in vivo. The close spacing extended several kilobases into flanking chromatin, indicating that this is a domain property of active chromatin, not just a characteristic of regions disrupted by transcription. A simple interpretation of our results is that the nucleosomes of active chromatin are mobile in vivo and, not being constrained by linker histones, freely move closer together.

An apparent pause site in the transcription unit of the rabbit alpha-globin gene

Transcription of the rabbit alpha-globin gene begins primarily at the cap site, although some upstream start sites are also observed. Analysis by RNA polymerase run-on assays in nuclei shows that transcription continues at a high level past the polyadenylation site, after which the polymerase density actually increases in a region of about 400 nucleotides, followed by a gradual decline over the 700 nucleotides. These features are also observed in the transcription unit of the rabbit beta-globin gene. The region with the unexpectedly high nascent RNA hybridization signal in the 3' flank contains a conserved sequence, KGCAGCWGGR (K = G or T, W = A or T, R = A or G), followed by an inverted repeat. The inverted repeat (perhaps with the conserved sequence) may be a pause site for RNA polymerase II, thus accounting for the increase in polymerase density. This sequence and inverted repeat are found in the 3' flank of several globin genes and the simian virus 40 (SV40) early genes, as well as in the regions implicated in pausing or termination of transcription of eight different genes. Deletion of the conserved sequence and inverted repeat from the 3' flank of the SV40 early region causes a small increase in the levels of transcription downstream from this site. Replacement with the conserved sequence and inverted repeat from the rabbit alpha-globin gene causes an accumulation of polymerases, supporting the hypothesis that polymerases pause at this site. This proposed pause site may affect the efficiency of termination at some sites further downstream, perhaps by loss of a processivity factor.

The DNA intercalator, ethidium bromide, alters the pattern of DNAse I hypersensitive sites of the beta A-globin gene in chicken erythrocytes

We have analysed the effects of a DNA intercalator, ethidium bromide (EB), on chromatin structure in nuclei from both chicken mature erythrocytes (RBC) and reticulocytes (Ret). A differential release of nuclear proteins was obtained from both types of nuclei exposed to EB. Among these proteins, a species of 45 kDa is the major component. Furthermore, in the 10 mM EB-treated nuclei, the pattern of DNAse I hypersensitive sites (DHS) around the chicken beta A-globin gene were significantly altered, i.e., the original set was replaced by a new set of DHS. We have discussed the implications of our observations, in the light of current concepts of functional aspects of the conformational heterogeneity of DNA in both protein-DNA interactions and chromatin structure, as well as the effects of DNA intercalators on DNA conformation.

EM analysis of Drosophila chorion genes: amplification, transcription termination and RNA splicing

We have used the electron microscope to examine ultrastructurally several events occurring during the biogenesis of two very abundant chorion (eggshell) mRNA molecules in the follicle cells of Drosophila melanogaster--namely, selective gene amplification, transcription initiation and termination, and RNA processing. We find that the highly transcribed s36 and s38 genes are positioned in the central region of large, multi-forked amplified DNA structures. Transcript morphology is consistent with the known presence of a small intron at the 5' end of each gene. Mature transcripts are associated with spliceosomes, demonstrating that splice site selection occurs co-transcriptionally but that splicing is completed after transcript release from the template. We have also mapped the termination sites for the genes. The two genes exhibit efficient termination very near their poly(A) sites--within a 210 bp region for s36 and a 360 bp region for s38.

How RNA polymerase II terminates transcription in higher eukaryotes

The termination of transcription of eukaryotic genes by RNA polymerase II, at first sight, appears to be a rather random process, with the heterogeneous transcripts produced being processed to generate their correct 3' ends. However, recent studies have revealed that specific termination or pause sites may influence the process. The mechanism of termination may even play a role in eukaryotic gene regulation.