Functional differences between the two splice variants of the nucleolar transcription factor UBF: the second HMG box determines specificity of DNA binding and transcriptional activity

Regulation of ribosomal DNA transcription during contraction-induced hypertrophy of neonatal cardiomyocytes

Cardiac hypertrophy requires protein accumulation. This results largely from an increased capacity for protein synthesis, which in turn is the result of an elevated rate of ribosome biogenesis. The process of ribosome formation is regulated at the level of transcription of the ribosomal RNA genes. In this study, we examined the amounts and activities of various components of the ribosomal DNA transcription apparatus in contraction-arrested neonatal cardiomyocytes and in spontaneously contracting cardiomyocytes that hypertrophy. Nuclear run-on assays demonstrated that spontaneously contracting cardiomyocytes supported a 2-fold increased rate of ribosomal DNA transcription. However, enzymatic assay of total solubilized RNA polymerase I and Western blots demonstrated that contraction-induced increases in ribosomal RNA synthesis were not accompanied by increased activity or amounts of RNA polymerase I. In contrast, accelerated ribosome biogenesis was accompanied by an increased amount of the ribosomal DNA transcription factor, UBF. Immunoprecipitation of [32P]orthophosphate-labeled UBF from hypertrophying, neonatal cardiomyocytes indicated that the accumulated UBF protein was phosphorylated and, thus, in the active form. UBF mRNA levels began to increase within 3-6 h of the initiation of contraction and preceded the elevation in rDNA transcription. Nuclear run-on assays demonstrated increased rates of transcription of the UBF gene. Transfection of chimeric reporter constructs containing deletions of the 5'-flanking region of the UBF gene revealed the presence of contraction response elements between -1189 and -665 relative to the putative start of transcription. These results are consistent with the hypothesis that UBF is an important factor in the regulation of rDNA transcription during contraction-mediated neonatal cardiomyocyte hypertrophy.

Differences in the DNA-binding properties of the HMG-box domains of HMG1 and the sex-determining factor SRY

High-mobility-group protein 1 (HMG1) is an abundant, non-sequence-specific, chromosomal protein with two homologous, HMG-box, DNA-binding domains, A and B, and an acidic tail. The HMG-box motif also occurs, as a single copy, in some sequence-specific transcription factors, e.g. the sex-determining factor, SRY. We have investigated whether or not there are differences in the DNA-binding properties of the isolated A and B HMG-box domains of HMG1 and SRY and whether, in the case of A and B, there might also be differences due to different sequence contexts within the native protein. The basic regions that flank the HMG1 B box, giving B', enhance its DNA-binding, supercoiling and DNA-bending activities, and promote the self-association of the DNA-bound B-box. All the HMG-box domains bind with structure specificity to four-way junctions, but the structure selectivity is significantly greater for A and the SRY box than for the HMG1 B or B' domains, as judged by competition with excess plasmid DNA. The domains self-associate to different extents on supercoiled DNA and this may explain differences in the ability to discriminate between four-way junctions and supercoiled DNA. The HMG1 A, B and B' domains constrain negative superhelical turns in DNA, but the SRY HMG box does not. Only the full B domain (B') bends DNA in a ligase-mediated circularisation assay; the minimal B box, the A domain and the SRY box do not. Thus, despite a common global fold, the HMG box appears to have been adapted to various functions in different protein contexts.

Regulation of rDNA transcription factors during cardiomyocyte hypertrophy induced by adrenergic agents

Ribosomal DNA transcription is important to the regulation of cardiomyocyte ribosome content and, as a consequence, the rate of protein synthesis and accumulation during cardiac hypertrophy. We studied the regulation of ribosomal RNA synthesis and the levels of RNA polymerase I and the ribosomal DNA transcription factor, UBF, during norepinephrine-induced hypertrophy of contraction-arrested neonatal cardiomyocytes in culture. Nuclear run-on assays and Western blots demonstrated that, concomitant with hypertrophy, norepinephrine (1 microM) increased the rate of ribosomal DNA transcription, without causing an increase in the amount of RNA polymerase I. However, the elevated rate of rRNA synthesis was accompanied by an increased cellular content of UBF protein as determined by Western analysis. Northern blots demonstrated norepinephrine-induced increases in UBF mRNA in neonatal cardiomyocytes indicating that the response was regulated, at least in part, at the pretranslational stage. Both alpha- and beta-adrenergic agents increased the level of UBF mRNA. The beta-adrenergic response was mimicked by forskolin (1 microM) and the cyclic AMP analog dibutyryl cAMP (10 microM). However, activation of protein kinase C by phorbol 12-myristate 13-acetate (0.1 microM) did not increase expression of UBF. These results implicate UBF as a possible regulatory factor of the accelerated rDNA transcription observed during norepinephrine-mediated cardiomyocyte hypertrophy.

Actinomycin D stimulates the transcription of rRNA minigenes transfected into mouse cells. Implications for the in vivo hypersensitivity of rRNA gene transcription

The in vivo hypersensitivity of eukaryotic rRNA gene transcription to actinomycin D has long been known, but this effect could not be reproduced in model systems and its molecular mechanisms remain uncertain. We studied the action of actinomycin D using mouse rRNA minigenes (with RNA polymerase I promoter and terminator signals), carrying truncated mouse or human rDNA inserts, which are faithfully transcribed upon transient transfection into mouse cells. Low concentrations (0.01-0.08 micrograms/ml) of actinomycin D caused within 1-2 h a 2-7-fold stimulation of the transcription of rRNA minigenes which is inversely related to the size of the rDNA transcript. With transcripts longer than 3 kb the effect was reversed and at 4 kb a practically complete inhibition of the formation of full-length transcripts was observed, accompanied, however, by an enhanced accumulation of unfinished rDNA transcripts. The dependence of actinomycin D action on transcript length was also observed with lacZ gene segments of different size inserted into the mouse rRNA minigenes. The transcription initiation of endogenous rRNA genes was also stimulated by the low doses of actinomycin D as indicated by the enhanced synthesis of unfinished rDNA transcripts (spanning mainly the 5' external transcribed spacer), whereas the synthesis of full-length transcripts was abolished. Removal of actinomycin D from the medium caused within 8-24 h a dramatic increase of the transcription from all rRNA minigenes tested. This stimulation was also inversely related to the size of the transcripts and varied from twofold to fivefold for the 3-4-kb transcripts to about 50-80-fold for the basic minigene transcript (395 nucleotides). The amount of endogenous aborted rDNA transcripts was also markedly increased, but the synthesis of full-length transcripts was not restored even 24 h after removal of the drug. The present results reproduce in a model cellular system the in vivo hypersensitivity of rRNA gene transcription to actinomycin D and reveal that the major factor involved is the size of the rRNA gene transcript. This effect requires only the basic rRNA gene promoter and terminator signals and does not depend on the G + C content of the RNA polymerase I transcripts. We suggest that at low concentrations, the intercalation of actinomycin D changes the conformation of DNA in the promoter region in a manner that stimulates the transcription of both endogenous and transfected rRNA genes.(ABSTRACT TRUNCATED AT 400 WORDS)

The RNA polymerase I transcription factor UBF is the product of a primary response gene

Transcription of the ribosomal RNA genes by RNA polymerase I is tightly coordinated with the rate of cell growth. The RNA polymerase I transcription factor, UBF, activates transcription by binding to elements within the promoter and enhancer elements within the intergenic spacer but is not required for basal transcription. To assess the role of UBF in modulating ribosomal DNA transcription, we studied its expression in NIH3T6 fibroblasts when transcription was repressed in response to serum starvation and stimulated following refeeding. Our results demonstrate a correlation between the amounts of UBF protein and the rates of ribosomal DNA transcription in quiescent and serum-stimulated cells. Nuclear run-on assays and Northern blot analyses demonstrated that the UBF gene was a primary response gene, exhibiting characteristics similar to those of c-myc and SRF. These results suggest that the regulation of transcription of the UBF gene by polymerase II represents a pathway by which cells modulate transcription by RNA polymerase I.

Identification of two splice isoforms of mRNA for mouse hepatocyte nuclear factor 4 (HNF-4)

Hepatocyte nuclear factor 4 (HNF-4) is a liver-enriched transcription factor involved in the expression of many liver-specific genes. In the preceding communication (Hata, S., Tsukamoto, T. and Osumi, T. (1992) Biochim. Biophys. Acta 1131, 211-213), we reported the presence of two isoforms of mRNA for HNF-4 in rat liver and kidney. The longer isoform contained a segment of 30 bases which was not present in the shorter one. As an initial step to determine whether or not other mammals have these mRNA isoforms, we isolated a cDNA for mouse HNF-4 using the rat HNF-4 gene as a probe. The cDNA had an open reading frame for a 465 amino acid polypeptide. The deduced amino acid sequence was remarkably conserved between mouse HNF-4 and rat HNF-4 (99.6% identical). Moreover, like the cDNA for the larger rat isoform, the mouse cDNA contained an extra segment of 30 bp in the coding region near the C-terminus. Blotting analyses showed that the mRNA is about 3.7 kb in size and that a single copy of the gene is present in the mouse genome. Next we carried out the polymerase chain reaction (PCR) using primers located just upstream and downstream of the extra segment. Two PCR products were amplified from a mouse liver cDNA library. Determination of their nucleotide sequences proved that they exactly corresponded to the two rat isoforms. Finally, we amplified a DNA fragment (1.1 kb in size) from mouse genomic DNA using the same PCR primers as above. Its nucleotide sequence unequivocally confirmed that different splice donor sites were used to generate the two isoforms.

E1BF/Ku interacts physically and functionally with the core promoter binding factor CPBF and promotes the basal transcription of rat and human ribosomal RNA genes

We have previously characterized an RNA polymerase (pol) I transcription factor, E1BF, from rat cells. This protein is immunologically related to Ku autoantigen and is required in pol-I directed transcription of rodent ribosomal RNA gene (rDNA). Glycerol density gradient fractionation and in situ UV cross-linking analysis of the purified factor showed directly that it consists of a heterodimer of 85 and 72 kDa polypeptides. E1BF also interacted with the human core promoter and augmented transcription of human rDNA as much as fivefold in HeLa nuclear extract, whereas transcription from adenovirus major late promoter, CMV or SV40 early promoters by pol II and of U6 and 5S RNA genes by pol III were either unaffected or minimally inhibited by the antibodies. Purified rat E1BF partially restored the suppression of human rDNA transcription by anti-Ku antibodies. Immunoprecipitation of rat cell extract with the anti-Ku antibodies followed by SDS-PAGE of the precipitated proteins and Southwestern analysis showed that E1BF interacts with CPBF, a core promoter binding factor. When the majority of CPBF and E1BF was removed from the reaction mixture by preincubation with a core promoter oligo nucleotide fragment, rDNA transcription was severely impaired. Addition of exogenous CPBF or E1BF to such a reaction resulted in significant restoration of the transcription, whereas inclusion of both factors caused further enhancement of rDNA transcription. These data demonstrate that E1BF is a basal pol I transcription factor that interacts with a core promoter binding factor both physically and functionally, and that is not a general pol II or pol III transcription factor.