Biomedical subjects

P J Farnham

Publications and source records attributed to P J Farnham.

At least 55 records · Page 3Linked to original sources

PubMed1993

A protein synthesis-dependent increase in E2F1 mRNA correlates with growth regulation of the dihydrofolate reductase promoter.

Enhanced expression of genes involved in nucleotide biosynthesis, such as dihydrofolate reductase (DHFR), is a hallmark of entrance into the DNA synthesis (S) phase of the mammalian cell cycle. To investigate the regulated expression of the DHFR gene, we stimulated serum-starved NIH 3T3 cells to synchronously reenter the cell cycle. Our previous results show that a cis-acting element at the site of DHFR transcription initiation is necessary for serum regulation. Recently, this element has been demonstrated to bind the cloned transcription factor E2F. In this study, we focused on the role of E2F in the growth regulation of DHFR. We demonstrated that a single E2F site, in the absence or presence of other promoter elements, was sufficient for growth-regulated promoter activity. Next, we showed that the increase in DHFR mRNA at the G1/S-phase boundary required protein synthesis, raising the possibility that a protein(s) lacking in serum-starved cells is required for DHFR transcription. We found that, similar to DHFR mRNA expression, levels of murine E2F1 mRNA were low in serum-starved cells and increased at the G1/S-phase boundary in a protein synthesis-dependent manner. Furthermore, in a cotransfection experiment, expression of human E2F1 stimulated the DHFR promoter 22-fold in serum-starved cells. We suggest that E2F1 may be the key protein required for DHFR transcription that is absent in serum-starved cells. Expression of E2F also abolished the serum-stimulated regulation of the DHFR promoter and resulted in transcription patterns similar to those seen with expression of the adenoviral oncoprotein E1A. In summary, we provide evidence for the importance of E2F in the growth regulation of DHFR and suggest that alterations in the levels of E2F may have severe consequences in the control of cellular proliferation.

3T3 Cells↗

PubMed1993

Site-specific initiation of transcription by RNA polymerase II.

RNA polymerase II initiates transcription at specific DNA sequences. Studies using sequence analysis and molecular genetics suggest a simple and universal model of start-site selection by RNA polymerase II. Two consensus sequences occur at fixed positions in promoters from higher eukaryotes and their viruses: the TATA box around -30 and the initiator at the start site of transcription. Both consensus sequences function as positioning elements that control site-specific initiation. As a first step during initiation, the basal transcription factor TFIID binds to the TATA box; regulatory transcription factors can tether TFIID bind to the TATA box; regulatory transcription factors can tether TFIID to promoters without a consensus TATA box. TFIID then directs the assembly of other basal transcription factors and RNA polymerase II into a preinitiation complex. Finally, RNA polymerase II searches for the best match to the initiator consensus about 30 base pairs downstream of the TATA box to select the exact start site. The transcriptional activity of a start-site sequence generally correlates with its similarity to the initiator consensus, suggesting that there is only one type of initiator.

Base Sequence↗

PubMed1992

Expression cloning of a cDNA encoding a retinoblastoma-binding protein with E2F-like properties.

An expression vector was modified to permit the rapid synthesis of purified, 32P-labeled, glutathione S-transferase (GST)-retinoblastoma (RB) fusion proteins. The products were used to screen lambda gt11 expression libraries, from which we cloned a cDNA encoding a polypeptide (RBAP-1) capable of binding directly to a putative functional domain (the pocket) of the retinoblastoma gene product (RB). The RB "pocket" is known to bind, directly or indirectly, to the cellular transcription factor, E2F, implicated in cell growth control. We have found that RBAP-1 copurifies with E2F, interacts specifically with the adenovirus E4 ORF 6/7 protein, binds specifically and directly to a known E2F DNA recognition sequence, and contains a functional tranasactivation domain. Therefore, RBAP-1 is a species of E2F and can bind specifically to the RB pocket.

Amino Acid Sequence↗

PubMed1992

Heat sensitivity and Sp1 activation of complex formation at the Syrian hamster carbamoyl-phosphate synthase (glutamine-hydrolyzing)/aspartate carbamoyltransferase/dihydroorotase promoter in vitro.

To study the regulation of transcription of the carbamoyl-phosphate synthase (glutamine-hydrolyzing)/aspartate carbamoyltransferase/dihydroorotase (CAD) gene from the Syrian hamster, Mesocricetus auratus, we developed a homologous in vitro transcription system on the basis of nuclear extract from Syrian hamster kidney cells. We optimized the reaction temperature and the concentrations of DNA template, KCl, and MgCl2 simultaneously with the response surface method and found an unusually low temperature optimum of 20 degrees C. We therefore investigated whether CAD transcription in vitro depended on a heat-labile component of nuclear extract. Preincubating extract alone at 30 degrees C reduced transcription from the CAD promoter but not from the major late promoter of adenovirus 2. The formation of stable initiation complexes at the CAD promoter was diminished in heat-treated extract; run-off transcripts, however, accumulated at the same rate as in untreated extract. The heat sensitivity of complex formation correlated with the heat sensitivity of DNA binding by transcription factor Sp1, which binds to two sites in the CAD promoter; moreover, both preformed initiation complexes and DNA-bound Sp1 were heat-resistant. Adding purified Sp1 to heat-treated extract restored complex formation. We propose that Sp1 activates CAD transcription by stabilizing initiation complexes at the CAD promoter.

Animals↗

PubMed1992

krox 20 messenger RNA and protein expression in the adult central nervous system.

krox 20 is an inducible immediate early response gene. To determine if krox 20 has a physiological role in the adult central nervous system (CNS), this study sought to demonstrate the presence of krox 20 in adult rat brain. RNA analysis showed the presence of krox 20 transcripts in the CNS, including the cortex. Polyclonal antibodies to a Krox 20 fusion protein demonstrated 79 and 55 kDa antigens in nuclear CNS homogenates. Neither RNA nor protein analysis was able to demonstrate an induction of krox 20 by a seizure at times when other immediate early response genes are known to be induced. Immunohistochemical analysis revealed staining at several levels throughout the nervous system. This staining was predominantly nuclear, consistent with the role of krox 20 as a transcription factor. These data show that krox 20 is present in the adult CNS, yet differs in response to stimuli as compared to other related transcription factors with a zinc finger motif, such as NGFI-A and NGFI-C.

Animals↗

PubMed1992

The HIP1 binding site is required for growth regulation of the dihydrofolate reductase gene promoter.

The transcription rate of the dihydrofolate reductase (DHFR) gene increases at the G1/S boundary of the proliferative cell cycle. Through analysis of transiently and stably transfected NIH 3T3 cells, we have now demonstrated that DHFR promoter sequences extending from -270 to +20 are sufficient to confer similar regulation on a reporter gene. Mutation of a protein binding site that spans sequences from -16 to +11 in the DHFR promoter resulted in loss of the transcriptional increase at the G1/S boundary. Purification of an activity from HeLa nuclear extract that binds to this region enriched for a 180-kDa polypeptide (HIP1). Using this HIP1 preparation, we have identified specific positions within the binding site that are critical for efficient protein-DNA interactions. An analysis of association and dissociation rates suggests that bound HIP1 protein can exchange rapidly with free protein. This rapid exchange may facilitate the burst of transcriptional activity from the DHFR promoter at the G1/S boundary.

3T3 Cells↗

PubMed1992

The HIP1 initiator element plays a role in determining the in vitro requirement of the dihydrofolate reductase gene promoter for the C-terminal domain of RNA polymerase II.

We examined the ability of purified RNA polymerase (RNAP) II lacking the carboxy-terminal heptapeptide repeat domain (CTD), called RNAP IIB, to transcribe a variety of promoters in HeLa extracts in which endogenous RNAP II activity was inhibited with anti-CTD monoclonal antibodies. Not all promoters were efficiently transcribed by RNAP IIB, and transcription did not correlate with the in vitro strength of the promoter or with the presence of a consensus TATA box. This was best illustrated by the GC-rich, non-TATA box promoters of the bidirectional dihydrofolate reductase (DHFR)-REP-encoding locus. Whereas the REP promoter was transcribed by RNAP IIB, the DHFR promoter remained inactive after addition of RNAP IIB to the antibody-inhibited reactions. However, both promoters were efficiently transcribed when purified RNAP with an intact CTD was added. We analyzed a series of promoter deletions to identify which cis elements determine the requirement for the CTD of RNAP II. All of the promoter deletions of both DHFR and REP retained the characteristics of their respective full-length promoters, suggesting that the information necessary to specify the requirement for the CTD is contained within approximately 65 bp near the initiation site. Furthermore, a synthetic minimal promoter of DHFR, consisting of a single binding site for Sp1 and a binding site for the HIP1 initiator cloned into a bacterial vector sequence, required RNAP II with an intact CTD for activity in vitro. Since the synthetic minimal promoter of DHFR and the smallest REP promoter deletion are both activated by Sp1, the differential response in this assay does not result from upstream activators. However, the sequences around the start sites of DHFR and REP are not similar and our data suggest that they bind different proteins. Therefore, we propose that specific initiator elements are important for determination of the requirement of some promoters for the CTD.

Animals↗

PubMed1991

Cell cycle analysis of Krox-20, c-fos, and JE expression in proliferating NIH3T3 fibroblasts.

We have shown that early growth response genes which were identified on the basis of their expression during the G0 to G1 transition can also be induced in proliferating fibroblasts. The expression of Krox-20 and c-fos mRNAs increased dramatically upon stimulation of cell populations of increasing density and correlated with the percentage of cells in the G0-G1 stages of the cell cycle. However, fractionation of serum-stimulated cultures into cell cycle stage-specific subpopulations using fluorescence-activated cell sorting revealed that the levels of Krox-20 and c-fos mRNAs were equal in all stages of the cell cycle. This result was corroborated by serum and cycloheximide stimulation of stage-specific fractions separated by centrifugal elutriation. Expression of the immediate-early gene JE was also induced in all stages of the cell cycle in the elutriated fractions. Thus, although the amount of induced Krox-20, c-fos, and JE mRNA correlated with the number of quiescent cells in a proliferating population, expression of all three genes occurred to the same extent in all stages of the cell cycle at a given culture density. Possible explanations for the density-associated increase in induced expression are discussed. We have demonstrated that there are both transcriptional and posttranscriptional components to the stimulated expression of the Krox-20 and c-fos genes in proliferating fibroblasts. Since the increased expression of these genes has the same steady-state and transcription rate kinetics as serum response factor-mediated induction, we are currently investigating the role of serum response factor in serum-induced expression in proliferating cells.

3T3 Cells↗

PubMed1991

Sp1 activation of RNA polymerase II transcription complexes involves a heat-labile DNA-binding component.

We have identified a component of the eukaryotic RNA polymerase II transcriptional machinery that is more heat-labile than TFIID. DHFR transcriptional activity was severely reduced in 40 degrees C heat-treated extracts in which TFIID was fully active. This heat-labile activity was required for the transcription of both TATA box and non-TATA box promoters that are activated by the transcription factor Sp1. Gel mobility shifts indicated that Sp1 DNA binding activity was heat-labile, and the addition of purified Sp1 to 40 degrees C heat-treated extracts fully restored DHFR transcriptional activity. In contrast, the addition of Sp1 to 47 degrees C heat-treated extract did not result in transcriptional activity from the DHFR promoter. We conclude that reduction in Sp1 DNA binding activity is partially responsible for the heat-sensitive loss of DHFR transcriptional activity, but that a second essential activity is also inactivated by 47 degrees C heat-treatment. The discovery of this heat-labile component of Sp1 activation has two important implications in the analysis of transcriptional regulation. First, it demonstrates that heat-treated extracts are not appropriate for examination of the involvement of TFIID in the transcription of Sp1-activated promoters. Second, it explains the previously reported low-temperature optima for transcription from the DHFR promoter and demonstrates that transcriptional studies of Sp1-activated promoters should not be performed at 30 degrees C.

Base Sequence↗

PubMed1990

Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site.

We have identified a sequence element that specifies the position of transcription initiation for the dihydrofolate reductase gene. Unlike the functionally analogous TATA box that directs RNA polymerase II to initiate transcription 30 nucleotides downstream, the positioning element of the dihydrofolate reductase promoter is located directly at the site of transcription initiation. By using DNase I footprint analysis, we have shown that a protein binds to this initiator element. Transcription initiated at the dihydrofolate reductase initiator element when 28 nucleotides were inserted between it and all other upstream sequences, or when it was placed on either side of the DNA helix, suggesting that there is no strict spatial requirement between the initiator and an upstream element. Although neither a single Sp1-binding site nor a single initiator element was sufficient for transcriptional activity, the combination of one Sp1-binding site and the dihydrofolate reductase initiator element cloned into a plasmid vector resulted in transcription starting at the initiator element. We have also shown that the simian virus 40 late major initiation site has striking sequence homology to the dihydrofolate reductase initiation site and that the same, or a similar, protein binds to both sites. Examination of the sequences at other RNA polymerase II initiation sites suggests that we have identified an element that is important in the transcription of other housekeeping genes. We have thus named the protein that binds to the initiator element HIP1 (Housekeeping Initiator Protein 1).

Base Sequence↗

PubMed1990

Sequences downstream of the transcription initiation site modulate the activity of the murine dihydrofolate reductase promoter.

The murine dihydrofolate reductase gene is regulated by a bidirectional promoter that lacks a TATA box. To identify the DNA sequences required for dihydrofolate reductase transcription, the activities of various templates were determined by in vitro transcription analysis. Our data indicate that sequences both upstream and downstream of the transcription initiation site modulate the activity of the dihydrofolate reductase promoter. We have focused on two regions downstream of the transcription initiation site that are important in determining the overall efficiency of the promoter. Region 1, which included exon 1 and part of intron 1, could stimulate transcription when placed in either orientation in the normal downstream position and when inserted upstream of the transcription start site. This region could also stimulate transcription in trans when the enhancer was physically separate from the promoter. Deletion of region 2, spanning 46 nucleotides of the 5' untranslated region, reduced transcriptional activity by fivefold. DNase I footprinting reactions identified protein-binding sites in both downstream stimulatory regions. Protein bound to two sites in region 1, both of which contain an inverted CCAAT box. The protein-binding site in the 5' untranslated region has extensive homology to binding sites in promoters that both lack (simian virus 40 late) and contain (adenovirus type 2 major late promoter and c-myc) TATA boxes.

Animals↗

PubMed1990

Identification of the serum-responsive transcription initiation site of the zinc finger gene Krox-20.

The Krox-20 gene is rapidly and transiently induced when quiescent 3T3 cells are stimulated to reenter the proliferative cycle. We identified the major serum-responsive transcription initiation site and found that it differs from the initiation sites previously identified for the Krox-20 gene. Transcripts from the major serum-responsive initiation site increased at least 40-fold in serum-stimulated cells compared with logarithmically growing cells.

Animals↗

PubMed1990

Characterization of the 5' end of the growth-regulated Syrian hamster CAD gene.

The carbamoylphosphate synthetase-aspartate transcarbamylase-dihydroorotase (CAD) gene encodes a tri-functional protein catalyzing the first three steps in de novo pyrimidine biosynthesis. Studies correlating CAD gene expression with cellular proliferation indicate the importance of understanding the regulation of the CAD gene. As a first step, the structure of the promoter region of the Syrian hamster CAD gene has been determined. Sequence analysis of 1671 base pairs of DNA revealed that the CAD promoter region is very GC rich. Primer extension analysis indicated that the transcription initiation site of the CAD gene is downstream from two GC boxes (consensus binding sites for the transcription factor Sp1). There is no TATA box appropriately spaced upstream from the transcription initiation site. Using RNase protection mapping, S1 nuclease analysis, and comparison to consensus splice donor/acceptor sites, the 5' end of the CAD gene has been determined to consist of a 241-base pair first exon, a 187-base pair first intron, a 140-base pair second exon, and a second intron that extends at least three kilobase pairs. Using conditions optimized for this GC-rich promoter, accurate transcription can be achieved in vitro. Analysis of CAD promoter deletions indicated that sequences extending only 114 base pairs upstream and 225 base pairs downstream from the transcription initiation site are sufficient for accurate and efficient transcription in vitro. DNase I footprinting reactions using this promoter fragment have identified three regions that bind proteins in a HeLa nuclear extract.

Animals↗

PubMed1989

Identification of a new promoter upstream of the murine dihydrofolate reductase gene.

In vitro reactions identified a transcription initiation site located 740 nucleotides upstream of the dihydrofolate reductase translational start. Transcription from this site proceeded in the direction opposite to that of dihydrofolate reductase mRNA. Deletion mapping indicated that this new promoter can be separated from the dihydrofolate reductase promoter and that separation increased transcription at -740. Transcripts that initiate at -740 were also detected in cellular RNA, indicating that this is a bona fide transcription initiation site in vivo.

Animals↗

PubMed1986

Murine dihydrofolate reductase transcripts through the cell cycle.

The murine dihydrofolate reductase gene codes for mRNAs that differ in the length of their 3' untranslated region as well as in the length of their 5' leader sequence. In addition, the dihydrofolate reductase promoter functions bidirectionally, producing a series of RNAs from the opposite strand than the dihydrofolate reductase mRNAs. We have examined the production of these RNAs and their heterogeneous 5' and 3' termini as mouse 3T6 cells progress through a physiologically continuous cell cycle. We found that all of the transcripts traverse the cell cycle in a similar manner, increasing at the G1/S boundary without significantly changing their ratios relative to one another. We conclude that cell-cycle regulation of dihydrofolate reductase is achieved without recruiting new transcription initiation sites and without a change in polyadenylation sites. It appears that the mechanism responsible for the transcriptional cell-cycle regulation of the dihydrofolate reductase gene is manifested only by transiently increasing the efficiency of transcription at the dihydrofolate reductase promoter.

Animals↗

PubMed1986

In vitro transcription and delimitation of promoter elements of the murine dihydrofolate reductase gene.

We have developed an in vitro transcription system for the murine dihydrofolate reductase gene. Although transcription in vitro from a linearized template was initiated at the same start sites as in vivo, the correct ratios were more closely approximated when a supercoiled template was used. In addition, whereas the dihydrofolate reductase promoter functions bidirectionally in vivo, the initiation signals directed unidirectional transcription in this in vitro system. The dihydrofolate reductase gene does not have a typical TATA box, but has four GGGCGG hexanucleotides within 300 base pairs 5' of the AUG codon. Deletion analysis suggested that, although sequences surrounding each of the GC boxes could specify initiation approximately 40 to 50 nucleotides downstream, three of the four GC boxes could be removed without changing the accuracy or efficiency of initiation at the major in vivo site. The dihydrofolate reductase promoter initiated transcription very rapidly in vitro, with transcripts visible by 1 min and almost maximal by 2 min at 30 degrees C with no preincubation. Nuclear extracts prepared from cells blocked in the S phase by aphidicolin or from adenovirus-infected cells at 16 h postinfection had enhanced dihydrofolate reductase transcriptional activity. This increased in vitro transcription mimicked the increase in dihydrofolate reductase mRNA seen in S-phase cells and suggested the presence of a cell-cycle-specific factor(s) which stimulated transcription from the dihydrofolate reductase gene.

Adenoviridae↗

PubMed1985

Transcriptional regulation of mouse dihydrofolate reductase in the cell cycle.

We have studied transcription of the dihydrofolate reductase gene as cells progress through the cell cycle. We used the techniques of DNA-excess filter hybridization and in vivo pulse labeling of a synchronous population of cells to measure the transcription rate of the dihydrofolate reductase gene in different phases of the cell cycle. Our results indicate that the dihydrofolate reductase gene is cell cycle regulated at the transcriptional level. The transcription rate is low in G1, increases 7-fold at the beginning of S phase, decreases almost immediately thereafter, and remains low throughout the remainder of S and into G2. This cell cycle regulation seen in the G1 to S phase transition is achieved by increasing the rate of transcription from a single promoter region. The fact that this region is similar to promoter regions of other housekeeping genes suggests that this type of regulation may not be unique to dihydrofolate reductase.

Animals↗

PubMed1985

Heterogeneity at the 5' termini of mouse dihydrofolate reductase mRNAs. Evidence for multiple promoter regions.

We have determined the sequence of the 1000 base pairs of DNA preceding the coding region of the mouse dihydrofolate reductase gene. 700 base pairs upstream of the translation start codon (position + 1) is the sequence CAACT, separated by 50 base pairs from the sequence TAATAA; these sequences resemble controlling elements responsible for accurate and efficient transcription initiation in a variety of eukaryotic genes. The region between -244 and -101 consists of a 3-fold tandem repeat of a 48-base pair sequence. S1 mapping results indicate that the 5' termini of the multiple dihydrofolate reductase mRNAs are heterogeneous, with the major terminus at -115 and with minor termini in the regions of -275 and -450. In addition, a portion of the 5'-ward region of the gene from -543 to -405 is represented differentially in some, but not all, mouse dihydrofolate reductase mRNAs. The above findings are consistent with the presence of two transcription promoter elements in the 5' end of the mouse dihydrofolate reductase gene. This has been substantiated by inserting portions of the 5'-ward 1000 base pairs of the gene into modular dihydrofolate reductase plasmids. When such constructs are transfected into Chinese hamster ovary cells lacking dihydrofolate reductase, function can be restored with equal transfection frequency when sequences surrounding the 5' CAACT-TAATAA region at -700 or a complete 48-base pair repeat from the region of -148 to -101 are present in the plasmid construct.

Animals↗