Transcriptional activity of the Rous sarcoma virus long terminal repeat correlates with binding of a factor to an upstream CCAAT box in vitro

Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y?

The Y box is an important sequence motif found in promoters and enhancers containing a CCAAT box - one of the few elements enriched in promoters of large sets of genes overexpressed in cancer. The search for the transcription factor(s) acting on it led to the biochemical purification of the nuclear factor Y (NF-Y) heterotrimer, and to the cloning - through the screening of expression libraries - of Y box-binding protein 1 (YB-1), an oncogene, overexpressed in aggressive tumors and associated with drug resistance. These two factors have been associated with Y/CCAAT-dependent activation of numerous growth-related genes, notably multidrug resistance protein 1. We review two decades of data indicating that NF-Y ultimately acts on Y/CCAAT in cancer cells, a notion recently confirmed by genome-wide data. Other features of YB-1, such as post-transcriptional control of mRNA biology, render it important in cancer biology.

NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors

NF-Y, a trimeric transcription factor (TF) composed of two histone-like subunits (NF-YB and NF-YC) and a sequence-specific subunit (NF-YA), binds to the CCAAT motif, a common promoter element. Genome-wide mapping reveals 5000–15,000 NF-Y binding sites depending on the cell type, with the NF-YA and NF-YB subunits binding asymmetrically with respect to the CCAAT motif. Despite being characterized as a proximal promoter TF, only 25% of NF-Y sites map to promoters. A comparable number of NF-Y sites are located at enhancers, many of which are tissue specific, and nearly half of the NF-Y sites are in select subclasses of HERV LTR repeats. Unlike most TFs, NF-Y can access its target DNA motif in inactive (nonmodified) or polycomb-repressed chromatin domains. Unexpectedly, NF-Y extensively colocalizes with FOS in all genomic contexts, and this often occurs in the absence of JUN and the AP-1 motif. NF-Y also coassociates with a select cluster of growth-controlling and oncogenic TFs, consistent with the abundance of CCAAT motifs in the promoters of genes overexpressed in cancer. Interestingly, NF-Y and several growth-controlling TFs bind in a stereo-specific manner, suggesting a mechanism for cooperative action at promoters and enhancers. Our results indicate that NF-Y is not merely a commonly used proximal promoter TF, but rather performs a more diverse set of biological functions, many of which are likely to involve coassociation with FOS.

Molecular epidemiology of avian leukosis virus subgroup J and evolutionary history of its 3' untranslated region

Avian leukosis subgroup J (ALV-J) causes a variety of tumors and mortality in meat-type chickens. Since its discovery in the late 1980s, ALV-J has spread to breeding stock produced by most primary breeding companies of North America, the European Union, and Asia. ALV-J seems to have been eradicated from elite breeding stock produced by most primary breeders, albeit ALV-J still circulates in some commercial poultry. This study was undertaken to examine the molecular epidemiology and evolution of ALV-J detected in breeding stock and broiler chickens representing eight primary breeding companies over a period of approximately 20 yr (1988-2007). The redundant transmembrane region of the envelope gene has been deleted in some isolates, suggesting that this region is dispensable for viral fitness. Within the 3' untranslated region (3' UTR), the direct repeat 1 was present in 100% of the ALV-J isolates studied. In contrast, the E element has undergone substantial deletions in >50% of the ALV-J proviruses studied. Overall, the unique region 3 was the least conserved within the 3' long terminal repeat (LTR), albeit the transcriptional regulatory elements typical of avian retroviruses (CAAT, CArG, PRE, TATA, and Y boxes) were highly conserved. The direct repeat region of the LTR was identical in all of the proviruses, and the 3' unique region 5 was relatively well conserved. Thus, the 3' UTR of ALV-J has evolved rapidly, reflecting significant instability of this region. Some of the mutations in the 3' UTR have resulted in the emergence of moderately distinct genetic lineages representing each primary breeding company from which ALV-J was isolated.

Dissection of silencer elements in first intron controlling the human renin gene

OBJECTIVE

A silencer within the renin first intron (intron A) was identified using Calu-6 cells, a pulmonary carcinoma cell line which produced renin. In the present study, a dissection of the first intron was performed to determine precisely the cis-regulatory elements involved in the silencer transcriptional effects.

MATERIALS AND METHODS

Intron A was completely sequenced to characterize potential binding sites for known transcription factors. Partial portions of intron A were subcloned upstream the 892 bp of the renin promoter and transfected in different models of renin-producing cells: primary culture of human chorionic cells, human Calu-6 cells and mouse As4.1 cells.

RESULTS

There is significant DNA homology (67%) between the 3' and 5' ends of the human and rat renin first intron. Several transcription factor binding sites identified in human first intron, but not in rat intron, do not contribute to the reported silencer activity. Transfections of renin/ luciferase constructs containing partial portions of first intron inserted upstream of the 892 bp in both renin-producing cells do not allow the precise characterization of cis-elements involved in the silencer effect.

CONCLUSIONS

The silencer located renin intron A is cell specific. The integrity of the human first intron seems necessary for its repressor activity on renin proximal promoter in renin-producing cells.

Role of the transcription start site core region and transcription factor YY1 in Rous sarcoma virus long terminal repeat promoter activity

The Rous sarcoma virus (RSV) long terminal repeat (LTR) contains a transcriptionally potent enhancer and promoter that functions in a variety of cell types. Previous studies have identified the viral sequences required for enhancer activity, and characterization of these elements has provided insight into the mechanism of RSV transcriptional activity. The objective of this study was to better define the RSV LTR promoter by examining the transcription start site core (TSSC) region. Deletion of the TSSC resulted in complete loss of transcriptional activity despite the presence of a functional TATA box, suggesting that the TSSC is required for viral expression. Homologies within the TSSC to the DNA binding motif of YY1 suggested that it might regulate promoter activity. YY1 has been shown to regulate transcription in some cellular genes and viral promoters by binding to sites overlapping the transcription start site. Gel shift assays using YY1 antibody identified YY1 as one of three complexes that bound to the TSSC. Mutation of the YY1 binding site reduced RSV transcriptional activity by more than 50%, suggesting that YY1, in addition to other TSSC-binding factors, regulates RSV transcription. Furthermore, in vitro transcription assays performed with Drosophila embryo extract (devoid of YY1 activity) showed decreased levels of RSV transcription, while transient transfection experiments overexpressing YY1 demonstrated that YY1 could transactivate the RSV LTR approximately 6- to 7-fold. We propose that the TSSC plays a vital role in RSV transcription and that this function is partially carried out by the transcription factor YY1.

Identification of two Y-box binding proteins that interact with the promoters of columbid annexin I genes

Two annexin I (anxI) genes, called cp35 and cp37, are expressed from the pigeon (Columba livia) genome, but they are regulated differently at both the transcriptional and post-transcriptional levels. The proximal promoter elements of these two genes are very similar. A conserved sequence from the cp35 and cp37 promoters bound specifically with proteins present in cropsac cell extracts. This sequence of DNA was used to screen a lambdagt11 cDNA expression library. Clones encoding two pigeon Y-box binding proteins (YB) were isolated. One of the pigeon YB cDNAs was found to be most similar to YB1 from other species, and the other was most similar to chicken YB2. Each YB is encoded by a single-copy gene in the pigeon, and their mRNAs are expressed in many tissues. On Northern blots, the sizes of the mRNAs encoding pigeon YB1 (pYB1) and pigeon YB2 (pYB2) were 1.8 and 1.7kb, respectively. The sequences of both pYB1 and pYB2 diverge from their previously identified relatives in the N-terminal domain 'A'. Antisera were developed to unique peptide epitopes in YB1 or 2. Affinity-purified anti-YB1 and anti-YB2 detected immunoreactive proteins in extracts from a variety of pigeon tissues, including the cropsac. To confirm that pYB1 and pYB2 interact with the cp35 promoter, electrophoretic gel mobility shift reactions were carried out in the presence or absence of YB antibodies. Binding to the cp35 promoter was specifically neutralized by either anti-pYB1 or anti-pYB2. These results are the first evidence that two YB proteins simultaneously bind to a promoter element, and thereby may interact during regulation of gene expression.

Characterization of the DNA-binding domain of the avian Y-box protein, chkYB-2, and mutational analysis of its single-strand binding motif in the Rous sarcoma virus enhancer

chkYB-2 is a sequence-specific, single-stranded DNA binding chicken Y-box protein that promotes Rous sarcoma virus long terminal repeat (RSV LTR)-driven transcription in avian fibroblasts. The DNA-binding domain of chkYB-2 has been mapped by characterizing the DNA binding properties of purified recombinant chkYB-2 mutant polypeptides. The data indicate that the invariant cold shock domain (CSD) is necessary but not sufficient for association with DNA and suggest that another conserved region, adjacent to the carboxyl boundary of the CSD, plays a role in high-affinity DNA binding. chkYB-2 binds to a tandem repeat of the 5'-GTACCACC-3' motif on the RSV LTR. Mutational analysis of this recognition sequence revealed the requirement of an essentially unaltered template for both high-affinity binding by chkYB-2 as well as maximal transcriptional activity of the RSV LTR in vivo. The single-stranded DNA binding activity of chkYB-2 is augmented by Mg2+. The possible significance of this finding for transactivation by a single-strand DNA binding protein is discussed.

Chicken YB-2, a Y-box protein, is a potent activator of Rous sarcoma virus long terminal repeat-driven transcription in avian fibroblasts

We have previously reported on the cloning and characterization of chk-YB-2, a novel member of the Y-box family of proteins, that binds to the sequence 5'-GTACCACC-3' present on the noncoding strand of the Rous sarcoma virus (RSV) long terminal repeat (LTR) in a single-strand-specific manner. Here, we demonstrate that deletion or mutation of this motif not only eliminates chk-YB-2 binding in vitro but also down-regulates RSV LTR-driven transcription in avian cells. Selective abrogation of chk-YB-2 expression by using antisense oligonucleotides decreased RSV LTR-driven transcription in a promoter-specific manner. This inhibition was not observed when a reporter construct with a deletion in the chk-YB-2 binding site was used. Depletion of cellular chk-YB-2 by transfecting the cells with excess of its recognition sequence oligonucleotides also resulted in reduced transcription from the RSV LTR. Taken together, these results suggest that chk-YB-2 acts as an activator of LTR-promoted transcription in avian cells and that this activation is mediated primarily through the sequence 5'-GTACCACC-3'.

Unique long terminal repeat U3 sequences distinguish exogenous jaagsiekte sheep retroviruses associated with ovine pulmonary carcinoma from endogenous loci in the sheep genome

Ovine pulmonary carcinoma (OPC) is a contagious lung cancer of sheep that is presumed to be caused by an exogenous retrovirus of sheep, jaagsiekte sheep retrovirus (JSRV). The sheep genome carries 15 to 20 copies of endogenous sheep retrovirus (ESRV) loci that hybridize to JSRV DNA probes. In order to clarity the etiologic roles of ESRV and an exogenous JSRV-like retrovirus (exJSRV) in OPC, we assessed sequence differences between ESRV and JSRV. Molecular characterization of six ESRV loci revealed restriction sites specific for JSRV. Nucleotide sequences of ESRVs from sheep of different breeds were similar to those of JSRV in structural genes but divergent in U3. Therefore, primers specific for the U3 sequences of exJSRV were designed for use in the PCR. Of 13 tumor DNAs tested by PCR with these exogenous-virus U3 primers, 8 produced DNA fragments that hybridized with the JSRV gag probe, but neither lung DNAs from healthy sheep nor DNAs from nontumor tissues of diseased sheep produced similar DNA fragments. exJSRV PCR products from tumor DNAs of sheep with OPC from three continents had restriction profiles similar to each other but different from those of ESRVs upon digestion with EcoRI, HindIII, NdeI, KpnI, and ScaI. These exjSRVs could be classified into two genotypes according to U3 sequences and restriction profiles. U3 sequences of exJSRV proviruses in tumors strongly resembled those of JSRV but differed from those of ESRVs, suggesting that exJSRVs, rather than ESRVs, are primarily associated with oncogenesis in OPC.

Identification of EFIV, a stable factor present in many avian cell types that transactivates sequences in the 5' portion of the Rous sarcoma virus long terminal repeat enhancer

We define a protein complex present in avian nuclear extracts that interacts with the Schmidt-Ruppin strain of the Rous sarcoma virus (RSV) long terminal repeat (LTR) between positions -197 and -168 relative to the transcriptional start site. We call this complex EFIV and demonstrate that the EFIV protein(s) is present in several avian cell types examined, including B cells (S13 and DT40), T cells (MSB), and chicken embryo fibroblasts. We also report that the EFIV binding site activates transcription of reporter constructs after transfection into avian B cells and chicken embryo fibroblasts, demonstrating that the EFIV region constitutes a functional transactivator sequence. By chemical interference footprinting and mutational analyses we define the EFIV binding site as including the sequence GCAACATG, which is present in two copies between positions -197 and -168, as well as sequences that lie between the two repeats. Electrophoretic mobility shift competition experiments suggest that the EFIV protein(s) may be related to members of the CCAAT/enhancer-binding protein family of transcription factors that interact with different regions of the RSV and the avian leukosis virus (ALV) LTRs. However, as defined by differences in sensitivity to protein synthesis inhibitors and footprinting patterns, EFIV is clearly distinct from these previously defined LTR binding factors. In addition, the finding that EFIV binding activity is stable in B cells indicates either that the lability of all 5' LTR binding activities is not required for B-cell transformation by the ALV/RSV family of viruses or that nonacute transforming viruses that include an RSV LTR may use a mechanism to effect cellular transformation different from that proposed for ALV.

The transcriptional regulatory protein, YB-1, promotes single-stranded regions in the DRA promoter

YB-1 is a member of a newly defined family of DNA- and RNA-binding proteins, the Y box factors. These proteins have been shown to affect gene expression at both the transcriptional and translational levels. Recently, we showed that YB-1 represses interferon-gamma-induced transcription of class II human major histocompatibility (MHC) genes (1). Studies in this report characterize the DNA binding properties of purified, recombinant YB-1 on the MHC class II DRA promoter. The generation of YB-1-specific antibodies further permitted an analysis of the DNA binding properties of endogenous YB-1. YB-1 specifically binds single-stranded templates of the DRA promoter with greater affinity than double-stranded templates. The single-stranded DNA binding sites of YB-1 were mapped to the X box, whereas the double-stranded binding sites were mapped to the Y box of the DRA promoter, by methylation interference analysis. Most significantly, YB-1 can induce or stabilize single-stranded regions in the X and Y elements of the DRA promoter, as revealed by mung bean nuclease analysis. In concert with the findings that YB-1 represses DRA transcription, this study of YB-1 binding properties suggests a model of repression in which YB-1 binding results in single-stranded regions within the promoter, thus preventing loading and/or function of other DRA-specific transactivating factors.

Multiple forms of C/EBP beta bind the EFII enhancer sequence in the Rous sarcoma virus long terminal repeat

In this report we demonstrate that C/EBP beta is a major component of three EFII DNA binding complexes, EFIIa, EFIIb, and EFIIc, which we have previously shown to specifically recognize a C/EBP consensus binding site found in the EFII enhancer sequence from the Rous sarcoma virus long terminal repeat (R. C. Sears and L. Sealy, J. Virol. 66:6338-6352, 1992). Three different forms of C/EBP beta, p42, p35, and p20, can bind the EFII DNA sequence as homodimers, and dimerization experiments show that EFIIa is a homodimer of p20 C/EBP beta, EFIIb is primarily composed of a p20/p35 heterodimer with minor amounts of p20/p42 heterodimer and p35 homodimer, and EFIIc is composed of p20 and/or p35 heterodimerized with a novel 60-kDa protein. p20 C/EBP beta is likely equivalent to the internally initiated translation product of C/EBP beta, LIP (liver inhibitor protein), described by P. Descombes and U. Schibler (Cell 67:569-579, 1991). In contrast to the low level of LIP expressed in liver, postulated to occur because of leaky ribosome scanning, we found high levels of expression of p20 C/EBP beta in fibroblasts and lymphocytes. In murine fibroblasts, p20 C/EBP beta has an extended half-life, four times longer than those of p42 and p35 C/EBP beta, which could contribute to its abundant accumulation in this cell type, even though its synthesis by leaky ribosome scanning might be inefficient. Interestingly, overexpression of either the long or short form of C/EBP beta represses EFII-mediated transcription, suggesting that another unidentified EFII transactivator(s) exists, which may be dominantly inhibited by C/EBP beta proteins, and/or that transactivation by C/EBP beta proteins requires posttranslational modifications that were lacking in the transient overexpression experiments.

Multiple forms of C/EBP beta bind the EFII enhancer sequence in the Rous sarcoma virus long terminal repeat

In this report we demonstrate that C/EBP beta is a major component of three EFII DNA binding complexes, EFIIa, EFIIb, and EFIIc, which we have previously shown to specifically recognize a C/EBP consensus binding site found in the EFII enhancer sequence from the Rous sarcoma virus long terminal repeat (R. C. Sears and L. Sealy, J. Virol. 66:6338-6352, 1992). Three different forms of C/EBP beta, p42, p35, and p20, can bind the EFII DNA sequence as homodimers, and dimerization experiments show that EFIIa is a homodimer of p20 C/EBP beta, EFIIb is primarily composed of a p20/p35 heterodimer with minor amounts of p20/p42 heterodimer and p35 homodimer, and EFIIc is composed of p20 and/or p35 heterodimerized with a novel 60-kDa protein. p20 C/EBP beta is likely equivalent to the internally initiated translation product of C/EBP beta, LIP (liver inhibitor protein), described by P. Descombes and U. Schibler (Cell 67:569-579, 1991). In contrast to the low level of LIP expressed in liver, postulated to occur because of leaky ribosome scanning, we found high levels of expression of p20 C/EBP beta in fibroblasts and lymphocytes. In murine fibroblasts, p20 C/EBP beta has an extended half-life, four times longer than those of p42 and p35 C/EBP beta, which could contribute to its abundant accumulation in this cell type, even though its synthesis by leaky ribosome scanning might be inefficient. Interestingly, overexpression of either the long or short form of C/EBP beta represses EFII-mediated transcription, suggesting that another unidentified EFII transactivator(s) exists, which may be dominantly inhibited by C/EBP beta proteins, and/or that transactivation by C/EBP beta proteins requires posttranslational modifications that were lacking in the transient overexpression experiments.

Characterization of rat pseudogenes for enhancer factor I subunit A: ripping provides clues to the evolution of the EFIA/dbpB/YB-1 multigene family

Genomic Southern blot analysis of rat EFIA (gene encoding enhancer factor I subunit A) reveals a complex band pattern when cDNA subfragment probes are used. Screening a rat genomic library with a rat EFIA cDNA probe yields two different processed EFIA pseudogenes, designated rat psi EFIA#(2/3) and #(4/7), in addition to two other different, but less extensively characterized clones. psi EFIA#(4/7) has no open reading frame (ORF) sequences. psi EFIA#(2/3) contains two ORFs (83 and 178 codons), the products of which (if expressed) might be negative-acting EFIA transcription factors. Located nearly 0.6 kb upstream from psi EFIA#(2/3) is a perfect 69-bp dinucleotide (CT) tandem repeat, a sequence element associated with other isolated pseudogenes. Additionally, the 3' end of this processed gene is interrupted by an unusual retroposon, an inverted dimeric B1-like short interspersed repetitive element (SINE). The isolation of several independent clones of the same EFIA processed pseudogenes indicates that they comprise a significant component of the rat EFIA copy multiplicity. The phenomenon of repeat induced point mutagenesis (ripping) at rat EFIA pseudogene CpG doublets occurs at a frequency at least 6.5 times higher than predicted from random mutagenesis. This is consonant with the proposal that ripping may be the mechanism which inactivates the ectopic recombination potential of the rat EFIA pseudogenes.

Cloning and characterization of chicken YB-1: regulation of expression in the liver

A cDNA expression library constructed from day 9 embryonic liver was screened with a previously identified protein binding site in the flanking region of the liver-specific, estrogen-dependent avian apoVLDLII gene. Two of the clones isolated were shown to encode the chicken homolog of the Y-box binding protein, YB-1 (dbpb), which we have designated chkYB-1. This protein was originally identified in avian extracts by virtue of its ability to bind to two reverse CCAAT motifs in the Rous sarcoma virus enhancer. Since its identification, additional nucleic acid binding properties have been ascribed to its homologs, or closely related proteins, in other species. We have determined the sequence of chkYB-1, investigated its ability to bind to sites known to be involved in tissue-specific expression in the liver, and examined factors influencing its hepatic expression. These studies have demonstrated that the level of chkYB-1 mRNA in the liver decreases steadily throughout embryogenesis and for several weeks posthatching until adult levels are attained. We present several lines of evidence that YB-1 expression in the liver is positively associated with DNA synthesis or cell proliferation. Its binding characteristics indicate that the protein can interact specifically with a number of binding sites for liver-enriched or specific factors. In addition, although it is not particularly asymmetric in terms of base composition, we find a marked preference in binding to the pyrimidine-rich strand of these sites regardless of the presence or polarity of an intact CCAAT box. The increased levels of expression of YB-1 during proliferation combined with its binding characteristics suggest that it may be involved in the reduced expression of liver-specific genes observed at early stages of development or during liver regeneration.

Cloning and characterization of chicken YB-1: regulation of expression in the liver

A cDNA expression library constructed from day 9 embryonic liver was screened with a previously identified protein binding site in the flanking region of the liver-specific, estrogen-dependent avian apoVLDLII gene. Two of the clones isolated were shown to encode the chicken homolog of the Y-box binding protein, YB-1 (dbpb), which we have designated chkYB-1. This protein was originally identified in avian extracts by virtue of its ability to bind to two reverse CCAAT motifs in the Rous sarcoma virus enhancer. Since its identification, additional nucleic acid binding properties have been ascribed to its homologs, or closely related proteins, in other species. We have determined the sequence of chkYB-1, investigated its ability to bind to sites known to be involved in tissue-specific expression in the liver, and examined factors influencing its hepatic expression. These studies have demonstrated that the level of chkYB-1 mRNA in the liver decreases steadily throughout embryogenesis and for several weeks posthatching until adult levels are attained. We present several lines of evidence that YB-1 expression in the liver is positively associated with DNA synthesis or cell proliferation. Its binding characteristics indicate that the protein can interact specifically with a number of binding sites for liver-enriched or specific factors. In addition, although it is not particularly asymmetric in terms of base composition, we find a marked preference in binding to the pyrimidine-rich strand of these sites regardless of the presence or polarity of an intact CCAAT box. The increased levels of expression of YB-1 during proliferation combined with its binding characteristics suggest that it may be involved in the reduced expression of liver-specific genes observed at early stages of development or during liver regeneration.

Functional and defective components of avian endogenous virus long terminal repeat enhancer sequences

Oncogenic avian retroviruses, such as Rous sarcoma virus (RSV) and the avian leukosis viruses, contain a strong enhancer in the U3 portion of the proviral long terminal repeat (LTR). The LTRs of a second class of avian retroviruses, the endogenous viruses (ev) lack detectable enhancer activity. By creating ev-RSV hybrid LTRs, we previously demonstrated that, despite the lack of independent enhancer activity in the ev U3 region, ev LTRs contain sequences that are able to functionally replace essential enhancer domains from the RSV enhancer. A hypothesis proposed to explain these data was that ev LTRs contain a partial enhancer that includes sequences necessary but not sufficient for enhancer activity and that these sequences were complemented by RSV enhancer domains present in the original hybrid constructs to generate a functional enhancer. Studies described in this report were designed to define sequences from both the ev and RSV LTRs required to generate this composite enhancer. This was approached by generating additional ev-RSV hybrid LTRs that exchanged defined regions between ev and RSV and by directly testing the requirement for specific motifs by site-directed mutagenesis. Results obtained demonstrate that ev enhancer sequences are present in the same relative location as upstream enhancer sequences from RSV, with which they share limited sequence similarity. In addition, a 67-bp region from the internal portion of the RSV LTR that is required to complement ev enhancer sequences was identified. Finally, data showing that CArG motifs are essential for high-level activity, a finding that has not been previously demonstrated for retroviral LTRs, are presented.

Isolation of the CCAAT transcription factor subunit EFIA cDNA and a potentially functional EFIA processed pseudogene from Bos taurus: insights into the evolution of the EFIA/dbpB/YB-1 gene family

The genomic copy multiplicity of the CCAAT transcription complex component enhancer factor I subunit A (EFIA) has been examined. When a mammalian genomic Southern blot was hybridized to a rat EFIA cDNA, a complex pattern consisting of numerous related sequences was found in all the species examined, with Bos taurus being the least complex. An EFIA#1 cDNA from Bos taurus was isolated from a primary lung endothelial cell cDNA library by screening with the 1489-bp rat EFIA cDNA. The deduced bovine EFIA#1 amino acid (aa) sequence is 98% identical to rat EFIA and 100% identical to human EFIA/DbpB/YB-1 family member DNA-binding protein B (DbpB). In addition, a processed EFIA pseudogene from Bos taurus, designated bovine psi EFIA#1, was obtained from a genomic library by screening with a rat EFIA cDNA probe. The bovine psi EFIA#1 gene has an ORF which, if expressed, would encode a 140-aa sequence, with aa 31-140 having 84% identity to bovine EFIA#1. The genomic cloning data indicate that processed pseudogenes are partially responsible for the complexity of the EFIA genomic Southern blots. The phenomenon of 'repeat induced point mutation' (ripping) at bovine psi EFIA#1 gene CpG dinucleotides occurs at a 6.5-fold higher frequency than expected from random mutagenesis. Therefore, ripping is likely to be the mechanism by which the bovine EFIA#1 pseudogene's ectopic recombination potential was inactivated.

CArG, CCAAT, and CCAAT-like protein binding sites in avian retrovirus long terminal repeat enhancers

A strong enhancer element is located within the long terminal repeats (LTRs) of exogenous, oncogenic avian retroviruses, such as Rous sarcoma virus (RSV) and the avian leukosis viruses. The LTRs of a second class of avian retroviruses, the endogenous viruses (evs), lack detectable enhancer function, a property that correlates with major sequence differences between the LTRs of these two virus groups. Despite this lack of independent enhancer activity, we previously identified sequences in ev LTRs that were able to functionally replace essential enhancer domains from the RSV enhancer with which they share limited sequence similarity. To identify candidate enhancer domains in ev LTRs that are functionally equivalent to those in RSV LTRs, we analyzed and compared ev and RSV LTR-specific DNA-protein interactions. Using this approach, we identified two candidate enhancer domains and one deficiency in ev LTRs. One of the proposed ev enhancer domains was identified as a CArG box, a motif also found upstream of several muscle-specific genes, and as the core sequence of the c-fos serum response element. The RSV LTR contains two CArG motifs, one at a previously identified site and one identified in this report at the same relative location as the ev CArG motif. A second factor binding site that interacts with a heat-stable protein was also identified in ev LTRs and, contrary to previous suggestions, appears to be different from previously described exogenous virus enhancer binding proteins. Finally, a deficiency in factor binding was found within the one inverted CCAAT box in ev LTRs, affirming the importance of sequences that flank CCAAT motifs in factor binding and providing a candidate defect in the ev enhancer.

Transcription factor binding and spacing constraints in the human beta-actin proximal promoter

The human beta-actin promoter, including its 5' flanking region and 5' untranslated region, is ubiquitously active in mammalian cells in culture. In this report we investigated the transcriptional activity of, and the protein-DNA interactions that occur within, the proximal region of the human beta-actin promoter. Efficient beta-actin promoter activity in transfected human HeLa cells requires only 114bp of 5' flanking sequences. Two of the cis-actin regulatory elements within this region of the beta-actin promoter, the CCAAT box and proximal CCArGG box, are specific in vitro binding sites for the transcription factors, nuclear factor Y (NF-Y) and serum response factor (p67SRF), respectively. These two elements are required together to stimulate in vivo transcription from the homologous as well as a heterologous promoter. Finally, a particular spatial alignment between the CCAAT box and proximal CCArGG box is required for trans-activation in vivo. The above provides strong evidence for a functional interaction between NF-Y and p67SRF when bound to their respective binding sites in the beta-actin promoter.

Mapping the transcriptional transactivation function of simian virus 40 large T antigen

T antigen is able to transactivate gene expression from the simian virus 40 (SV40) late promoter and from several other viral and cellular promoters. Neither the mechanisms of transactivation by T antigen nor the regions of T antigen required for this activity have been determined. To address the latter point, we have measured the ability of a set of SV40 large T antigen mutants to stimulate gene expression in CV-1 monkey kidney cells from the SV40 late promoter and Rous sarcoma virus (RSV) long terminal repeat (LTR) promoter. Transactivation, although reduced, was retained by an N-terminal 138-amino-acid fragment of T antigen. Mutants with alterations at various locations within the N-terminal 85 amino acids transactivated the RSV LTR promoter less well than did wild-type T antigen. Most of these were also partially defective in their ability to transactivate the SV40 late promoter. Two mutants with lesions in the DNA-binding domain that were unable to bind to SV40 DNA were completely defective for transactivation of both promoter, while a third mutant with a lesion in the DNA-binding domain which retained origin-binding activity transactivated both promoters as well as did wild-type T antigen. Only a low level of transactivation was seen with mutant T antigens which had lesions in or near the zinc finger region (amino acids 300 to 350). Mutations which caused defects in ATPase activity, host range/helper function, binding to p53, binding to the retinoblastoma susceptibility protein, or nuclear localization had little or no effect on transactivation. These results suggest that N-terminal portion of T antigen possesses an activation activity. The data are consistent with the idea that the overall conformation of T antigen is important for transactivation and that mutations in other regions that reduce or eliminate transactivation do so by altering the conformation or orientation of the N-terminal region so that its ability to interact with various targets is diminished or abolished.

Activation of an endogenous retrovirus enhancer by insertion into a heterologous context

An enhancer element is located in the U3 portion of exogenous avian retrovirus long terminal repeats (LTRs). A similar element has not been detected in the LTRs of ev-1 and ev-2, two avian endogenous viruses (evs) that normally are not expressed in vivo. Experiments were initiated to determine whether minor nucleotide differences in the U3 region of a previously untested ev that is ubiquitously expressed in vivo (ev-3) might confer enhancer function on the LTR of this provirus. This question was addressed by inserting U3 regions from ev-3 and from ev-1 and/or ev-2 both upstream of the herpesvirus thymidine kinase gene promoter and in place of the major enhancer domains of the Rous sarcoma virus LTR and determining their relative effects on transcription. U3 regions from all evs tested were unable to enhance transcription from the thymidine kinase gene promoter, indicating that nucleotide differences in the ev U3 regions do not affect their relative enhancer function and therefore are unlikely to play a role in their differential expression in vivo. Unexpectedly, however, all ev U3 regions were able to augment transcription in an orientation-independent manner in the ev-Rous sarcoma virus hybrid LTRs. Further experiments conducted to determine why this enhancer activity is not detectable in intact ev LTRs demonstrated that it was not due to removal of repressor sequences in the ev fragments used that might normally be present in intact ev LTRs. The lack of detectable enhancer activity in intact ev LTRs also was not explained by a defect in ev promoters that makes them unresponsive to enhancers in cis. These experiments therefore identify sequences that, although unable to function detectably as enhancers in their natural context, can function efficiently in a heterologous context. Data are discussed in terms of the modularity of enhancer elements and possible interactions between enhancers and promoter-specific sequences.