Protein-nucleotide contacts in the immunoglobulin heavy-chain promoter region

A steroidogenic factor-1-binding site and cyclic adenosine 3',5'-monophosphate response element-like elements are required for the activity of the rat aromatase promoter in rat Leydig tumor cell lines

Although transcription initiation within CYP19 (cytochrome P450 aromatase) occurs immediately 5' to the initiator methionine (proximal promoter) in two rat Leydig tumor cell lines (R2C and H540) that express high aromatase activity and in rat ovary, the patterns of aromatase expression in the two cell types are distinctive. To define mechanisms controlling different patterns of expression of the rat aromatase proximal promoter, we performed transient transfection and gel mobility shift assays. Transfection experiments using different sized promoter fragments fused to a reporter gene were used to identify regions that are functionally important for transcriptional regulation in steroidogenic cell lines [R2C, H540, and Y1 (mouse adrenocortical cells that express low aromatase activity)]. These experiments indicate that the cAMP response element (CRE) at -231 and the steroidogenic factor-1 (SF1) motif are both required for expression of the reporter gene in each steroidogenic cell line and that the CRE at -169 is similarly required in R2C cells. Gel mobility shift assays confirm binding of nuclear proteins from the steroidogenic cell lines to the SF1 motif and to CRE (-231). Leydig tumor cells also contain nuclear proteins that bind to the CRE (-169), but nuclear extracts from R2C cells produce a uniquely shifted band compared with H540 cells. These results suggest that differences in proteins that bind to distinct elements within the rat aromatase promoter may be responsible for different patterns and levels of aromatase expression in these steroidogenic cell lines.

Regulatory Elements in the Promoter of a Murine TCRD V Gene Segment

TCRD V segments rearrange in an ordered fashion during human and murine thymic development. Recombination requires the accessibility of substrate gene segments, and transcriptional enhancers and promoters have been shown to regulate the accessible chromatin configuration. We therefore investigated the regulation of TCRD V rearrangements by characterizing the promoter of the first TCRD V segment to be rearranged, DV101S1, under the influence of its own enhancer. Sequences required for full promoter activity were identified by transient transfections of normal and mutated promoters into a human γδ lymphoma, and necessary elements fall between −86 and +66 nt, relative to the major transcription start site. They include a cAMP responsive element (CRE) at −62, an Ets site at −39, a TATA box at −26, the major transcriptional start site sequence (−8 to −5 and −2 to +11), and a downstream sequence (+12 to +33). Gel shift analyses and in vitro DNase I footprinting showed that nuclear proteins bind to the functionally relevant CRE, Ets, +1 to +10 sequence, and the +17 to +21 sequence. Nuclear proteins also bind to an E box at −52, and GATA-3 binds to a GATA motif at −5, as shown by Ab ablation-supershift experiments, but mutations that abrogated protein binding to these sites failed to affect DV101S1 promoter activity. We conclude that not all protein-binding sites within the DV101S1 minimal promoter are important for enhancer driven TCRD gene transcription. Further, the possibility remains that the GATA and E box sites function in enhancer independent DV101S1 germline transcription.

Interaction of the nuclear matrix-associated region (MAR)-binding proteins, SATB1 and CDP/Cux, with a MAR element (L2a) in an upstream regulatory region of the mouse CD8a gene

Matrix-associated regions (MARs), AT-rich DNA segments that have an affinity for the nuclear matrix, have been shown to play a role in transcriptional regulation of eukaryotic genes. The present study demonstrates that a DNA element, called L2a, which has been implicated in the transcriptional regulation of the mouse CD8a gene encoding an important T cell coreceptor, is a MAR. Moreover, the identities of two nuclear proteins, L2a-P1 and L2a-P2, previously shown to bind to the L2a element, have been determined. The L2a-P1 protein found to be present in all CD8-positive T cell lines tested is SATB1, a known MAR-binding protein. The widely expressed L2a-P2 protein is CDP/Cux, a MAR-binding protein that has been associated with repression of gene transcription. Interaction of both proteins with the L2a element was studied using the missing nucleoside approach, DNase I footprinting, and electrophoretic mobility shift assays with wild type and mutant L2a elements. The data suggest that CDP/Cux bound to the L2a element is displaced by binding of SATB1 and the accompanying conformational change in the DNA lying between the primary binding sites of SATB1 and CDP/Cux. We suggest that displacement of CDP/Cux by SATB1 favors transcription of the CD8a gene, possibly by enhancing or altering its association with the nuclear matrix.

Purification and characterization of a rat liver protein that recognizes CCAAT-homologous sequences of the metallothionein promoter and trans-activates this promoter

C'BP-1, a protein that binds to the MRE-c' region (-135 to -110) of the mouse metallothionein-I (MT-I) gene in metal-independent manner, was purified from rat liver nuclear extract by ion exchange and affinity chromatography. Analysis by SDS-PAGE, UV cross-linking, and glycerol gradient sedimentation, taken together, showed that C'BP-1 is a dimer of the 34-kDa polypeptides. Affinity-purified C'BP-1 could significantly stimulate transcription from mouse MT-I gene promoter. DNase I footprinting with the purified protein identified two binding sites for C'BP-1 located at positions -135 to -100 and -210 to -175 with respect to the start site of MT-I gene transcription. Both C'BP-1 binding sequences were found to contain imperfect dyad of the CCAAT homology. C'BP-1 was shown to make critical contacts with the CCAAT homology by methylation interference analysis and competition electrophoretic mobility shift assay with mutants harboring alterations in the CCAAT homology. An antibody that specifically recognizes C/EBP delta partially supershifted C'BP-1/MRE-c' complex, suggesting that C'BP-1 is identical to C/EBP delta or is closely related to C/EBP delta.

Xenobiotic responsive element-mediated transcriptional activation in the UDP-glucuronosyltransferase family 1 gene complex

We have isolated genomic DNA clones containing rat UDP-glucuronosyltransferase family 1 (UGT1) sequences and have shown drug-responsive and tissue-specific alternative expression of multiple first exons (Emi, Y., Ikushiro, S., and Iyanagi, T. (1995) J. Biochem. (Tokyo) 117, 392-399). The UGT1 locus encodes at least nine UGT1 isoforms. UGT1A1 is a major 3-methylcholanthrene (MC)-inducible form in rat liver. In this report, we have identified a cis-acting element necessary for transcriptional activation of UGT1A1 in hepatocytes. A promoter region was fused to a chloramphenicol acetyltransferase gene, and the resultant construct was transiently transfected into hepatocytes. A DNA fragment carrying 1,100 nucleotides derived from the 5'-flanking region of the UGT1A1 gene was enough for MC induction. Unidirectional deletion of this region revealed that there existed one xenobiotic responsive element (XRE), TGCGTG, between -134 and -129. When a single base substitution was introduced into the XRE, MC-induced expression of the UGT1A1 gene was completely abolished. In addition, an XRE-deleted construct failed to respond to MC. Gel mobility shift assays showed MC-inducible binding of the nuclear aromatic hydrocarbon receptor-ligand complex to this motif. Gel shift-coupled DNase I protection analyses revealed that the GCGTG-core sequence was a target site of the liganded aromatic hydrocarbon receptor. These results suggest that the XRE participates in induction of the rat UGT1A1 gene by MC.

NusG alters rho-dependent termination of transcription in vitro independent of kinetic coupling

To complement the recent discovery that rho-dependent termination in E. coli requires nusG protein in vivo, we have tested the effect of purified nusG protein on rho-dependent termination in vitro. With the well-characterized trp t' terminator of E. coli, and no other proteins than E. coli RNA polymerase and rho factor, nusG causes a proximal shift in the terminated RNA endpoints, compared to the endpoints generated by rho alone. The presence of nusG also enhances rho-mediated termination on partially defective mutant trp t' templates. We rule out explanations such as a change in the kinetic coupling between rho and RNA polymerase or a nusG-mediated increase in the affinity of rho for RNA. We also detect no difference in the helicase rate of rho in the presence of nusG. Even assays with completely stalled and isolated ternary complexes indicate that rho is able to effect the release of RNA with the assistance of nusG at points preceding the most proximal release sites observed in the absence of nusG. Our observations support a model in which nusG acts as a component of the transcription complex, possibly interacting with both rho and RNA polymerase as it governs accessibility to the nascent transcript.

A single transcription factor binds to two divergent sequence elements with a common function in cardiac myosin light chain-2 promoter

The cardiac myosin light chain-2 (MLC-2) gene promoter contains several positive and negative cis-acting sequences that are involved in the regulation of its expression. We describe here the properties of two activator sequences, elements A and P, and their DNA-binding factors (ABFs). Element A (CCAAAAGTGG), located at -61, has homology with the evolutionarily conserved sequence CC(A/T)6GG, present in the genes of many contractile proteins. Element P (TAACCTTGAAAGC), located 114 bp upstream of element A, is conserved in both chicken and rat cardiac MLC-2 gene promoters. Deletion mutagenesis demonstrated that these two elements are involved in the positive regulation of MLC-2 gene transcription. At least two sequence-specific element A-binding proteins, ABF-1 and ABF-2, were identified by gel shift analysis of the fractionated cardiac nuclear proteins. ABF-1 binds to element A with strict dependence on the internal element A sequence AAAAGT. In contrast, ABF-2 exhibits a relaxed sequence requirement, as it recognizes the consensus CArG and CCAAT box sequences as well. ABF-2 also recognizes the distal element P despite the fact that the sequences of elements A and P are divergent. DNase I footprinting, methylation interference, and gel shift analyses demonstrated unequivocally that the element A-DNA affinity-purified protein ABF-2 binds to element P with sequence specificity. Since both elements A and P play a positive regulatory role in MLC-2 gene transcription and bind to a single protein (ABF-2), it would appear that ABF-2 is a key transcription factor with the ability to recognize divergent sequence elements involved in a common regulatory pathway during myogenesis.

A single transcription factor binds to two divergent sequence elements with a common function in cardiac myosin light chain-2 promoter

The cardiac myosin light chain-2 (MLC-2) gene promoter contains several positive and negative cis-acting sequences that are involved in the regulation of its expression. We describe here the properties of two activator sequences, elements A and P, and their DNA-binding factors (ABFs). Element A (CCAAAAGTGG), located at -61, has homology with the evolutionarily conserved sequence CC(A/T)6GG, present in the genes of many contractile proteins. Element P (TAACCTTGAAAGC), located 114 bp upstream of element A, is conserved in both chicken and rat cardiac MLC-2 gene promoters. Deletion mutagenesis demonstrated that these two elements are involved in the positive regulation of MLC-2 gene transcription. At least two sequence-specific element A-binding proteins, ABF-1 and ABF-2, were identified by gel shift analysis of the fractionated cardiac nuclear proteins. ABF-1 binds to element A with strict dependence on the internal element A sequence AAAAGT. In contrast, ABF-2 exhibits a relaxed sequence requirement, as it recognizes the consensus CArG and CCAAT box sequences as well. ABF-2 also recognizes the distal element P despite the fact that the sequences of elements A and P are divergent. DNase I footprinting, methylation interference, and gel shift analyses demonstrated unequivocally that the element A-DNA affinity-purified protein ABF-2 binds to element P with sequence specificity. Since both elements A and P play a positive regulatory role in MLC-2 gene transcription and bind to a single protein (ABF-2), it would appear that ABF-2 is a key transcription factor with the ability to recognize divergent sequence elements involved in a common regulatory pathway during myogenesis.

The plasmacytoma J558L lacks constitutively active NF-kappa B and is deficient in early response gene activation

In mature B cells the nuclear factor NF-kappa B which binds within the kappa enhancer is constitutively present in the nucleus. However, the lambda light chain producing myeloma J558L has been found to lack constitutively functional NF-kappa B. Deoxycholate released functional NF-kappa B from cytoplasmic extracts and functional NF-kappa B was present in J558L following cycloheximide but not phorbol ester treatment. J558L was also unable to respond to phorbol ester stimulation with synthesis of mRNA from the early response gene TIS11. J558L differs from S107, another myeloma which was found to be deficient in the synthesis of NF-kappa B but not in the activation of TIS11. Somatic cell hybrids were used to further define the defect in J558L; hybrids were made with the myelomas S107 and S194 and the pre-B cell line 70Z/3. In general, complementation of the defect in J558L was observed; however there was not a direct correlation between the levels of TIS11 mRNA and NF-kappa B expression in the somatic cell hybrids, suggesting that the pathways of activation of these genes, while possibly sharing common elements, are not identical. The defect in J558L was surprising given that it has frequently been used for the expression of transfected light chain genes.

Sgs-3 chromatin structure and trans-activators: developmental and ecdysone induction of a glue enhancer-binding factor, GEBF-I, in Drosophila larvae

The transcription of the Drosophila melanogaster 68C salivary gland glue gene Sgs-3 involves the interaction of a distal and a proximal regulatory region. These are marked in vivo by a specific chromatin structure which is established sequentially during development, starting early in embryogenesis. The distal region is characterized by a stage- and tissue-specific DNase I hypersensitive site. A stage- and tissue-specific factor, GEBF-I, binds in this region and is missing in 2B5 mutant larvae which lack Sgs-3 transcripts. This binding involves the simultaneous interaction with two distinct DNA sequences which induces conformational changes in the protein. Salivary glands acquire competence to respond to ecdysone in the mid-third larval instar, whereafter the hormone rapidly induces both the GEBF-I protein and Sgs-3 transcription.

Sgs-3 chromatin structure and trans-activators: developmental and ecdysone induction of a glue enhancer-binding factor, GEBF-I, in Drosophila larvae

The transcription of the Drosophila melanogaster 68C salivary gland glue gene Sgs-3 involves the interaction of a distal and a proximal regulatory region. These are marked in vivo by a specific chromatin structure which is established sequentially during development, starting early in embryogenesis. The distal region is characterized by a stage- and tissue-specific DNase I hypersensitive site. A stage- and tissue-specific factor, GEBF-I, binds in this region and is missing in 2B5 mutant larvae which lack Sgs-3 transcripts. This binding involves the simultaneous interaction with two distinct DNA sequences which induces conformational changes in the protein. Salivary glands acquire competence to respond to ecdysone in the mid-third larval instar, whereafter the hormone rapidly induces both the GEBF-I protein and Sgs-3 transcription.

Interaction of a nuclear protein with a palindromic sequence of the mouse immunoglobulin lambda 2-chain gene promoter is important for its transcription

By using a gel mobility retardation assay, we detected the formation of three major complexes from the binding of nuclear proteins to the promoter of the immunoglobulin lambda 2-chain gene. Two of the complexes were generated by the presence of an unidentified nuclear factor(s) called herein NF-lambda 2. Although the sequences between lambda 2- and lambda 1-chain gene promoters are very similar, the lambda 1-chain promoter did not compete for the binding of NF-lambda 2 efficiently. The binding site of NF-lambda 2 was localized by DNase I footprinting to a 14-bp region which is about 30 bp upstream of the immunoglobulin octamer motif. This region, referred to as the NF-lambda 2 motif, is within an 18-bp region of twofold rotational symmetry. Experiments with oligomers containing either the NF-lambda 2 or the octamer motifs as competitors for binding and DNase I footprinting, showed that the third complex is the product of the simultaneous binding of an octamer-binding protein and NF-lambda 2. Changing the sequence of the NF-lambda 2 motif to that of the lambda 1-chain counterpart abolished the binding ability of NF-lambda 2. Concomitantly, the level of chloramphenicol acetyltransferase expression driven by the mutated lambda 2 promoter decreased by two- to fivefold when compared with that of the wild-type promoter. It is therefore concluded that the interaction of NF-lambda 2 with the NF-lambda 2 motif stimulates transcription of the lambda 2-chain gene.

Interaction of a nuclear protein with a palindromic sequence of the mouse immunoglobulin lambda 2-chain gene promoter is important for its transcription

By using a gel mobility retardation assay, we detected the formation of three major complexes from the binding of nuclear proteins to the promoter of the immunoglobulin lambda 2-chain gene. Two of the complexes were generated by the presence of an unidentified nuclear factor(s) called herein NF-lambda 2. Although the sequences between lambda 2- and lambda 1-chain gene promoters are very similar, the lambda 1-chain promoter did not compete for the binding of NF-lambda 2 efficiently. The binding site of NF-lambda 2 was localized by DNase I footprinting to a 14-bp region which is about 30 bp upstream of the immunoglobulin octamer motif. This region, referred to as the NF-lambda 2 motif, is within an 18-bp region of twofold rotational symmetry. Experiments with oligomers containing either the NF-lambda 2 or the octamer motifs as competitors for binding and DNase I footprinting, showed that the third complex is the product of the simultaneous binding of an octamer-binding protein and NF-lambda 2. Changing the sequence of the NF-lambda 2 motif to that of the lambda 1-chain counterpart abolished the binding ability of NF-lambda 2. Concomitantly, the level of chloramphenicol acetyltransferase expression driven by the mutated lambda 2 promoter decreased by two- to fivefold when compared with that of the wild-type promoter. It is therefore concluded that the interaction of NF-lambda 2 with the NF-lambda 2 motif stimulates transcription of the lambda 2-chain gene.

Purification and characterization of a novel factor which stimulates rat ribosomal gene transcription in vitro by interacting with enhancer and core promoter elements

Previous studies in our laboratory have characterized a 174-base-pair (bp) enhancer sequence in the rat ribosomal DNA spacer region that exhibits all of the characteristics of a polymerase (Pol) II enhancer. Further studies showed that at least half of the enhancer activity resides in a 37-bp motif (E1) within the 174-bp spacer sequence that is located between positions -2.183 and -2.219 kilobase pairs upstream of the initiation site. To identify the factor(s) that binds specifically to the 37-bp enhancer domain, we fractionated whole-cell extract from rat adenocarcinoma ascites cells by chromatography on a series of columns, including an oligodeoxynucleotide affinity column. The final preparation contained two polypeptides of molecular weights 79,400 and 89,100 and was completely devoid of RNA Pol I activity. Electrophoretic mobility shift analysis showed that the polypeptides in the purified preparation (designated E1BF) interacted with both the enhancer element and the core promoter. To determine whether each polypeptide can separately bind to the core promoter and the enhancer, the individual components were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, renatured, and subjected to gel retardation analysis. This experiment demonstrated that both polypeptides interacted with the two cis-acting sequences. The specificity of the binding was demonstrated by competition with unlabeled 37-bp and core promoter fragments and lack of competition with nonspecific DNAs in the mobility shift assay. The 37-bp enhancer as well as the downstream sequence of the core promoter were protected by E1BF in the DNase I footprinting assay. Addition of E1BF to limiting amounts of fraction DE-B, which contains all factors essential for Pol I-directed transcription, resulted in three- to fourfold stimulation of ribosomal DNA transcription. Comparison of molecular weights and footprinting profiles did not reveal any relationship between E1BF and other Pol I trans-acting factors.

Purification and characterization of a novel factor which stimulates rat ribosomal gene transcription in vitro by interacting with enhancer and core promoter elements

Previous studies in our laboratory have characterized a 174-base-pair (bp) enhancer sequence in the rat ribosomal DNA spacer region that exhibits all of the characteristics of a polymerase (Pol) II enhancer. Further studies showed that at least half of the enhancer activity resides in a 37-bp motif (E1) within the 174-bp spacer sequence that is located between positions -2.183 and -2.219 kilobase pairs upstream of the initiation site. To identify the factor(s) that binds specifically to the 37-bp enhancer domain, we fractionated whole-cell extract from rat adenocarcinoma ascites cells by chromatography on a series of columns, including an oligodeoxynucleotide affinity column. The final preparation contained two polypeptides of molecular weights 79,400 and 89,100 and was completely devoid of RNA Pol I activity. Electrophoretic mobility shift analysis showed that the polypeptides in the purified preparation (designated E1BF) interacted with both the enhancer element and the core promoter. To determine whether each polypeptide can separately bind to the core promoter and the enhancer, the individual components were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, renatured, and subjected to gel retardation analysis. This experiment demonstrated that both polypeptides interacted with the two cis-acting sequences. The specificity of the binding was demonstrated by competition with unlabeled 37-bp and core promoter fragments and lack of competition with nonspecific DNAs in the mobility shift assay. The 37-bp enhancer as well as the downstream sequence of the core promoter were protected by E1BF in the DNase I footprinting assay. Addition of E1BF to limiting amounts of fraction DE-B, which contains all factors essential for Pol I-directed transcription, resulted in three- to fourfold stimulation of ribosomal DNA transcription. Comparison of molecular weights and footprinting profiles did not reveal any relationship between E1BF and other Pol I trans-acting factors.

Involvement of a second lymphoid-specific enhancer element in the regulation of immunoglobulin heavy-chain gene expression

To determine whether enhancer elements in addition to the highly conserved octamer (OCTA)-nucleotide motif are important for lymphoid-specific expression of the immunoglobulin heavy-chain (IgH) gene, we have investigated the effect of mutating the binding site for a putative additional lymphoid-specific transcription factor, designated NF-microB, in the murine IgH enhancer. We demonstrate that the NF-microB-binding site plays a critical role in the IgH enhancer, because mutation of the microB DNA motif decreased transcriptional activity of the IgH enhancer in cells of the B-cell lineage but not in nonlymphoid cells. This effect was comparable to or even stronger than the effect of a mutation in the OCTA site. Moreover, combined mutation of both microB and OCTA sites further reduced enhancer activity in lymphoid cells. Interestingly, alteration of either the microB or E3 site in a 70-base-pair fragment of the IgH enhancer that lacks the binding site for OCTA abolished enhancer activity in lymphoid cells completely. Nevertheless, a multimer of the microB motif alone showed no enhancer activity. DNase footprinting analysis corroborated the functional data showing that a lymphoid-specific protein binds to the microB DNA motif. Our results suggest that the microB element is a new crucial element important for lymphoid-specific expression of the IgH gene but that interaction with another enhancer element is essential for its activity.

Involvement of a second lymphoid-specific enhancer element in the regulation of immunoglobulin heavy-chain gene expression

To determine whether enhancer elements in addition to the highly conserved octamer (OCTA)-nucleotide motif are important for lymphoid-specific expression of the immunoglobulin heavy-chain (IgH) gene, we have investigated the effect of mutating the binding site for a putative additional lymphoid-specific transcription factor, designated NF-microB, in the murine IgH enhancer. We demonstrate that the NF-microB-binding site plays a critical role in the IgH enhancer, because mutation of the microB DNA motif decreased transcriptional activity of the IgH enhancer in cells of the B-cell lineage but not in nonlymphoid cells. This effect was comparable to or even stronger than the effect of a mutation in the OCTA site. Moreover, combined mutation of both microB and OCTA sites further reduced enhancer activity in lymphoid cells. Interestingly, alteration of either the microB or E3 site in a 70-base-pair fragment of the IgH enhancer that lacks the binding site for OCTA abolished enhancer activity in lymphoid cells completely. Nevertheless, a multimer of the microB motif alone showed no enhancer activity. DNase footprinting analysis corroborated the functional data showing that a lymphoid-specific protein binds to the microB DNA motif. Our results suggest that the microB element is a new crucial element important for lymphoid-specific expression of the IgH gene but that interaction with another enhancer element is essential for its activity.

Initiation and processing of two kappa immunoglobulin germ line transcripts in mouse B cells

The splicing patterns and sequences of two processed kappa immunoglobulin germ line mRNAs are presented. A 1.1-kilobase (kb) mRNA appeared to be derived from splicing of the previously characterized 8.4-kb germ line transcript, while a 0.8-kb mRNA was the splice product of a second 4.7-kb germ line transcript that initiated 50 base pairs upstream of J kappa 1. The interaction of the two kappa germ line promoters with nuclear binding factors is also examined. The potential role of these germ line transcripts in establishing the rearrangement potential of the locus is discussed.

Initiation and processing of two kappa immunoglobulin germ line transcripts in mouse B cells

The splicing patterns and sequences of two processed kappa immunoglobulin germ line mRNAs are presented. A 1.1-kilobase (kb) mRNA appeared to be derived from splicing of the previously characterized 8.4-kb germ line transcript, while a 0.8-kb mRNA was the splice product of a second 4.7-kb germ line transcript that initiated 50 base pairs upstream of J kappa 1. The interaction of the two kappa germ line promoters with nuclear binding factors is also examined. The potential role of these germ line transcripts in establishing the rearrangement potential of the locus is discussed.

The regulatory VirG protein specifically binds to a cis-acting regulatory sequence involved in transcriptional activation of Agrobacterium tumefaciens virulence genes

Virulence genes of Agrobacterium tumefaciens are induced in parallel in the presence of plant phenolic compounds such as acetosyringone and the two regulatory vir genes virA and virG. In this study we identified a cis-acting regulatory sequence in the 5'-noncoding region of the virE operon that is essential for this activation. To do this, we constructed a series of deletion mutants by using exonuclease Bal 31. Western blot (immunoblot) analysis showed that the 70 base pairs upstream of the transcriptional start site were sufficient for full virE gene induction. A conserved dodecadeoxynucleotide sequence (vir box), which was previously identified in the nontranscribed sequences of all vir genes, was located at 5' end of the minimum required promoter sequence. Deletion of this vir box only completely abolished induction of the virE gene. This demonstrates that the vir box functions as an upstream regulatory sequence. To study the role of the VirG protein in the activation process, we overproduced the native-sized VirG protein in Escherichia coli by fusing the lacZ' start codon ATG with the second virG codon AAA using site-directed mutagenesis. The VirG protein was purified and renatured from E. coli and was shown to bind to a specific sequence in two vir gene promoters. Footprinting analysis of the virE and virB promoters identified the 12-base-pair vir box as the VirG-binding core sequence.

A two-base change in a POU factor-binding site switches pituitary-specific to lymphoid-specific gene expression

The structurally related POU homeo domain proteins Pit-1 and Oct-2 activate pituitary- and lymphoid-specific transcription, respectively, by binding to similar AT-rich motifs in their target genes. In this study we identify bases critical for recognition and activation by Pit-1 and examine how small differences in Pit-1 and Oct-2-binding sites can impart differential transcriptional responses in pituitary and B-lymphoid cells. Scanning mutagenesis of Pit-1 response elements in both the rat prolactin and growth hormone genes reveals a critical binding motif recognized in an identical manner by the native Pit-1 protein and cloned Pit-1 gene product. This motif, ATTATTCCAT, differs by only two bases from the octamer element, ATTTGCAT, required for Oct-2-dependent activation of immunoglobulin genes. Cross recognition of Pit-1 and Oct-2 sites by both factors can be demonstrated in competitive binding assays, in which an oligometric Pit-1 site from the prolactin gene is converted to an Oct-2 site by a double point mutation. In contrast to the binding data, no cross activation of transcription is detectable in cultured cell lines. When inserted immediately 5' to a prolactin TATA box, the wild-type prolactin element enhances transcription strongly in pituitary cells but is inactive in B cells, whereas the octamer variant of the prolactin site activates expression in B cells but is silent in pituitary lines. Both elements are nonfunctional in heterologous cell lines that lack Pit-1 and Oct-2.(ABSTRACT TRUNCATED AT 250 WORDS)

Effects of anti-IgM suppression on polyclonally activated murine B cells: analysis of immunoglobulin mRNA, gene specific nuclear factors and cell cycle distribution

Polyclonal activation of murine B cells with bacterial lipopolysaccharide (LPS) and dextran sulfate (DxS) results in cell proliferation as well as increased immunoglobulin gene transcription and antibody secretion. When added to B cell cultures during mitogen activation, anti-mu antibody suppresses the rate of proliferation and immunoglobulin gene expression. Using this model system we show that co-cultures of B cells with LPS/DxS and anti-mu resulted in a decrease of both mu and kappa chain mRNA. Suppression did not prevent B cell entry into cycle nor a significant alteration in the distribution of cells in phases of cell cycle, although it did prolong the cycle transit time in a dose dependent fashion as determined by bromodeoxyuridine pulse labelling. Analysis of B cell specific nuclear binding factors, which previously have been shown to be important in regulating immunoglobulin gene transcription were examined. Results show that the kappa-specific enhancer binding activity of NF-kappa B was induced in activated as well as suppressed cultures. The lymphoid specific factor NF-A2, which recognizes the octamer sequence motif in the promoters of immunoglobulin genes, was induced by the polyclonal activation but was selectively lost in extracts from suppressed cells. Thus, specific regulation of the nuclear factor which plays a critical role in both heavy and light chain immunoglobulin gene expression may contribute to the transcriptional suppression observed in anti-mu treated B cells.

Overlapping octamer and TAATGARAT motifs in the VF65-response elements in herpes simplex virus immediate-early promoters represent independent binding sites for cellular nuclear factor III

Expression of the immediate-early (IE) genes of herpes simplex virus (HSV) is specifically stimulated by a 65-kilodalton virion transcription factor (VF65 or VP16) that is introduced as a component of infecting virions. In both the IE175(ICP4) and IE110(ICP0) promoters, this activation requires an upstream cis-acting target response element that contains a single TAATGARAT consensus element. Furthermore, many HSV IE TAATGARAT elements overlap with ATGCTAAT octamer motifs that are similar to the OTF-1-binding sites found in both immunoglobulin and histone H2b genes and to the nuclear factor III (NFIII)-binding site within the adenovirus type 2 origin of DNA replication. Purified HeLa cell NFIII protein proved to form specific DNA-protein complexes with several upstream regions from both the IE110 and IE175 promoters, and this interaction was subject to efficient competition with an adenovirus type 2 DNA fragment containing an intact NFIII-binding site. Surprisingly, the NFIII protein bound to synthetic oligonucleotides containing only the TAATGARAT consensus elements as well as to those containing the ATGCTAAT octamer sequence, although the former exhibited lower affinity and gave complexes with slightly different electrophoretic mobility. The ATGCTAAT oligonucleotide also competed more efficiently than the TAATGARAT sequence itself for binding to a TAATGARAT probe, indicating that the same protein species binds to both sites. The oligonucleotides also formed novel supershifted complexes with lysed virion proteins, but only in the presence of a crude nuclear extract and not with affinity-purified NFIII alone. We conclude that the cellular NFIII protein can recognize both the ATGCTAAT and TAATGARAT elements independently but that only the interaction with TAATGARAT represents an intermediate step in the transcriptional stimulation of IE genes by the HSV virion factor.

Octamer transcription factors 1 and 2 each bind to two different functional elements in the immunoglobulin heavy-chain promoter

Immunoglobulin heavy-chain genes contain two conserved sequence elements 5' to the site of transcription initiation: the octamer ATGCAAAT and the heptamer CTCATGA. Both of these elements are required for normal cell-specific promoter function. The present study demonstrates that both the ubiquitous and lymphoid-cell-specific octamer transcription factors (OTF-1 and OTF-2, respectively) interact specifically with each of the two conserved sequence elements, forming either homo- or heterodimeric complexes. This was surprising, since the heptamer and octamer sequence motifs bear no obvious similarity to each other. Binding of either factor to the octamer element occurred independently. However, OTF interaction with the heptamer sequence appeared to require the presence of an intact octamer motif and occurred with a spacing of either 2 or 14 base pairs between the two elements, suggesting coordinate binding resulting from protein-protein interactions. The degeneracy in sequences recognized by the OTFs may be important in widening the range over which gene expression can be modulated and in establishing cell type specificity.

Octamer transcription factors 1 and 2 each bind to two different functional elements in the immunoglobulin heavy-chain promoter

Immunoglobulin heavy-chain genes contain two conserved sequence elements 5' to the site of transcription initiation: the octamer ATGCAAAT and the heptamer CTCATGA. Both of these elements are required for normal cell-specific promoter function. The present study demonstrates that both the ubiquitous and lymphoid-cell-specific octamer transcription factors (OTF-1 and OTF-2, respectively) interact specifically with each of the two conserved sequence elements, forming either homo- or heterodimeric complexes. This was surprising, since the heptamer and octamer sequence motifs bear no obvious similarity to each other. Binding of either factor to the octamer element occurred independently. However, OTF interaction with the heptamer sequence appeared to require the presence of an intact octamer motif and occurred with a spacing of either 2 or 14 base pairs between the two elements, suggesting coordinate binding resulting from protein-protein interactions. The degeneracy in sequences recognized by the OTFs may be important in widening the range over which gene expression can be modulated and in establishing cell type specificity.

B-cell control region at the 5' end of a major histocompatibility complex class II gene: sequences and factors

Transcription of major histocompatibility complex class II genes is elaborately regulated. Mouse class II genes are transcribed primarily in B cells, peripheral macrophages and interdigitating cells, and thymic cortical and medullary cells. In this study, we began to identify the DNA sequences and protein factors that control expression of a class II gene in B cells, addressing in particular how closely they resemble those that regulate immunoglobulin gene expression. We describe a region upstream of the E alpha gene that is crucial for its transcription in the B cells of transgenic mice but is less important in cultured B-cell lines. The sequence of this region reveals several familiar motifs, including a second X-Y pair reminiscent of that residing in the promoter-proximal region of all class II genes, a B motif strikingly homologous to that associated with the immunoglobulin kappa gene enhancer, several Ephrussi motifs, and a Pu box-like sequence very similar to that implicated in simian virus 40 and lymphotrophic papovavirus expression in B cells. Careful study of the proteins that bind specifically to these different motifs prompts us to suggest that major histocompatibility complex class II and immunoglobulin genes rely on quite different factors to achieve B-cell-specific expression.

Identification of a novel lymphoid specific octamer binding protein (OTF-2B) by proteolytic clipping bandshift assay (PCBA)

The octamer sequence ATGCAAAT is found in the promoters of immunoglobulin (Ig) heavy and light chain genes and in the heavy chain enhancer and is a major determinant of the cell type specific expression of Ig genes in B cells. An apparent paradox is that the same sequence serves as an upstream promoter or enhancer element in a variety of housekeeping genes such as the histone H2B and U snRNA genes. The differential usage of this regulatory sequence motif is thought to be mediated by different species of octamer binding proteins. One species of 100 kd, designated OTF-1, is present in all cell types and may exert its activating function only when it can interact with additional adjacent transcription factors. The lymphoid cell specific octamer binding protein of 60 kd (OTF-2A) specifically stimulates Ig promoters which consist essentially of a TATA-box and an octamer sequence upstream of it. Here we present evidence for yet another B cell specific octamer binding protein of 75 kd (OTF-2B). From several findings, including the absence of OTF-2B (but not OTF-2A) from a lymphocyte line that cannot respond to the IgH enhancer, we propose a role of the novel octamer factor in the long range activation by the IgH enhancer. We have used the proteolytic clipping bandshift assay (PCBA) technique to distinguish the three different forms found in B cells. This analysis indicates that the 75 kd-species OTF-2B is closely related to the 60 kd species OTF-2A.

B-cell control region at the 5' end of a major histocompatibility complex class II gene: sequences and factors

Transcription of major histocompatibility complex class II genes is elaborately regulated. Mouse class II genes are transcribed primarily in B cells, peripheral macrophages and interdigitating cells, and thymic cortical and medullary cells. In this study, we began to identify the DNA sequences and protein factors that control expression of a class II gene in B cells, addressing in particular how closely they resemble those that regulate immunoglobulin gene expression. We describe a region upstream of the E alpha gene that is crucial for its transcription in the B cells of transgenic mice but is less important in cultured B-cell lines. The sequence of this region reveals several familiar motifs, including a second X-Y pair reminiscent of that residing in the promoter-proximal region of all class II genes, a B motif strikingly homologous to that associated with the immunoglobulin kappa gene enhancer, several Ephrussi motifs, and a Pu box-like sequence very similar to that implicated in simian virus 40 and lymphotrophic papovavirus expression in B cells. Careful study of the proteins that bind specifically to these different motifs prompts us to suggest that major histocompatibility complex class II and immunoglobulin genes rely on quite different factors to achieve B-cell-specific expression.

DNA-binding factors of B lymphoid cells are susceptible to limited proteolytic cleavage during nuclear extract preparation

DNA-binding proteins that interact with the 3' end of the mouse mu immunoglobulin heavy chain gene were identified by the electrophoretic mobility shift assay. Complexes of distinctly different mobilities were formed by extracts prepared from B lymphoid lines representing different stages of maturation. The apparent stage-specific differences are shown to be due to proteolytic events that occurred during extract preparation.

A conserved heptamer upstream of the IgH promoter region octamer can be the site of a coordinate protein-DNA interaction

Immunoglobulin genes contain a conserved eight base sequence element 5' to the site of transcription initiation. This octamer can serve as a site for the binding of nuclear proteins which are presumably involved in the cell type specific expression of this family of genes. In studying the binding of nuclear proteins to this conserved sequence element, we have detected a protein interaction that involves, in addition to the octamer, nucleotides which are immediately upstream. We have characterized this additional contact as a sequence specific interaction with a heptameric sequence element (CTCATGA) that is conserved among Ig heavy chain promoters. Protein binding to the heptamer is unique in that it is dependent upon the proximity and orientation of, as well as protein interaction with, the conserved octamer.

Identification of murine nuclear proteins that bind to the conserved octamer sequence of the immunoglobulin promoter region

Sequence-specific DNA-affinity chromatography was used to purify a nuclear protein from the B-cell leukemia cell line BCL1 that specifically binds to the octamer sequence ATTTGCAT, previously shown to be important in the regulation of immunoglobulin genes. This protein has a molecular mass of approximately 70 kDa and is responsible for the protein-DNA interaction specific to lymphoid cells. Other proteins of molecular mass 80-90 kDa and 50-55 kDa that specifically bind to the octamer sequence were also identified. These results demonstrate that the octamer is recognized by several biochemically distinct nuclear proteins, perhaps to differentially regulate the expression of immunoglobulin genes.

DNA-binding factors of B lymphoid cells are susceptible to limited proteolytic cleavage during nuclear extract preparation

DNA-binding proteins that interact with the 3' end of the mouse mu immunoglobulin heavy chain gene were identified by the electrophoretic mobility shift assay. Complexes of distinctly different mobilities were formed by extracts prepared from B lymphoid lines representing different stages of maturation. The apparent stage-specific differences are shown to be due to proteolytic events that occurred during extract preparation.

Purification of an octamer sequence (ATGCAAAT)-binding protein from human B cells

The highly conserved octamer sequence ATGCAAAT or its inverse complement found in all human and murine immunoglobulin gene promoters has been demonstrated to be necessary in the lymphoid-specific transcription by deletion analysis. Trans-acting factors that interact with the octamer motif are thought to be involved in this tissue-specific expression. Using a gel mobility shift assay, we have identified both lymphoid-specific and ubiquitous nuclear factors that interact with a human gamma 1 heavy chain gene promoter region containing the octamer motif, consistent with the results obtained with murine heavy or light chain promoter regions. We have purified an octamer binding protein from human B cells by sequence-specific DNA affinity chromatography. Renaturation of gel-purified protein allowed the identification of a polypeptide with a molecular weight of 74 kilodaltons (kD) that is capable of recognizing and binding to the octamer motif. This 74 kD protein seems to be also present in T-cells and non-lymphoid cells. The possible function of the factor is discussed.

A mouse renin promoter containing the conserved decanucleotide element binds the same B-cell factors as an authentic immunoglobulin heavy chain promoter

A mouse renin-1 gene promoter fragment, normally inactive in B-cells, becomes a potent promoter in these cells after insertion of the highly conserved decanucleotide (dc/cd sequence) of immunoglobulin heavy and light chain promoters [(1987) EMBO J. 6, 1685-1690]. We observe retarded complexes of the same electrophoretic mobility when the cd-containing renin promoter fragment or an authentic immunoglobulin heavy chain promoter fragment is incubated with a nuclear extract from myeloma cells, suggesting that the renin promoter is activated due to its acquired ability to bind a B-cell-specific positive factor. No retarded complexes are observed with the original renin promoter fragment thus questioning the presence of a repressor as an explanation for its lack of activity in B-cells.