Cell type-specificity elements of the immunoglobulin heavy chain gene enhancer

Extinction of an immunoglobulin kappa promoter in cell hybrids is mediated by the octamer motif and correlates with suppression of Oct-2 expression

When immunoglobulin-expressing B cells are fused with fibroblasts, immunoglobulin expression is rapidly and selectively suppressed. here we demonstrate that the conserved octamer motif of a kappa light chain gene promoter plays a crucial role in mediating this "extinction" phenomenon. Replacement of this octamer site by an Sp1 or NF1 binding site is sufficient to bypass extinction. Furthermore, in early cell hybrids, immunoglobulin suppression is correlated with absence of the cell-specific transcription factor Oct-2 and its transcripts. Such hybrids cannot support transcription of a transiently introduced reporter plasmid, driven by an octamer-containing promoter, unless an expression vector encoding Oct-2 is cotransfected. Transfection of the same Oct-2 expression vector into hybrid cells is also sufficient to "reactivate" an integrated kappa promoter construct. Thus, our data further establish the role of Oct-2 for immunoglobulin transcription and show that in B cell x fibroblast hybrids, the lack of a necessary cell-specific transcription factor is involved in the extinction of immunoglobulin expression.

A novel B-cell lineage-specific transcription factor present at early but not late stages of differentiation

A novel B-cell-specific transcription factor, BSAP, was identified as a mammalian homolog of the sea urchin protein TSAP, which interacts with the promoters of four tissue-specific late histone H2A-2 and H2B-2 genes. As shown by mobility-shift, methylation interference, and mutational analyses, the mammalian protein BSAP recognizes all four sea urchin binding sites in a manner indistinguishable from TSAP; however, the two proteins differ in molecular weight. BSAP is exclusively restricted to the B-cell lineage of lymphoid differentiation. Its expression appears to be activated during pro-B-cell development, is abundant at the pre-B- and mature B-cell stages, but is absent in terminally differentiated plasma cells. Moreover, BSAP is clearly a B-cell-specific transcription factor, as a wild-type but not a mutant TSAP-binding site of the sea urchin functions only in transfected B cells as an upstream promoter element. Competition experiments did not reveal any high-affinity binding site for BSAP in known regulatory regions of immunoglobulin and class II major histocompatibility (MHC) genes, suggesting that BSAP is a regulator of a different set of B-lymphoid-specific genes.

A second B cell-specific enhancer 3' of the immunoglobulin heavy-chain locus

The expression of immunoglobulin heavy-chain (IgH) genes is generally thought to be regulated by the combination of the VH promoter with the enhancer element which is located in the JH-CH intron. This is probably an oversimplification: there are cell lines that transcribe IgH genes despite the deletion of the intron-enhancer. These findings could imply that other enhancer element(s) exist in the IgH locus. Here we show that a strong B-cell-specific enhancer is indeed located at the 3'-end of the rat IgH locus, 25 kilobases downstream of C alpha. This enhancer should be retained downstream of all rearranged IgH genes, regardless of the VH or CH segment used. Taken together with analogous findings for the mouse kappa locus, the results prompt a re-evaluation of the mechanism of regulation of immunoglobulin gene transcription. Furthermore, unlike the intron-enhancer, the IgH 3' enhancer would become linked to a c-myc that rearranges into an IgH switch region. The IgH 3' enhancer could therefore play a part in the activation of the translocated c-myc genes in rat immunocytomas, mouse plasmacytomas and Burkitt lymphomas.

Structural analyses of human developmentally regulated Vh3 genes

In mice, a restricted set of the Jh-proximal Vh genes are preferentially expressed during early ontogeny. Recently, analyses of human Ig cDNA from a fetal liver revealed a restricted set of Vh genes which belong to the Vh1, 3, 4, and 6 families. Although the Vh6 and some Vh5 genes are proximal to the Jh region, no Vh5 gene was found in the fetal liver, suggesting that the distance between the Jh genes and some early-expressed Vh genes may not be the only factor responsible for Vh gene expression during early development. As an initial step in searching for other underlying mechanisms, we characterized two human germline Vh3 genes which belong to the developmentally restricted Vh repertoire, and found that they contain many enhancer-like sequences which are identical, or highly homologous to, various transcriptional enhancer motifs. Hence, it is conceivable that, in addition to the established positional effects, cis regulatory elements may be important in the programmed expression of some Vh genes during early B-lymphocyte development.

A factor known to bind to endogenous Ig heavy chain enhancer only in lymphocytes is a ubiquitously active transcription factor

The transcriptional enhancer located in the first intron of the immunoglobulin heavy chain constant region is a major determinant of B-cell-specific expression of immunoglobulin genes. Like other enhancers, the Ig heavy chain enhancer contains several short sequence motifs that bind specific transcription factors. Each binding site contributes to the overall activity of the enhancer, however no single element seems absolutely required for activity. For a better understanding of the Ig heavy chain enhancer components, we have cloned and analyzed individual sequence elements. We find that the factor that binds to the E3 enhancer motif, CATGTGGC, is a ubiquitous transcription factor. It is present in an active form in both B cells and non-B cells, where it can mediate transcriptional activation in vitro and in vivo. However, despite its ability to activate transcription of a transfected reporter gene, the factor is apparently unable to bind to the endogenous Ig heavy chain enhancer in non-lymphoid cells: In previous experiments by others, the characteristic in vivo footprint of this factor, designated NF-muE3, was detected in B cells but not in non-B cells. From this and other findings the picture emerges that there are at least three categories of factors which mediate cell-type-specific transcription in B lymphocytes: (a) cell-specific factors such as Oct-2A and Oct-2B that are not expressed in most other cell types: (b) ubiquitous factors such as NF-kappa B that are constitutively active in B cells but are sequestered in an inactive form in other cells; (c) ubiquitously active factors, exemplified by the one binding to the E3 sequence motif. This factor is present in an active form in a variety of cell types but is apparently unable to bind to the endogenous Ig heavy chain enhancer in non-B cells, perhaps due to a non-permissive chromatin structure of the Ig heavy chain locus.

Analysis of the expression of murine lambda genes transfected into immunocompetent cell lines

Hybridoma cell lines were transfected with plasmids containing either a rearranged lambda 1 or a rearranged lambda 2 mouse gene. The levels of lambda-chains synthesized by these transfectants were very low or undetectable. Activation of the expression of the lambda 2 gene was achieved artificially by deleting a portion of the region upstream of the promoter. Analogous deletions in the fragment containing the lambda 1 gene did not result in gene activation suggesting that the upstream sequences of lambda 1 and lambda 2 genes have diverged enough to allow differential regulation of their expression. However, both genes were activated by insertion, at a position upstream of the promoter, of a fragment containing the K-chain gene enhancer. These results suggest that the complete set of sequence elements that mediate lambda gene activation during normal B-cell differentiation are not all contained in the fragments of genomic DNA cloned so far, and thus, at least some of them must be located at a considerable distance from the promoter.

TFE3: a helix-loop-helix protein that activates transcription through the immunoglobulin enhancer muE3 motif

The muE3 motif within the immunoglobulin heavy-chain enhancer is required for full enhancer activity and is known to bind one, or perhaps a family, of related ubiquitous nuclear proteins. Here, we present the isolation of a cDNA that encodes an apparently novel microE3-binding protein designated TFE3. The major open reading frame of the cDNA predicts a protein of 59 kD, with a leucine zipper situated adjacent to an myc-related motif that has been proposed to assume a helix-loop-helix structure. Both of these motifs have been shown (for other proteins) to facilitate protein-protein interactions and DNA binding. Expression of the cDNA in 3T3 cells stimulates transcription from an artificial promoter consisting of four muE3 sites linked to a TATA box and also augments transcription of a reporter gene when it is linked to multiple copies of a particular heavy-chain enhancer subfragment but not when it is linked to the intact enhancer. Using GAL4 fusion proteins, we mapped a strong transcription activation domain within TFE3 that is distinct from the leucine zipper and helix-loop-helix motifs and includes a potential negative amphipathic helix. Like the other muE3-binding proteins detected in nuclear extracts, in vitro-synthesized TFE3 also binds to the USF/MLTF site found in the adenovirus major late promoter.

Identification of a third protein factor which binds to the Rous sarcoma virus LTR enhancer: possible homology with the serum response factor

We have identified a new protein factor (EFIII) in nuclear extracts of quail fibroblasts and chick embryos which binds specifically in vitro to a 26-bp region of the Rous sarcoma virus (RSV) long terminal repeat (LTR) enhancer. The EFIII binding site in the RSV LTR exhibits a strong sequence homology to the serum response element (SRE). The SRE is a 22-bp cis-acting DNA sequence element, first identified upstream of the human c-fos gene, which can confer serum inducibility to heterologous promotors. The binding site for EFIII in the RSV LTR enhancer is also of interest because this region has been implicated in mediating trans-activation of the RSV LTR enhancer by the protein product of the v-fos gene. We show that avian EFIII binds with equal efficiency to both its binding sites in the RSV LTR and the human c-fos SRE. A dyad symmetry element in the c-fos SRE, previously shown to be critical for binding of the cognate human serum response factor (SRF), is also critical for EFIII binding to the LTR SRE-homologous sequences; similarly, EFIII and the human SRF exhibit identical protein-DNA contacts with their corresponding recognition sequences. We suggest that EFIII may be the avian homolog of the mammalian SRF and, in fact, have evidence to indicate that the RSV LTR is serum responsive.

General repression of enhanson activity by the adenovirus-2 E1A proteins

It has been shown previously that the adenovirus 2 (Ad2) E1A proteins repress activation of transcription by the SV40, polyomavirus and immunoglobulin gene enhancers. Here, we demonstrate that the repression of the SV40 enhancer is not specifically mediated by one of its constituent enhansons and/or proto-enhancers, but that each is subject to repression individually. This inhibitory effect of the E1A proteins is also observed with the AP-1 factor-binding enhansons from the polyomavirus and human metallothionein enhancers, and the MHC class I gene H-2Kb enhanson, which binds the KBF1/H2TF1/TC-IIB protein. Repression by the E1A gene products may, in fact, extend to all enhancer trans-activators, because the transcriptional activities of nuclear receptors (e.g., the estrogen and glucocorticoid receptors), of the yeast enhancer factor GAL4 expressed in HeLa cells, and of chimeric trans-activators (such as GAL-VP16) are all similarly inhibited. The E1A protein domains 2 and 3, including the acidic amino acid stretch that has been shown previously to be necessary for E1A-mediated trans-activation, are not required for repression. These results indicate that the amino-terminal region of the protein, which contains domain 1, plays a crucial role in repression, possibly by interfering in the transcriptional activation process at a step common to all trans-acting enhancer factors.

Regulation of the immunoglobulin gene transcription

The transcription of the immunoglobulin heavy (IGH), kappa (IGK) and lambda (IGL) chain genes is coordinate and B lymphocyte specific. This expression of the immunoglobulin genes is under the control of regulatory elements: the promoters located 5' of each variable (V) gene and the enhancers located between the joining and constant genes in the IGH and IGK locus and downstream on the C kappa gene. These sequences represent sites for the binding of transcription factors. A 90-100 kDa ubiquitous proteins (NF-A1) as well as two specific B cell proteins (NF-A2, OTF-2B) bind to the octamer site of the V promoter and IGH enhancer. The NF-kB protein binds to the kB site in the intron kappa enhancer, but also to kB-like sites found in the promoter regions of other genes. This paper reviews the recent data on these factors and other transcription factors which bind to the promoters and enhancers of the immunoglobulin genes and control their expression.

The SV40 TC-II(kappa B) and the related H-2Kb enhansons exhibit different cell type specific and inducible proto-enhancer activities, but the SV40 core sequence and the AP-2 binding site have no enhanson properties

The enhancer activity of the oligomerized SV40 TC-I and TC-II sequences has been investigated in lymphoid and non-lymphoid cell lines. While the TC-I sequence had no demonstrable enhanson activity, a class C enhanson (proto-enhancer), 5'-GGAAAGTCCCC-3', overlapping the TC-II sequence and the GT-I enhanson was identified. This TC-II enhanson, which is identical to the kappa B motif from the kappa chain enhancer, was active in both lymphoid and non-lymphoid cells, which contrasts with the previously reported lymphoid cell specificity of the kappa B motif. However, its activity in non-lymphoid cells is in agreement with our previous reports describing the effect of mutations in the 'TC region' within the total SV40 enhancer in lymphoid and non-lymphoid cells. The activity of the TC-II enhanson could be moderately increased in HeLa by 12-O-tetradecanoyl-phorbol-13-acetate (TPA) and cycloheximide treatment, indicating that the protein(s) mediating its activity may be partially repressed by the previously described inhibitor protein I kappa B. The TC-II related, H-2Kb element, 5'-TGGGGATTCCCCA-3', of the histocompatibility class I H-2Kb gene promoter is also a class C enhanson which is active in both lymphoid and non-lymphoid cells. However, in contrast to the TC-II enhanson, the H-2Kb enhanson exhibits a very low activity in HeLa cells, but can be strongly induced by TPA and/or cycloheximide treatments which suggests that its cognate factor is inactivated (repressed) by an inhibitor protein. Interestingly, cycloheximide, but not TPA treatment, could induce the activity of both the TC-II and H-2Kb enhansons in F9 embryonal carcinoma cells, suggesting that these cells lack some component(s) of the protein kinase C signal transduction pathway. We also show that oligomers of the SV40 'core' sequence, which overlaps the TC-II enhanson, had no enhanson activity in any of the cell types studied, which questions the possible role of the AP-3 protein in SV40 enhancer activity in these cell types. In addition, oligomers of the AP-2 binding sites which are present in the SV40 TC region and in the human metallothionein IIA promoter show no enhanson activity, irrespective of whether the cells are treated with TPA.(ABSTRACT TRUNCATED AT 400 WORDS)

Immunoglobulin gene transcription: molecular mechanisms

Recently, many of the proteins involved in transcriptional regulation of immunoglobulin genes have been identified, purified and their cDNAs cloned. This detailed molecular information has revealed fascinating similarities among different classes of DNA-binding proteins and has dramatically expanded the number of potential mechanisms for achieving precise tissue- and developmental stage-specific immunoglobulin transcription.

The Oct-2 protein binds cooperatively to adjacent octamer sites

Recombinant proteins derived from the cloned human oct-2 gene were used to investigate cooperative binding by Oct-2 to adjacent DNA-binding sites. Oct-2, a B-cell-specific transcription factor, binds tightly to the octamer sequence in immunoglobulin promoters. A second apparently unrelated consensus sequence in heavy chain promoters, the heptamer site, also is recognized by the Oct-2 protein but with 1000-fold lower affinity. Simultaneous occupancy of both the octamer and heptamer sites is favored by cooperative interactions. The heptamer site is probably recognized by the same binding surface in the Oct-2 protein as the octamer site and thus is conserved as a lower-affinity binding site. This permits the immunoglobulin promoter to respond to a much broader range of levels of Oct-2 protein. Substitution of prototype octamer sequences for heptamer sequences yields a probe with two octamer sites spaced by 2 nucleotides, which also binds Oct-2 protein cooperatively. Only the POU domain in the Oct-2 protein is required for this cooperative interaction. Similar protein-protein interactions between bound Oct-2 proteins may promote promoter-enhancer synergism in the heavy chain gene.

Role of the octamer motif in hybrid cell extinction of immunoglobulin gene expression: extinction is dominant in a two enhancer system

We have shown previously that genes activated by the immunoglobulin heavy chain (IgH) enhancer or promoter in mouse myeloma cells are extinguished upon fusion of the myeloma with a mouse T cell lymphoma. Here we show that the conserved octamer sequence shared by the IgH enhancer and promoter, when multimerized to form a tissue-specific enhancer, can also render a gene extinguishable under the same experimental conditions. Extinction, however, is not correlated with either absence of the tissue-specific transcription factor OTF-2 or loss of its ability to bind the octamer sequence. It was also found that extinction mediated by the IgH enhancer is dominant to transcriptional activation by the SV40 enhancer. We propose, therefore, that the T cell-negative regulator responsible for IgH gene extinction does not simply prevent IgH enhancer activation but interferes with gene expression more directly, perhaps by disrupting the transcription complex established as a result of tissue-specific enhancer activation.

A developmental-specific factor binds to suppressor sites flanking the immunoglobulin heavy-chain enhancer

We identified a novel nuclear protein, NF-mu NR, that binds to multiple sites flanking the immunoglobulin heavy-chain enhancer. The expression of NF-mu NR shows a unique developmental pattern; the activity is present in all cells representing early stages of B-cell development, but is absent from more mature cells that express a high level of immunoglobulin heavy chains. NF-mu NR also is present in most cell lines outside of the B-cell lineage (e.g., T cells, macrophages, and fibroblasts). The binding sites for NF-mu NR correlate very well with cis-acting negative regulatory elements of the heavy-chain enhancer defined previously. Indeed, when the segments bound by NF-mu NR are deleted from the enhancer, it is now found to function as a positive transcription element in T cells and macrophages. Taken together, these results suggest that NF-mu NR may function as a negative regulator of enhancer function. The observation that the segments bound by NF-mu NR correspond to the segments bound to the nuclear matrix suggests an intriguing model not only of how enhancers might function but also of how negative regulation might occur.

Developmental and tissue-specific regulation of a novel transcription factor of the sea urchin

We have identified a novel transcription factor that interacts with the promoter of four tissue-specific late histone H2A-2 and H2B-2 genes of the sea urchin by DNase I footprint, mobility shift, and methylation interference analyses. The binding site for this factor is required for efficient transcription of the H2B-2.1 gene both in vitro in nuclear extracts of gastrula embryos and in vivo in microinjected sea urchin embryos. This factor binds with equal affinity to the recognition sequences of all four histone genes in cross-competition assays. Moreover, the binding site of the H2B-2.2 promoter can functionally substitute for that of the H2B-2.1 gene in in vivo expression experiments. Nevertheless, all four binding sites share little sequence homology with each other. This transcription factor increases in abundance during embryogenesis and has been detected in the adult sea urchin only in the tube feet, where the late H2A-2 and H2B-2 genes are expressed specifically. Therefore, we refer to this factor as tissue-specific activator protein (TSAP). The close correlation between the presence of TSAP and the expression pattern of the late H2A-2 and H2B-2 genes suggests that this transcription factor is directly responsible for the developmental and tissue-specific regulation of these genes.

Numerous nuclear proteins bind the long control region of human papillomavirus type 16: a subset of 6 of 23 DNase I-protected segments coincides with the location of the cell-type-specific enhancer

The long control region of the human papillomavirus type 16 genome is 856 base pairs (bp) long. It contains a cell-type-specific enhancer, a glucocorticoid response element, and sequences mediating the response to the viral gene products of open reading frame E2; all three regulate the promoter P97. We mapped binding sites of trans-acting proteins relevant for the cell-type-specific enhancer and other cis-acting elements by DNase I footprint experiments with nuclear extracts from HeLa cells. Throughout the human papillomavirus type 16 long control region 23 footprints protect 557 of 900 bp. Nine footprints fall into a 400-bp segment that was previously identified to contain the cell-type-specific enhancer. Variations of the protein concentration in the footprint reaction do not affect six of these nine footprints. At high protein concentrations, three footprints fuse to a 106-bp protected region, suggesting that this segment specifically binds several proteins of lower affinity or abundance. Unexpectedly, extracts from human MCF7 and mouse 3T3 cells, in which the enhancer is inactive, give footprints identical to those obtained with HeLa extracts. Seven footprints contain the sequence 5'-TTGGC-3'. Footprint competition experiments suggest that factor NFI binds to these seven motifs. Competition with cloned oligonucleotides in transfections suggests that these elements contribute to the enhancer function. Subcloning identifies a 232-bp fragment between positions 7524 and 7755 as sufficient for full enhancer activity. Several of the six footprinted elements on this segment may cooperate functionally, since subclones of this region show decreased or no cell-type-specific enhancer function.

Functional cooperativity between protein molecules bound at two distinct sequence elements of the immunoglobulin heavy-chain promoter

Immunoglobulin heavy-chain gene promoters contain two conserved upstream sequence elements, octamer and heptamer, both of which are required for normal cell type-specific promoter function in vivo. The octamer sequence motif 5'-ATGCAAAT-3', and its precise inverse, are strongly conserved in heavy- and light-chain gene promoters and are important determinants for the lymphoid-specific function of these promoters and of the heavy-chain enhancer. The heptameric sequence element with the consensus 5'-CTCATGA-3' (refs 3 and 4) is also required in addition to the octamer for full lymphoid-specific activity of heavy-chain promoters. Although these two elements have no sequence similarity, they are both recognized in vitro by the ubiquitous octamer transcription factor OTF-1 (reviewed refs 13 and 14) and the lymphoid-specific OTF-2 (reviewed in refs 15 and 16). Here we show that purified OTF-2 binds cooperatively to the immunoglobulin heptamer and octamer elements so that interaction with the octamer element facilitates binding of OTF-2 to the heptamer motif. More important, cooperativity in OTF-2 binding is closely mirrored by functional cooperation between the heptamer and octamer elements in activating transcription from the heavy-chain promoter in vitro.

Ubiquitous and lymphocyte-specific factors are involved in the induction of the mouse interleukin 2 gene in T lymphocytes

The immediate upstream region of the mouse interleukin 2 (Il-2) gene harbors a strong transcriptional enhancer. This enhancer contains most, if not all of the sequence elements necessary for the T cell specific induction of the Il-2 gene by the phorbol ester TPA and the plant lectin Concanavalin A. DNase I footprinting studies with fractionated extracts obtained from induced and uninduced E14 T cells revealed numerous recognition sites for potential trans-acting factors. Five of these sites are also recognized by the TPA-activated HeLa cell factors AP-1 and AP-3. Other sites including two TATA-boxes, two purine-rich sequence motifs and two copies of the GGGPuTTTCAA motif are recognized by lymphocyte specific factors. The latter motif is highly conserved between several lymphokine genes and is therefore designated as a T cell element (TCE). In E14 T cells, pentamers of the distal TCEd confer an activity similar to that of the entire Il-2 enhancer, whereas in B and HeLa cells, the TCEd-pentamer is inactive as is the Il-2 enhancer. These data indicate the involvement of the TCEd and its recognition factor(s) in the cell type specific induction of the Il-2 gene during T cell activation.

Repression of the IgH enhancer in teratocarcinoma cells associated with a novel octamer factor

Embryonal carcinoma (EC) cell lines are models for early cells in mouse embryogenesis. A 300-base pair fragment of the heavy chain enhancer was inactive in F9 EC cells, unlike in other nonlymphoid cells where it has significant activity. Alterations of the octamer motif increased enhancer activity. Nuclear extracts from F9 cells contained an octamer binding protein (NF-A3) that was unique to EC cells; the amount of NF-A3 decreased upon differentiation. It is proposed that NF-A3 represses specific regulatory sequences that contain the octamer motif. Thus, the same DNA sequence mediates either negative or positive transcriptional effects, depending on the cell type.

Myeloma kappa gene transcription is blocked upon fusion with fibroblasts

Numerous studies on somatic cell hybrids have shown that expression of tissue-specific functions can be suppressed as a consequence of fusion with cells that do not express the given functions. We have further investigated this phenomenon, using as a model system the regulation of expression of kappa light chain genes in intraspecific hybrids between mouse myeloma cells and mouse fibroblasts. Hybrids containing only one genome equivalent from each parent cell (1s:1s) were isolated by fluorescence-activated cell sorting from within 10 h after fusion, and they were grown for no more than 16 days thereafter in order to ensure maximum integrity of the genomic constitution. Here we report that in hybrid cells, kappa gene transcription was specifically turned off as demonstrated by nuclear run-on assays performed on 16-day-old proliferating hybrids. Furthermore, a mechanism affecting mRNA stability may also contribute, at least initially, to the rapid depletion of cytoplasmic kappa transcripts, observed during the first few hours after fusion. Suppression was dominant and could not be overridden by increasing the relative myeloma ploidy at either the heterokaryon or the synkaryon stage. Nor could suppression be relieved by treating hybrids with cycloheximide.

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.

Direct combinatorial interaction between a herpes simplex virus regulatory protein and a cellular octamer-binding factor mediates specific induction of virus immediate-early gene expression

We provide evidence for a novel mechanism of transcriptional regulation in which the immediate-early (IE) transactivating protein of herpes simplex virus, Vmw65, is assembled into a specific DNA-binding complex together with a cellular octamer-binding factor (TRF). The assembly of Vmw65/TRF complex requires not only the core TRF recognition site, but also flanking sequences which are dispensable for TRF binding alone. We show from functional analyses that TRF binding by a motif is required but not sufficient to confer induction on a heterologous promoter, and it is the ability of the motif to allow TRF/Vmw65 complex assembly which correlates with functional activity. Thus, for the induction of HSV IE expression, Vmw65 forms a complex with TRF by recognition of the specific subset of appropriately flanked TRF binding sites present in each of the IE genes. This mechanism may provide a paradigm for the selective utilization of the same transcription factor in differential gene expression.

A human lymphoid-specific transcription factor that activates immunoglobulin genes is a homoeobox protein

The human lymphoid-specific transcription factor OTF-2 contains a homoeodomain that is required for DNA binding and binds specifically to DNA elements that are recognized by Drosophila homoeodomain proteins, suggesting coevolutionary relationships between mammalian and invertebrate homoeodomain proteins and their DNA recognition elements.

A cloned octamer transcription factor stimulates transcription from lymphoid-specific promoters in non-B cells

The complementary DNA coding for a lymphocyte-specific transcription factor binding to the DNA 'octamer' sequence TNATTTGCAT has been cloned. The nucleotide sequence shows homology to the homoeobox domain. Expression of this cDNA in HeLa cells is sufficient for a strong transcriptional activation of B-cell-specific promoters.

OBP100 binds remarkably degenerate octamer motifs through specific interactions with flanking sequences

We have used the 100-kD HeLa cell octamer-binding protein OBP100 as a model to study flexible DNA sequence recognition by promoter-binding proteins. OBP100 binds to the conserved octamer motif ATGCAAAT found in numerous promoters and additionally to two degenerate octamer motifs (sites I and II) within the SV40 enhancer region. We show here that OBP100 binds the herpes simplex virus immediate early promoter TAATGARAT (R = purine) motif itself, extending the flexibility of OBP100 sequence recognition to sequences that bear very little resemblance (four matches over a 14-bp region). Nevertheless, a progression of OBP100-binding sites can be established that links the sequences of these two apparently unrelated binding sites by incremental steps. Mutational and chemical modification interference analyses of a degenerate octamer binding site (SV40 site II) show that specific sequences, which are not normally conserved but flank the degenerate octamer motif, can compensate for the degeneracy in the octamer core sequence. Thus, different regions of the binding site sequence (core or flanking) can diverge separately but not independently of one another. These results suggest that flexible DNA sequence recognition arises because there are few obligatory contact sites for OBP100 binding, but, rather, specific binding reflects the sum of many independent interactions.

A human protein specific for the immunoglobulin octamer DNA motif contains a functional homeobox domain

The homeobox domain is shared by Drosophila homeotic proteins, yeast mating type proteins, and some functionally uncharacterized mammalian proteins. A lymphoid-restricted human protein that binds to the immunoglobulin octamer regulatory motif was shown to contain an amino acid sequence that has 33% amino acid identity with the consensus sequence of the previously cloned homebox domains. This homeobox gene was localized to chromosome 19, thus mapping separately from other human homebox genes. A mutant protein containing amino acid substitutions within a putative helix-turn-helix motif in the homeobox domain did not bind DNA detectably. This human homeobox protein was shown to bind the same DNA sequence as the homeobox domains of the yeast mating type proteins and Drosophila homeotic protein, suggesting that homeobox proteins may have closely related DNA binding characteristics.

Octamer-binding proteins from B or HeLa cells stimulate transcription of the immunoglobulin heavy-chain promoter in vitro

The B-cell-type specificity of the immunoglobulin (Ig) heavy-chain and light-chain promoters is mediated by an octanucleotide (OCTA) element, ATGCAAAT, that is also a functional component of other RNA polymerase II promoters, such as snRNA and histone H2B promoters. Two nuclear proteins that bind specifically and with high affinity to the OCTA element have been identified. NF-A1 is present in a variety of cell types, whereas the presence of NF-A2 is essentially confined to B cells, leading to the hypothesis that NF-A2 activates cell-type-specific transcription of the Ig promoter and NF-A1 mediates the other responses of the OCTA element. Extracts of the B-cell line, BJA-B, contain high levels of NF-A2 and specifically transcribe Ig promoters. In contrast, extracts from HeLa cells transcribed the Ig promoter poorly. Surprisingly, addition of either affinity-enriched NF-A2 or NF-A1 to either a HeLa extract or a partially purified reaction system specifically stimulates the Ig promoter. This suggests that the constitutive OCTA-binding factor NF-A1 can activate transcription of the Ig promoter and that B-cell-specific transcription of this promoter, at least in vitro, is partially due to a quantitative difference in the amount of OCTA-binding protein. Because NF-A1 can stimulate Ig transcription, the inability of this factor to activate in vivo the Ig promoter to the same degree as the snRNA promoters probably reflects a difference in the context of the OCTA element in these two types of promoters.

Cooperativity and hierarchical levels of functional organization in the SV40 enhancer

We have investigated the cell-specific activity of the GT-IIC, GT-I, Sph-II, Sph-I, and octamer motifs of the SV40 enhancer in four cell lines (HeLa cells, MPC11 plasmocytoma B cells, and non-differentiated and retinoic acid-differentiated F9 embryonal carcinoma cells). Our present results reveal the existence of three classes of motifs that interact with cell-specific enhancer factors but that have no enhancer activity of their own: those (class A) that generate enhancer activity following oligomerization of tandem repeats of the motif; those (class B) that cannot enhance transcription when oligomerized as a tandem repeat but whose association with a second motif results in transcription activation after oligomerization; and those (class C) that exhibit enhancer activity when a single copy of the motif is oligomerized. Three levels of functional organization of enhancers can also be defined. The possible implications for enhancer functions are discussed.

The HeLa cell protein TEF-1 binds specifically and cooperatively to two SV40 enhancer motifs of unrelated sequence

We have purified a protein (TEF-1) that specifically binds to two sequence unrelated motifs (GT-IIC and Sph) of the simian virus 40 (SV40) enhancer. TEF-1 binds cooperatively to templates containing tandem but not inverted or spaced repeats of its cognate motifs. This cooperative binding correlates with the ability of the tandem repeats to generate enhancer activity in vivo. In contrast, TEF-1 and a second SV40 enhancer binding protein, TEF-2, bind independently to templates containing the cognate motifs of both proteins (GT-I and either GT-IIC or Sph motifs) even though these motifs cooperate in enhancer activity in vivo. These results allow us to distinguish different classes of enhancer factors.

Cloning of a lymphoid-specific cDNA encoding a protein binding the regulatory octamer DNA motif

An octamer DNA sequence plays a critical role in directing transcription of immunoglobulin genes in B lymphocytes. A new technique of direct binding of radioactive DNA was used to screen a complementary DNA expression library from the BJAB cell line in lambda gt11 phage to derive molecular cDNA clones representing a putative B lymphocyte-specific octamer binding protein. The plaques were screened with DNA containing four copies of the octamer sequence and positive phage recombinants were identified. The fusion protein produced on inducing a lysogen of one phage bound to a monomeric octamer probe. The cDNA insert from this phage hybridized to messenger RNA found in B lymphocytes, but not in most other cells. Thus, this cDNA derives from a gene (oct-2) that specifies an octamer binding protein expressed preferentially in B lymphocytes, proving that, for at least one gene, a cell-specific transcription factor exists and its amount is controlled through messenger RNA availability.

Purification of a nuclear trans-acting factor involved in the regulated transcription of a human immunoglobulin heavy chain gene

The expression of the rearranged human immunoglobulin gamma 1 heavy chain gene (HIG1) was shown to be induced through its enhancer by the positive regulatory trans-acting factor(s) that was contained only in cells of B lineage. The trans-acting factors were purified from mouse myeloma NS1 cells, and HIG1-inducing activity was found mainly in fractions of molecular weight 53-127 kd and in a fraction eluted from a heparin-Sepharose column with 0.5 M KCI. This semipurified fraction contained proteins binding to the conserved octamer sequence, ATGCAAAT, in the promoter region, as well as to sequences in the enhancer region. The 0.5 M KCI eluates from a heparin-Sepharose column were applied to a DNA affinity column of synthetic oligonucleotides of the octamer sequence and the sequence TATTTTAGGAAGCAAA in the HpaII-BgIII region of the HIG1 gene enhancer. The protein eluted from the enhancer sequence-specific DNA affinity column showed a strong inducing activity for the HIG1 gene, and the molecular weight of a predominant protein was 96 kd.

Redundancy of information in enhancers as a principle of mammalian transcription control

In contrast to prokaryotes, in which strong transcriptional signals can be located within very short DNA segments, typical mammalian enhancers are about 200 base-pairs long. We reasoned that a minimal length of enhancer-active DNA is required for a high transcription rate in higher eukaryotes, and that segments from a single enhancer or from different enhancers might be multimerized or combined to satisfy such a requirement. To test this, enhancer fragments from different viruses were joined in a recombinant simian virus 40 (SV40) and screened for efficiency of viral growth. The 48 combinations tested show that the hypothesis is basically correct. For example, two subfunctional heterologous enhancer fragments can together form a functional enhancer. No enhancer shorter than 84 base-pairs could promote SV40 growth, i.e. in no case did we find a short "superstrong" enhancer segment. To test whether multimerization of a short fragment would result in a strong enhancer, we have synthesized a 50 base-pair enhancer segment derived from Herpesvirus saimiri. One to six copies of this oligonucleotide gave an incremental increase in enhancer activity. We propose, therefore, that mammalian gene regulation is based on a redundancy of information that can be provided either by a combination of different DNA sequence elements, or by multiple copies of the same element. Also, the finding of strong and weak enhancers suggests that in most cases an enhancer is permanently required for transcription of a gene, rather than acting in an all-or-none fashion to establish a transcription complex, after which it becomes dispensable.

Herpes simplex virus regulatory elements and the immunoglobulin octamer domain bind a common factor and are both targets for virion transactivation

Functional upstream activator sequences (TAATGARAT motifs) of herpes simplex virus immediate-early genes were identified and shown both to bind a factor (TRF) present in uninfected HeLa cells and to confer inducibility by the virus regulatory protein, Vmw65, on a normally nonresponsive promoter. Point-mutation analyses demonstrated binding specificity and correlated binding with Vmw65 induction. Furthermore, the octamer domains of the adenovirus DNA replication origin, the histone H2B, and the immunoglobulin light chain genes bound and competed for TRF. The immunoglobulin octamer also conferred Vmw65 inducibility on the TK promoter. In addition, a modified form of TRF was specifically detected in infected cells. We conclude that TRF is similar or identical to the previously described octamer binding protein and is likely to be the target for coordinate induction of immediate-early gene expression by Vmw65.

Identification and purification of a human lymphoid-specific octamer-binding protein (OTF-2) that activates transcription of an immunoglobulin promoter in vitro

The octamer sequence 5'-ATGCAAAT, in either orientation, serves as an upstream element in a variety of promoters and also occurs as a modular enhancer element. It is of particular interest in immunoglobulin genes since it is found in the upstream regions of all heavy and light chain promoters and in the heavy chain enhancer, both of which are known to be necessary for cell-specific expression. We report here the chromatographic separation of ubiquitous and B cell-specific octamer-binding proteins. The B cell factor was purified to homogeneity using affinity chromatography and consists of three peptides of 62, 61, and 58.5 +/- 1.5 kd. Each of the polypeptides was renatured after SDS-PAGE and shown to bind to the octamer sequence. The specific DNA binding activity of the pure B cell-specific factor was indistinguishable from that of the affinity-purified ubiquitous factor. This B cell-specific octamer-binding factor, in pure form, activated transcription from a kappa light chain promoter in vitro, thus demonstrating that it is indeed a B cell-specific transcription factor for this gene. In addition to the ubiquitous and B cell-specific octamer-binding factors, we identified several additional proteins, one of which is B cell-specific, that interact with the kappa promoter.

Human proto-oncogene c-jun encodes a DNA binding protein with structural and functional properties of transcription factor AP-1

Nuclear oncogene products have the potential to induce alterations in gene regulation leading to the genesis of cancer. The biochemical mechanisms by which nuclear oncoproteins act remain unknown. Recently, an oncogene, v-jun, was found to share homology with the DNA binding domain of a yeast transcription factor, GCN4. Furthermore, GCN4 and the phorbol ester-inducible enhancer binding protein, AP-1, recognize very similar DNA sequences. The human proto-oncogene c-jun has now been isolated, and the deduced amino acid sequence indicates more than 80 percent identity with v-jun. Expression of cloned c-jun in bacteria produced a protein with sequence-specific DNA binding properties identical to AP-1. Antibodies raised against two distinct peptides derived from v-jun reacted specifically with human AP-1. In addition, partial amino acid sequence of purified AP-1 revealed tryptic peptides in common with the c-jun protein. The structural and functional similarities between the c-jun product and the enhancer binding protein suggest that AP-1 may be encoded by c-jun. These findings demonstrate that the proto-oncogene product of c-jun interacts directly with specific target DNA sequences to regulate gene expression, and therefore it may now be possible to identify genes under the control of c-jun that affect cell growth and neoplasia.

A 100-kD HeLa cell octamer binding protein (OBP100) interacts differently with two separate octamer-related sequences within the SV40 enhancer

Numerous eukaryotic upstream promoter and enhancer regions contain a functional octamer sequence ATGCAAAT. We have examined the interactions between an octamer binding protein isolated from HeLa cells and the SV40 and immunoglobulin heavy-chain (IgH) gene enhancers. A partially purified octamer binding activity forms a single complex with the IgH enhancer octamer in a gel retardation assay, but two complexes with a SV40 enhancer fragment containing a single 72-bp element. By using point mutants and both dimethyl sulfate and diethyl pyrocarbonate modification interference assays, we show that the SV40 complexes result from binding of a factor to the octamer-related sequence ATGCAAAG (Octa1) and to an adjacent previously unidentified octamer-related sequence ATGCATCT (Octa2). The base-specific interactions with Octa1 and Octa2 differ; chemical modifications over a 10-bp sequence TATGCAAAGC affect Octa1 binding whereas Octa2 binding is affected by modifications spanning a 13-bp sequence ATGCATCTCAATT in which the octamer-like sequence is not centered. The octamer binding activity has been purified extensively by a DNA affinity precipitation procedure and SDS-polyacrylamide gel electrophoresis. The purified protein, OBP100, has an apparent molecular weight of 100 kD and binds both SV40 Octa1 and Octa2, as well as the IgH enhancer. The distinct interactions of OBP100 with the differently sized Octa1 and Octa2 binding sites suggest remarkably flexible sequence recognition between OBP100 and its binding sites.

Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors

Using in vivo dimethylsulfate footprinting, we have analyzed protein-DNA interactions within two regions upstream of the tyrosine aminotransferase (TAT) gene that are characterized by an altered chromatin structure in TAT-expressing as compared to nonexpressing cells. All the identified protein contacts to DNA are found exclusively in the TAT-expressing hepatoma cells. In vitro analyses of specific DNA-binding factors in crude nuclear extracts yield DNAase I footprints that correlate well with the binding sites in vivo. Surprisingly, all DNA-binding activities are present in nuclei of TAT-expressing and nonexpressing cells, indicating that the mere presence of factors is not sufficient for their interaction with a binding site in vivo. Genomic sequencing reveals methylation of CpG dinucleotides in the regions analyzed in nonexpressing cells, whereas no methylation is found in TAT-expressing cells. In vitro methylation at a cytosine residue within a footprint region prevents the interaction of a factor with its binding site.

A purine-rich DNA sequence motif present in SV40 and lymphotropic papovavirus binds a lymphoid-specific factor and contributes to enhancer activity in lymphoid cells

The enhancer of simian virus 40 (SV40) is active in a wide variety of tissues and hosts and thus has been called a general enhancer. Previous work has established that this region contains a number of subsegments, each with a different cell type specificity. By analyzing enhancer deletion mutants of SV40 with a restricted cell type specificity, we have identified a purine-rich DNA motif (Pu box) that is essential for activity of the mutant enhancer in lymphoid cells and also obtained evidence for an independent element that confers activity in kidney CV-1 cells. The Pu box element is positively regulated since binding of a cognate factor(s) was only observed in lymphoid cell extracts. The Pu box is also present in the 63-bp enhancer repeat of lymphotropic papovavirus (LPV), and competition experiments show that the SV40 and LPV sequences bind the same factor(s). Thus, the Pu box is likely to be a major determinant of the lymphotropic host range of LPV. In SV40, however, the Pu box is one of several enhancer elements with different cell specificities. We suggest that such an arrangement reflects a diversification strategy of SV40 to maximize its chance of adaptation to various types of host cells.