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

Transcription factor Spi-B binds unique sequences present in the tandem repeat promoter/enhancer of JC virus and supports viral activity

Progressive multifocal leukoencephalopathy (PML) is an often fatal demyelinating disease caused by lytic infection of oligodendrocytes with JC virus (JCV). The development of PML in non-immunosuppressed individuals is a growing concern with reports of mortality in patients treated with mAb therapies. JCV can persist in the kidneys, lymphoid tissue and bone marrow. JCV gene expression is restricted by non-coding viral regulatory region sequence variation and cellular transcription factors. Because JCV latency has been associated with cells undergoing haematopoietic development, transcription factors previously reported as lymphoid specific may regulate JCV gene expression. This study demonstrates that one such transcription factor, Spi-B, binds to sequences present in the JCV promoter/enhancer and may affect early virus gene expression in cells obtained from human brain tissue. We identified four potential Spi-B-binding sites present in the promoter/enhancer elements of JCV sequences from PML variants and the non-pathogenic archetype. Spi-B sites present in the promoter/enhancers of PML variants alone bound protein expressed in JCV susceptible brain and lymphoid-derived cell lines by electromobility shift assays. Expression of exogenous Spi-B in semi- and non-permissive cells increased early viral gene expression. Strikingly, mutation of the Spi-B core in a binding site unique to the Mad-4 variant was sufficient to abrogate viral activity in progenitor-derived astrocytes. These results suggest that Spi-B could regulate JCV gene expression in susceptible cells, and may play an important role in JCV activity in the immune and nervous systems.

Expression levels of FAS are regulated through an evolutionary conserved element in intron 2, which modulates cystic fibrosis disease severity

We have analyzed frequent naturally occurring variants in the autogene FAS in two independent cystic fibrosis (CF) patient populations. Analysis of FAS expression levels from intestinal epithelial biopsies from 16 unrelated F508del-CFTR homozygotes showed a correlation between FAS intron 2 SNP rs7901656 and signals for Affymetrix GeneChip U133 Plus 2.0 probeset 204781_s_at consistent with a dominant model (P=0.0009). Genotype and haplotype analysis at six informative SNPs spanning the FAS gene locus was carried out on 37 nuclear families representing extreme clinical phenotypes that were selected from the European CF Twin and Sibling Study population of more than 300 affected sibling pairs. Case-control comparison of the haplotype composed of rs2296603-rs7901656-rs1571019 encompassing intron 2 of FAS reached significance (P=0.0246). Comparative phylogenetic analysis and functional annotation of the FAS intron 2 sequence revealed a conserved non-coding sequence surrounding rs7901656 and predicted binding sites for four transcription factors whereby the binding site of c-Rel is altered by rs7901656. Taken together, these findings from two independent CF patient cohorts indicate that allelic variants within FAS intron 2 alter FAS gene expression and that these functional variants modulate the manifestation of CF disease.

Establishment and characterization of choroid plexus carcinoma cell lines: connection between choroid plexus and immune systems

Murine choroid plexus cell lines were produced from choroid plexus carcinoma generated in transgenic mice harboring the viral oncogene simian virus 40 large tumor antigen under transcriptional control of an intronic enhancer region from the human immunoglobulin heavy chain (IgH) gene. Two morphologically distinct cell lines have been cloned. These established cell lines retained the characteristics of choroid plexus cells in that they expressed such choroid plexus cell marker or related proteins as transthyretin and alpha2-macroglobulin. They were tumorigenic in nude mice. In the cell lines, the muA and muB (HE2) motifs within the IgH intronic enhancer were active and we also demonstrated the existence of the proteins binding to these motifs, suggesting a potential link between the choroid plexus and immune systems. It is considered that these binding proteins act as trans-activators for the enhancer and may belong to the class of ETS-related proteins. These cell lines and xenografts should be useful materials for analyses of choroid plexus functions.

Human HE2 (microB) and microA motifs show the same function as whole IgH intronic enhancer in transgenic mice

In the murine IgH gene intronic enhancer (ENHiH), two major functional domains were reported. One is the E4/octomer region and another includes the microA and microB motifs. In the human ENHiH, it was reported that the HE2, which corresponds to the murine microB, and E6 motifs play an important role in an enhancer activity and a tissue-specificity at cellular level. Here we examined the in vivo function of the E6, microA and HE2 motifs within the human ENHiH by using the transgenic mice technique. The microA and HE2 motifs together revealed almost the same enhancer function as the whole human ENHiH, but the E6 motif had lesser enhancer activity and tissue-specificity.

Pi, a pre-B-cell-specific enhancer element in the immunoglobulin heavy-chain enhancer

We have identified a new immunoglobulin heavy-chain enhancer element, designated pi, between the microE2 and microE3 elements. The pi enhancer element is transcriptionally active primarily during early stages of B-cell development but becomes virtually inactive during B-cell maturation at about the stage of immunoglobulin kappa light-chain gene rearrangement. Mutational analysis suggests that the pi element is crucial for immunoglobulin heavy-chain enhancer activity at the pre-B-cell stage but is almost irrelevant for enhancer activity at the mature B-cell or plasma-cell stage. The activity of the pi enhancer element correlates with the presence of an apparently pre-B-cell-specific protein-DNA complex. The similarity of the pi site to recognition sequences for members of the ets gene family suggests that the protein(s) interacting with the pi site most likely are ets-related transcription factors.

Pi, a pre-B-cell-specific enhancer element in the immunoglobulin heavy-chain enhancer

We have identified a new immunoglobulin heavy-chain enhancer element, designated pi, between the microE2 and microE3 elements. The pi enhancer element is transcriptionally active primarily during early stages of B-cell development but becomes virtually inactive during B-cell maturation at about the stage of immunoglobulin kappa light-chain gene rearrangement. Mutational analysis suggests that the pi element is crucial for immunoglobulin heavy-chain enhancer activity at the pre-B-cell stage but is almost irrelevant for enhancer activity at the mature B-cell or plasma-cell stage. The activity of the pi enhancer element correlates with the presence of an apparently pre-B-cell-specific protein-DNA complex. The similarity of the pi site to recognition sequences for members of the ets gene family suggests that the protein(s) interacting with the pi site most likely are ets-related transcription factors.

Functional analysis of defined mutations in the immunoglobulin heavy-chain enhancer in transgenic mice

We have analyzed the effect of defined mutations in the mouse immunoglobulin heavy-chain enhancer after introduction into the germline of transgenic mice. We have tested a mutation of the enhancer octamer motif, a double mutation of the octamer motif and the microB-site, and a triple mutation in the microE2, microE3 and microE4-sites. All constructs are expressed in the spleen of transgenic mice. Furthermore, expression is exclusively detectable in lymphoid organs and not in several nonlymphoid tissues. Whereas mutations in the microE-sites have a more pronounced effect on transgene activity in thymocytes as compared to bone marrow and spleen cells, the octamer/microB double mutation shows significantly reduced expression levels only in B-cells. Finally, our results demonstrate that the intronic heavy-chain enhancer element does not contribute to the increase steady state levels of heavy-chain mRNA after stimulation of spleen cells with LPS.

Regulation of immunoglobulin gene transcription

Analysis of the immunoglobulin gene suggests that their expression is controlled through the combinatorial action of tissue- and stage-specific factors (OTF-2, TF-microB, NF-kappa B), as well as more widely expressed E motif-binding factors such as E47/E12. Two basic issues cloud understanding of how these factors are involved in immunoglobulin gene regulation. First, cloning of these factors shows them to be members of families of proteins, all with similar DNA-binding specificities. OTF-2 is a member of the POU domain family, NF-kappa B is a related protein, and the microE5/kappa E2-binding factors are members of the bHLH family. Second, these binding sites and associated factors are involved in the regulation of many genes, not only the immunoglobulin genes, and in fact not only lymphoid-specific genes. These facts complicate understanding which member of a family is in fact responsible for interaction with, and activation of, a particular binding element in an enhancer/promoter. Recently, more detailed analysis of the interactions between such proteins and their related binding sites suggest that a certain level of specificity may in fact be encoded by the DNA element such that one family member of a protein is preferentially bound, or alternatively that the protein-DNA interactions that occur give subtle alterations in protein conformation that unmask an activation or protein-protein interactive domain. An additional level of regulation is imparted by combinatorial mechanisms such as adjacent DNA-binding elements and factors that may alter activity, as well as "cofactors" that, by forming a complex with the bound factor, affect its activation of a gene in a particular cell type. A third level of specificity may be obtained by factors such as NF-kappa B and the bHLH family due to their ability to create heterogeneous complexes, creating unique complexes in a tissue- or stage-specific manner. The multiple functions transcription factors such as NF-kappa B and OTF-2 play in the transcriptional regulation of multiple genes seems complex in contrast to a one factor, one gene regulation model. However, this type of organization may limit the number of factors lymphocytes would require if each lymphoid-specific gene were activated by a unique factor. Thus what appears to be complexity at the molecular level may reflect an economical organization at the cellular level. Investigation of the key factors controlling these genes suggests an ordered cascade of transcription factors becomes available in the cell during B cell differentiation.(ABSTRACT TRUNCATED AT 400 WORDS)

A pre-B- and B cell-specific DNA-binding protein, EBB-1, which binds to the promoter of the VpreB1 gene

The VpreB1 protein is thought to be expressed on the surface of pre-B cells in association with lambda 5 and mu heavy chain, and to play an important role on B cell differentiation. The expression of VpreB1 and lambda 5 is pre-B cell specific, and regulated at the initiation of transcription. We have identified at least two sequence-specific DNA-binding proteins which bind to the region -191 to -74 of the promoter of the mouse VpreB1 gene. These DNA-binding proteins also bind to the promoter of the mouse lambda 5 gene. One of the two DNA-binding proteins, called EBB-1, is restricted to pre-B and B cells, but not detected in plasma cells, T cells and cells of other lineages. Transient transfection analysis of reporter constructs revealed that the binding sites of these proteins play a significant role in the activity of the promoter, especially the binding site of EBB-1. Taken together these results suggest that EBB-1 might be one of the crucial factors which regulates a series of intracellular events in B cell differentiation.

LyF-1, a transcriptional regulator that interacts with a novel class of promoters for lymphocyte-specific genes

We have studied transcriptional control of the murine terminal deoxynucleotidyltransferase (TdT) gene, which is activated specifically in immature B and T lymphocytes. This analysis has led to the identification and purification of a 50-kDa sequence-specific DNA-binding protein, LyF-1, that interacts with the approximate consensus sequence PyPyTGGGAGPu and is enriched in cells at most stages of B- and T-cell differentiation. LyF-1 binds tightly to an element in the TdT promoter that we show is required for transcription in lymphocytes. LyF-1 also interacts with an element in the immunoglobulin mu enhancer, called microB, that was recently shown to be important for lymphocyte-specific enhancer activity. Moreover, LyF-1 binds to the promoters for the lymphocyte-specific genes lambda 5, VpreB, and lck, all of which we speculate have additional features in common with the TdT promoter. Thus, LyF-1 may be a general transcriptional activator for genes whose expression is restricted to the B- and/or T-lymphocyte lineages.

LyF-1, a transcriptional regulator that interacts with a novel class of promoters for lymphocyte-specific genes

We have studied transcriptional control of the murine terminal deoxynucleotidyltransferase (TdT) gene, which is activated specifically in immature B and T lymphocytes. This analysis has led to the identification and purification of a 50-kDa sequence-specific DNA-binding protein, LyF-1, that interacts with the approximate consensus sequence PyPyTGGGAGPu and is enriched in cells at most stages of B- and T-cell differentiation. LyF-1 binds tightly to an element in the TdT promoter that we show is required for transcription in lymphocytes. LyF-1 also interacts with an element in the immunoglobulin mu enhancer, called microB, that was recently shown to be important for lymphocyte-specific enhancer activity. Moreover, LyF-1 binds to the promoters for the lymphocyte-specific genes lambda 5, VpreB, and lck, all of which we speculate have additional features in common with the TdT promoter. Thus, LyF-1 may be a general transcriptional activator for genes whose expression is restricted to the B- and/or T-lymphocyte lineages.

Expression of immunoglobulin genes in common variable immunodeficiency

Five common variable immunodeficiency (CVI) patients were analyzed for expression of immunoglobulin (Ig) genes. In the pokeweed mitogen (PWM)-induced Ig-production assay, the combination of T and B cells showed that all patients' T cells had normal helper functions and all patients' B cells had profound defects. The defective B-cell maturation stages based on their Ig gene expression patterns were variable. One of five patients showed normal mu-chain gene expression and nearly normal IgM production, but neither IgG nor IgA production, which suggested that this patient's B-cell defects might lie on a mu- to gamma or mu- to alpha class-switch stage. B cells in another patient showed low mu-chain gene expression and low IgM production, but an Ig enhancer region, which is an important region for expression of Ig genes, was intact. Thus, this patient might have a transacting factor defect which interacts with the Ig enhancer region. The other three patients showed no mu-chain gene expression and no IgM production. Thus, their B-cell defects lay on the B-cell maturation stage, similar to X-linked agammaglobulinemia. These results showed that primary B-cell defects in CVI occurred at several B-cell differentiation stages, which could be recognized by expression of Ig genes.

Complex pattern of immunoglobulin mu gene expression in normal and transgenic mice: nonoverlapping regulatory sequences govern distinct tissue specificities

Analysis of normal mice and transgenic mice carrying a rearranged immunoglobulin mu gene revealed a more complex tissue-specific pattern of mu gene expression than anticipated from previous observations. Expression of the endogenous mu locus and the mu transgene was detected both in lymphoid tissues and in skeletal muscle. Analysis of the expression pattern of mu transgenes containing intragenic deletions or point mutations in binding sites for Oct transcription factors (OCTA sites) indicated that distinct regulatory sequences control lymphoid- and muscle-specific mu gene expression. Consistent with previous transfection experiments, mu gene expression in lymphoid tissues is dependent on the intragenic enhancer and the OCTA site in the promoter. However, neither of these regulatory sequences is required for mu gene expression in skeletal muscle that is governed by a muscle-specific control region located 3' of the enhancer. An "off-state" of the mu transgene was observed only in liver and embryonal fibroblasts, whereas enhancer-dependent mu transgene expression was detected at low levels in other nonlymphoid tissues. From these data we suggest a model for the regulation of tissue-specific mu gene expression in which a "ubiquitous" competence for basal transcription is up-regulated in lymphoid and muscle tissues by distinct cell type-specific regulatory sequences and down-regulated in liver and fibroblastic cells by putative negative sequence elements.

mRNA transcripts initiating within the human immunoglobulin mu heavy chain enhancer region contain a non-translatable exon and are extremely heterogeneous at the 5' end

Transcription events are thought to precede gene rearrangement in the immunoglobulin (Ig) loci and may be the mechanism by which the various gene regions are made accessible for recombination. If this is the case, identification and characterization of transcripts from the Ig loci should permit a better understanding of the gene rearrangement process. We have isolated a 2.3 kb cDNA clone from the human pre-B cell line Nalm-1 that contains enhancer-specific sequences from the Ig heavy (H) chain gene locus. The 2.3 kb transcript initiated within the enhancer region and showed extreme 5' heterogeneity, with more than 50 initiation sites mapping near the Ig-specific octamer ATTTGCGT. Sequencing of the cDNA clone demonstrated that 644 nucleotides from the Ig enhancer region were incorporated as a leader exon spliced to the mu constant (Cmu) region. This leader exon contained many translation termination codons and may function to inhibit the translation of sterile Cmu polypeptides. Using an enhancer-derived probe, we detected two low-abundancy mRNA transcripts with sizes of 2.3 and 12 kb. Northern blot analysis suggested that the 12 kb transcript was the unspliced precursor mRNA of a VDJ rearrangement. The potential role of these enhancer-containing transcripts in the opening of the IgH chain gene for rearrangement and for class switching is discussed.

Positive and negative regulation of immunoglobulin gene expression by a novel B-cell-specific enhancer element

A new B-cell-specific enhancer element has been identified 3' of E4 and the octamerlike motifs in the human immunoglobulin heavy-chain gene enhancer. Tandem copies of this 67-bp MnlI-AluI fragment, when fused to the chloramphenicol acetyltransferase gene driven by the conalbumin promoter, stimulated transcription in B cells but not in Jurkat T cells or HeLa cells. Footprinting analysis revealed that the identical sequence CCGAAACTGAAAAGG, designated E6, was protected by nuclear extracts from B cells, T cells, or HeLa cells. Gel mobility shift assays using a synthetic E6 motif detected a B-cell-specific complex in addition to a ubiquitous band found also in T cells and HeLa cells. In agreement with the results of gel retardation assays, tandem copies of the E6 motif stimulated transcription in ARH77 and Raji cells but not in Jurkat or HeLa cells. Furthermore, a mutant E6 motif lost both in vitro binding activity and in vivo enhancer activity. In striking contrast to the mouse Ig heavy-chain enhancer, in which the octamer motif acts as a B-cell-specific enhancer element, the human enhancer contains an octamerlike sequence with one base substitution which bound octamer-binding proteins with only very low affinity and showed no enhancer activity of its own. Interestingly, the MnlI-AluI fragment could suppress the basal-level activity of the conalbumin promoter in both Jurkat and HeLa cells. Moreover, simian virus 40 enhancer activity was blocked by the MnlI-AluI fragment in HeLa cells but not in B cells. Thus, the novel enhancer element identified in this study is probably a target site for both positive and negative factors.

Activation of octamer-containing promoters by either octamer-binding transcription factor 1 (OTF-1) or OTF-2 and requirement of an additional B-cell-specific component for optimal transcription of immunoglobulin promoters

Several distinct octamer-binding transcription factors (OTFs) interact with the sequence ATTTGCAT (the octamer motif), which acts as a transcription regulatory element for a variety of differentially controlled genes. The ubiquitous OTF-1 plays a role in expression of the cell cycle-regulated histone H2b gene as well as several other genes, while the tissue-specific OTF-2 has been implicated in the tissue-specific expression of immunoglobulin genes. In an attempt to understand the apparent transcriptional selectivity of these factors, we have investigated the physical and functional characteristics of OTF-1 purified from HeLa cells and both OTF-1 and OTF-2 purified from B cells. High-resolution footprinting and mobility shift-competition assays indicated that these factors were virtually indistinguishable in binding affinities and DNA-protein contacts on either the H2b or an immunoglobulin light-chain (kappa) promoter. In addition, each of the purified factors showed an equivalent intrinsic capacity to activate transcription from either immunoglobulin promoters (kappa and heavy chain) or the H2b promoter in OTF-depleted HeLa and B-cell extracts. However, with OTF-depleted HeLa extracts, neither factor could restore immunoglobulin gene transcription to the relatively high level observed in unfractionated B-cell extracts. Restoration of full immunoglobulin gene activity appears to require an additional B-cell regulatory component which interacts with the OTFs. The additional B-cell factor could act either by facilitating interaction of OTF activation domains with components of the general transcriptional machinery or by contributing a novel activation domain.

Modulation of the IgH enhancer's cell type specificity through a genetic switch

Using defined regions of the immunoglobulin heavy-chain enhancer linked to minimal promoters and cDNAs that encode the two helix-loop-helix transcription factors ITF-1 and TFE3, we demonstrate that activity of an otherwise repressed enhancer can be stimulated in nonlymphoid cells. Repression in non-B cells is mediated by the microE5 motif. Derepression occurs at two levels. First, overexpression of ITF-1, and E12/E47-related protein that binds the microE5 motif, leads to transcriptional activation itself. Second, binding of ITF-1 physically displaces a repressor that normally blocks the stimulatory activity of TFE3, which binds the neighboring microE3 motif. TFE3 can only stimulate enhancer activity in the presence of ITF-1 or in the absence of a microE5 motif. Hence, one component of the enhancer's cell type specificity can be artificially modulated through a "genetic switch" in which activity is dictated by the relative levels of ITF-1 and a competing repressor.

Positive and negative regulation of immunoglobulin gene expression by a novel B-cell-specific enhancer element

A new B-cell-specific enhancer element has been identified 3' of E4 and the octamerlike motifs in the human immunoglobulin heavy-chain gene enhancer. Tandem copies of this 67-bp MnlI-AluI fragment, when fused to the chloramphenicol acetyltransferase gene driven by the conalbumin promoter, stimulated transcription in B cells but not in Jurkat T cells or HeLa cells. Footprinting analysis revealed that the identical sequence CCGAAACTGAAAAGG, designated E6, was protected by nuclear extracts from B cells, T cells, or HeLa cells. Gel mobility shift assays using a synthetic E6 motif detected a B-cell-specific complex in addition to a ubiquitous band found also in T cells and HeLa cells. In agreement with the results of gel retardation assays, tandem copies of the E6 motif stimulated transcription in ARH77 and Raji cells but not in Jurkat or HeLa cells. Furthermore, a mutant E6 motif lost both in vitro binding activity and in vivo enhancer activity. In striking contrast to the mouse Ig heavy-chain enhancer, in which the octamer motif acts as a B-cell-specific enhancer element, the human enhancer contains an octamerlike sequence with one base substitution which bound octamer-binding proteins with only very low affinity and showed no enhancer activity of its own. Interestingly, the MnlI-AluI fragment could suppress the basal-level activity of the conalbumin promoter in both Jurkat and HeLa cells. Moreover, simian virus 40 enhancer activity was blocked by the MnlI-AluI fragment in HeLa cells but not in B cells. Thus, the novel enhancer element identified in this study is probably a target site for both positive and negative factors.

Activation of octamer-containing promoters by either octamer-binding transcription factor 1 (OTF-1) or OTF-2 and requirement of an additional B-cell-specific component for optimal transcription of immunoglobulin promoters

Several distinct octamer-binding transcription factors (OTFs) interact with the sequence ATTTGCAT (the octamer motif), which acts as a transcription regulatory element for a variety of differentially controlled genes. The ubiquitous OTF-1 plays a role in expression of the cell cycle-regulated histone H2b gene as well as several other genes, while the tissue-specific OTF-2 has been implicated in the tissue-specific expression of immunoglobulin genes. In an attempt to understand the apparent transcriptional selectivity of these factors, we have investigated the physical and functional characteristics of OTF-1 purified from HeLa cells and both OTF-1 and OTF-2 purified from B cells. High-resolution footprinting and mobility shift-competition assays indicated that these factors were virtually indistinguishable in binding affinities and DNA-protein contacts on either the H2b or an immunoglobulin light-chain (kappa) promoter. In addition, each of the purified factors showed an equivalent intrinsic capacity to activate transcription from either immunoglobulin promoters (kappa and heavy chain) or the H2b promoter in OTF-depleted HeLa and B-cell extracts. However, with OTF-depleted HeLa extracts, neither factor could restore immunoglobulin gene transcription to the relatively high level observed in unfractionated B-cell extracts. Restoration of full immunoglobulin gene activity appears to require an additional B-cell regulatory component which interacts with the OTFs. The additional B-cell factor could act either by facilitating interaction of OTF activation domains with components of the general transcriptional machinery or by contributing a novel activation domain.

The importance of the 3'-enhancer region in immunoglobulin kappa gene expression

The first enhancers to be identified in the immunoglobulin gene loci are located in the J-C intron. However, deletion of the immunoglobulin kappa intron-enhancer has little effect on the transcription of kappa transgenes. Here we ask whether the second kappa enhancer which we recently identified at the 3'-end of the locus plays a role in kappa gene expression. We show that its omission leads to 20-40 fold lower expression of kappa transgenes and to poor allelic exclusion. Transfection experiments show that activity of the 3'-enhancer, like that of the kappa-intron enhancer, can be induced in a pre-B cell line by incubation with bacterial lipopolysaccharide. Whereas induction of the kappa-intron enhancer is due to induction of NF-kappa B activity, deletion mapping of the 3'-enhancer localises its activity to a 50 nucleotide region that lacks an NF-kappa B site; indeed the 3'-enhancer allows kappa expression in a cell line which lacks NF-kappa B. Thus, both the 3'- and intron-enhancers can be induced at the same stage of differentiation but by distinct pathways. Furthermore, unlike the intron-enhancer, the 3'-enhancer plays a critical role in the transcription of rearranged immunoglobulin kappa genes.

Complex regulation of the immunoglobulin mu heavy-chain gene enhancer: microB, a new determinant of enhancer function

The B-lymphocyte-specific activity of the immunoglobulin mu heavy-chain gene enhancer has been attributed to the octamer motif (ATTTGCAT) present within the enhancer that binds a B-cell-specific factor designated NF-A2/OTF-2. However, significant residual enhancer activity even after deletion of this element has suggested the presence of a second critical functional determinant. We have used deletion and mutational analyses to define an element, microB (TTTGGGGAA), that is essential for B-cell-specific enhancer activity in S194 myeloma cells in the absence of the octamer. Transfection analysis in a panel of lymphoid cell lines suggests that the presence of either microB or octamer leads to considerable enhancer activity in cell lines representing later stages of B-cell differentiation, whereas both elements are needed for function in cell lines representing earlier stages. Furthermore, in contrast to the results in pre-B-cell lines, both microB and octamer elements function independently in certain T-cell lines in which the mu enhancer is active.

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.

Complex regulation of the immunoglobulin mu heavy-chain gene enhancer: microB, a new determinant of enhancer function

The B-lymphocyte-specific activity of the immunoglobulin mu heavy-chain gene enhancer has been attributed to the octamer motif (ATTTGCAT) present within the enhancer that binds a B-cell-specific factor designated NF-A2/OTF-2. However, significant residual enhancer activity even after deletion of this element has suggested the presence of a second critical functional determinant. We have used deletion and mutational analyses to define an element, microB (TTTGGGGAA), that is essential for B-cell-specific enhancer activity in S194 myeloma cells in the absence of the octamer. Transfection analysis in a panel of lymphoid cell lines suggests that the presence of either microB or octamer leads to considerable enhancer activity in cell lines representing later stages of B-cell differentiation, whereas both elements are needed for function in cell lines representing earlier stages. Furthermore, in contrast to the results in pre-B-cell lines, both microB and octamer elements function independently in certain T-cell lines in which the mu enhancer is active.

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.

Cell-type-specific control elements of the lymphotropic papovavirus enhancer

Lymphotropic papovavirus (LPV) exhibits a highly restricted host range, in which only cells of primate B-lymphocyte origin are permissive for infection. Its enhancer element contributes to this tropism, since transcriptional potentiation is confined to cells of the hematopoietic lineage. Nuclear extracts from B and T cells, but not from HeLa cells, contain protein factors that interact specifically with the LPV 63-base-pair enhancer repeat, as demonstrated by DNase I footprinting and gel retardation experiments. Within the repeat three sequence motifs were identified: the core motif, the Pu box, and a novel element named T motif. Functional analysis demonstrated that these motifs as well as some sequences upstream of the repeat contribute to the optimal activity of the enhancer. There are clear differences between the patterns of binding of the B and T lymphocyte nuclear proteins to the enhancer which are also reflected in the transcriptional activity of the enhancer in both cell types. Furthermore, the activity of the LPV enhancer and its interaction with nuclear proteins seem to be regulated during B-cell differentiation.

Octamer-binding proteins in diverse hemopoietic cells

The immunoglobulin genes have B-cell-specific promoter and enhancer elements. The regulation of these elements is thought to be mediated to a large degree by the trans-activating factor oct-2, which binds the octamer element (ATTTGCAT). We have further examined the role of this octamer element in directing the lymphoid-specific expression of the immunoglobulin H enhancer. No direct relationship was found between the levels of expression of the Cmu gene and oct-2. Indeed, variable amounts of oct-2 were detected in all of the hemopoietic lineage cells tested in this study.

Octamer-binding proteins in diverse hemopoietic cells

The immunoglobulin genes have B-cell-specific promoter and enhancer elements. The regulation of these elements is thought to be mediated to a large degree by the trans-activating factor oct-2, which binds the octamer element (ATTTGCAT). We have further examined the role of this octamer element in directing the lymphoid-specific expression of the immunoglobulin H enhancer. No direct relationship was found between the levels of expression of the Cmu gene and oct-2. Indeed, variable amounts of oct-2 were detected in all of the hemopoietic lineage cells tested in this study.

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.

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.

DNA recognition element required for PUF-I mediated cell-type-specific transcription of the rat prolactin gene

The cell-type-specific transcription of the prolactin gene in vitro is mediated through the interaction of prolactin upstream factor I (PUF-I) with a 28 basepair region of the gene promoter (-63 to -36) which contains an 18 bp A+T-rich imperfect palindrome (-63 to -46). Base substitutions were introduced into 16 of the 18 palindromic residues by targeted saturation mutagenesis. The GH3 binding and in vitro transcription assays of the mutated promoters showed that base substitutions within the 5'-ATATTCA-3' sequence located at -52 to -46 were detrimental to PUF-I binding and its cell-type-specific transcriptional enhancement activity. Transcription assays of the mutated promoters performed with several nonpituitary-derived extracts demonstrated that a distal TATA box located from -59 to -53 promotes initiation at -27. Thus, the cell-type-specific cis-acting element required by PUF-I for DNA recognition is immediately adjacent to a general TATA sequence. Base substitutions that decreased +1 transcription and PUF-I binding concomitantly increased -27 initiation of RNA in vitro. We suggest that PUF-I binding in pituitary cells potentiates +1 transcription and represses alternative TATA box activity for initiation events occurring at -27. This is the first known report of a eukaryotic DNA binding protein that has both an activator and repressor activity for a single transcription unit.

Multiple sequence elements in the c-fos promoter mediate induction by cAMP

Induction of c-fos by cyclic AMP in NIH-3T3 cells is distinct from induction by serum. Whereas induction by serum is mediated by the serum response element (SRE), induction by cAMP does not require this element. In fact, no single sequence element in the c-fos promoter/enhancer is stringently required for the cAMP response. Rather, multiple sequence elements in the c-fos promoter/enhancer can mediate induction by cAMP independently. These elements are: (1) the region from -72 to -54, which contains a binding site for a cellular activating transcription factor (ATF); (2) the region from -225 to -99; (3) the region from -303 to -281, which is homologous to the consensus binding site for the transcription factor AP1; and (4) the region from -317 to -298, which contains the SRE. These sequence elements convey cAMP inducibility when fused to the cAMP-unresponsive 'minimal' fos promoter (-53 to +42). In addition, the c-fos regions from -700 to -63 and from -71 to -48 can confer cAMP inducibility to a heterologous promoter.

A distinct octamer-binding protein present in malignant melanoma cells

The octamer-binding proteins present in HeLa cells, B-cells and malignant melanoma cells were compared by a gel-electrophoresis DNA-binding assay. Using an extract from the malignant melanoma cells a complex was formed using a variety of octamer containing probes that was distinct from those found using either a HeLa or B-cell extract. DNAase 1 footprints and methylation interference patterns of the melanoma-specific octamer-binding protein were indistinguishable from those obtained with the HeLa factor NF-A1, except for preferential binding of the melanoma-specific factor to DNA methylated at two G residues 16 base-pairs 3' to the octamer motif. Competition analyses using a variety of wild-type and mutant probes showed that mutations affecting binding of NF-A1 similarly affected binding of the melanoma octamer-binding factor. These data also revealed the extreme flexibility of the octamer-binding site, with one probe sharing only 4 bases with the 8 base consensus sequence binding efficiently.

The pituitary-specific transcription factor GHF-1 is a homeobox-containing protein

Growth hormone factor 1 (GHF-1) is a pituitary-specific transcription factor that plays a critical role in cell type-specific expression of the growth hormone (GH) gene. Here, we describe the isolation of bovine and rat GHF-1 cDNA clones. These cDNAs encode proteins whose molecular mass, 33K, is identical to purified GHF-1 and whose sequence agrees with a partial GHF-1 peptide sequence. The predicted GHF-1 sequence contains a region, near its C-terminus, that exhibits considerable similarity to a homeobox consensus sequence. DNAase I footprinting with bacterially expressed fusion protein containing a fragment of GHF-1 encompassing the homeobox indicates that this region of the protein functions as its DNA binding domain. Expression of GHF-1 is restricted to cells of the somatotropic lineage in the pituitary. This remarkable specificity of GHF-1 expression correlates with the selective transcription of its target, the GH gene. Other mammalian homeobox-containing proteins may function similarly as transcription factors controlling cell type-specific expression in other locations.