Restricted Transcription Research Articles

Regulation of the infraabdominal regions of the bithorax complex of Drosophila by gap genes.

The expression of the abdominal-A and Abdominal-B genes of the bithorax complex of Drosophila is controlled by cis-regulatory infraabdominal regions. The activation of these regions along the anteroposterior axis of the embryo determines where abdominal-A and Abdominal-B are transcribed. There is spatially restricted transcription of the infraabdominal regions (infraabdominal transcripts) that may reflect this specific activation. We show that the gap genes hunchback, Krüppel, tailless and knirps control abdominal-A and Abdominal-B expression early in development. The restriction of abdominal-A and Abdominal-B transcription is preceded by (and requires) the spatially localized activation of regulatory regions, which can be detected by the distribution of infraabdominal transcripts. The activation of these regions (except the infraabdominal-8 one) could require no specific gap gene. Instead, a general mechanism of activation, combined with repression by gap genes in the anteroposterior axis, seems to be responsible for delimiting infraabdominal active domains. The gradients of the hunchback and Krüppel products seem to be key elements in this restricted activation.

Regionalization of the developing forebrain: a comparison of FORSE-1, Dlx-2, and BF-1

The FORSE-1 monoclonal antibody (mAb) was generated using a strategy designed to produce mAbs against neuronal cell surface antigens that might be regulated by regionally restricted transcription factors in the developing CNS. To determine whether FORSE-1 has a labeling pattern similar to that of known transcription factors, the expression of BF-1 and Dlx-2 was examined by in situ hybridization on sections serial to those labeled with FORSE-1. We find a striking overlap between BF-1 and FORSE-1 in the telencephalon; both are expressed in the lateral but not the medial walls of the telencephalon, and the boundaries of expression are apparently identical. FORSE-1 staining is detected prior to BF-1 expression in the neural tube, however. FORSE-1 and Dlx-2 have very different patterns of expression in the forebrain, suggesting that regulation by Dlx-2 cannot by itself explain the distribution of FORSE-1. However, they share some sharp boundaries in the diencephalon. In addition, FORSE-1 identifies some previously unknown boundaries in the developing forebrain. These results indicate that a new cell surface marker can be used to subdivide the embryonic telencephalon and diencephalon into regions smaller than previously described, providing necessary complexity to the developmental patterning in the forebrain.

FORSE-1: a positionally regulated epitope in the developing rat central nervous system

We designed a protocol to identify cell surface molecules expressed in restricted spatial patterns in the developing central nervous system (CNS) that might be regulated by regionally restricted transcription factors. The immunogen was a membrane fraction from NT2/D1 embryocarcinoma cells that were induced to differentiate into neurons and upregulate Hox gene expression in response to retinoic acid. One monoclonal antibody (mAb), FORSE-1, specifically labels the rostral rat CNS from the earliest stages. Staining is observed in the rostral but not caudal neural folds of the embryo prior to neural tube closure. Staining is enriched in the forebrain as compared to the rest of the CNS, until E18. Between E11.5 and E13.5, only certain areas of the telencephalon and diencephalon are labeled. Later, up to E17.5, FORSE-1 labeling is specifically restricted to the telencephalon, where a correlation with mitotic activity is apparent: the ventricular zone labels with FORSE-1, while the cortical plate is negative. The staining of the neuroepithelium is intensified by acetone fixation, which also reveals, between E11.5 and E13.5, a dorsoventrally restricted, FORSE-1-positive region of the spinal cord. After E18, the entire CNS is labeled, through adulthood. The mAb labels the surfaces of dissociated, living cells. Other, non-CNS areas of FORSE-1 labeling are nasal and otic placodes, nasal epithelium, nasal glands, and early (E9.5-10.5) endoderm. mAb FORSE-1 recognizes an epitope present on both a high-molecular-weight (> 200 kDa) proteoglycan from embryonic and early postnatal brain, and on a 80 kDa doublet that is restricted to the CNS in the adult. These findings suggest the FORSE-1 antigen as a candidate cell surface molecule for mediating regional specification from the earliest stages of CNS development.

Latent infection with bovine herpesvirus type 1

As with other alphaherpesviruses, the molecular mechanisms that underlie bovine herpesvirus type 1 (BHV-1) latency and reactivation are poorly understood. Restricted transcription of the BHV-1 genome has been described in latently infected neurons of the natural host and in the rabbit latency model. BHV-1 latency-associated transcription (LAT) is predominantly nuclear, approximately 1.0 to 1.2 kb in size, and anti-parallel to and overlapping an immediate-early gene. Down-regulation of LAT expression observed in ganglia during dexamethasone-induced viral reactivation, together with altered reactivation characteristics of a LAT-promoter deletion mutant suggests that expression and/or proper regulation of LAT is necessary for efficient viral reactivation.

The interaction of GATA-binding proteins and basal transcription factors with GATA box-containing core promoters. A model of tissue-specific gene expression.

The core promoters of the rat platelet factor 4 (PF4), mouse erythropoietin and chicken beta globin genes contain a GATA motif in place of the consensus TATAAA site. In the case of the PF4 gene, this site has been shown to play a critical role in restricting transcription to the megakaryocyte lineage. In order to understand the mechanism of tissue specificity, we investigated the function of the GATA box-containing promoters in vitro. Our studies show that the TATA-binding protein of TFIID is required for initiation of transcription from the GATA box-containing promoters. GATA-1 interacts with the core promoter GATA motif and inhibits generation of preinitiation complexes. The functional significance of the inhibition of preinitiation complexes is supported by in vitro transcription assays in which transcription from the PF4 and erythropoietin core promoters is suppressed by GATA-1. We also demonstrate that GATA-2 inhibits initiation of transcription from the PF4 core promoter. Based on these results, we propose a model in which repression of PF4 expression in nonmegakaryocytes is mediated, in part, by competition between GATA-binding proteins and basal factors for the core promoter.

Replication of lymphocytic choriomeningitis virus is restricted in terminally differentiated neurons

We have investigated the replication of lymphocytic choriomeningitis virus (LCMV) before and after the nerve growth factor (NGF)-induced transdifferentiation of PC12 cells from the chromaffin to the neuron-like phenotype. Untreated and NGF-treated cells were equally susceptible to LCMV infection; however, the viral yield was found to be 1,000-fold lower in NGF-differentiated PC12 cells. The reduced viral yield correlated with restricted LCMV replication and transcription within the infected cell, which was not caused by the lack of cell proliferation in the NGF-treated cells but rather was related to the induction or changes in expression levels of specific gene product(s) associated with the cell commitment to a neuronal phenotype. The return to the chromaffin phenotype after withdrawal of NGF restored normal LCMV yields as well as levels of viral replication and transcription. The finding of reduced viral replication in terminally differentiated neuronal cells has important implications for understanding the mechanism by which neurotropic viruses, such as LCMV, are able to establish a long-term persistent infection in the central nervous system in the absence of severe pathological changes.

The molecular basis of latent infections by alphaherpesviruses

Paradoxically, alphaherpesviruses, which otherwise are extremely lytic, establish reactivatable latent infections in their natural hosts; primarily, in nervous tissue. To accomplish this, lytic replication must not occur in neurons during the latent phase of infection, but is probably necessary for viral reactivation. Progress has been made in the last few years in describing molecular aspects of viral latency and reactivation. Restricted transcription of the viral genome is seen in latently infected neurons, with latency-associated transcription being antiparallel and overlapping viral immediate early genes. Results in animal latency systems using viral mutants containing deletions in this region of the genome indicate that latency-associated transcription has a significant role in viral latency, probably in establishment or reactivation of latent infection. The challenges, however, of understanding the complexities underlying conditional permissiveness of neurons for viral replication still lie ahead.

A positive role for histone acetylation in transcription factor access to nucleosomal DNA

Acetylation of the N-terminal tails of the core histones directly facilitates the recognition by TFIIIA of the 5S RNA gene within model chromatin templates. This effect is independent of a reduction in the extent of histone-DNA interactions or a change in DNA helical repeat; it is also independent of whether a histone tetramer or octamer inhibits TFIIIA binding. Removal of the N-terminal tails from the core histones also facilitates the association of TFIIIA with nucleosomal templates. We suggest that the histone tails have a major role in restricting transcription factor access to DNA and that their acetylation releases this restriction by directing dissociation of the tails from DNA and/or inducing a change in DNA configuration on the histone core to allow transcription factor binding. Acetylation of core histones might be expected to exert a major influence on the accessibility of chromatin to regulatory molecules.

Restricted transcription of varicella-zoster virus in latently infected human trigeminal and thoracic ganglia.

Normal human trigeminal and thoracic ganglia latently infected with varicella-zoster virus (VZV) were identified by polymerase chain reaction (PCR). Total RNA was extracted from these ganglia and treated with DNase until ganglionic RNA was free of VZV DNA as determined by PCR. Radiolabeled cDNA synthesized by priming with random oligonucleotides was hybridized to Southern blots containing recombinant clones that spanned greater than 95% of the VZV genome. The single region of the VZV genome detected was the 12.5-kb SalI C fragment located in the unique long segment of the viral genome. Two additional regions of the VZV genome, EcoRI G and SalI B, were detected in RNA from adult dorsal root ganglia and infant nervous system tissue.

Synaptic basal lamina contains a signal for synapse-specific transcription

Nuclei in the synaptic region of multinucleated skeletal myofibers are transcriptionally distinct, since acetylcholine receptor genes are transcribed at a high rate by these nuclei, but not by nuclei elsewhere in the myofiber. Although this spatially restricted transcription pattern is presumably imposed by the motor nerve, the continuous presence of the nerve is not required, since synapse-specific transcription persists after denervation. These results suggest either that a transcriptional signal persists at synaptic sites after nerve terminals have degenerated, or that a transcriptional pattern in the myofiber, once established, is stable in the absence of a nerve-derived signal. To distinguish between these possibilities, we denervated muscle and damaged the myofibers and specialized cells located near synaptic sites, and then studied transcription of an acetylcholine receptor gene in myofibers that regenerated in their original basal lamina sheaths, but remained denervated. We show that synapse-specific transcription is re-induced in these regenerated myofibers, and we conclude that a signal for synapse-specific transcription is stably maintained in the synaptic basal lamina.

Spatial restriction of AChR gene expression to subsynaptic nuclei.

Acetylcholine receptors (AChRs) and the mRNAs encoding the four AChR subunits are highly concentrated in the synaptic region of skeletal myofibers. The initial localization of AChRs to synaptic sites is triggered by the nerve and is caused, in part, by post-translational mechanisms that involve a redistribution of AChR protein in the myotube membrane. We have used transgenic mice that harbor a gene fusion between the murine AChR delta subunit gene and the human growth hormone gene to show that innervation also activates two independent transcriptional pathways that are important for establishing and maintaining this non-uniform distribution of AChR mRNA and protein. One pathway is triggered by signal(s) that are associated with myofiber depolarization, and these signals act to repress delta subunit gene expression in nuclei throughout the myofiber. Denervation of muscle removes this repression and causes activation of delta subunit gene expression in nuclei in non-synaptic regions of the myofiber. A second pathway is triggered by an unknown signal that is associated with the synaptic site, and this signal acts locally to activate delta subunit gene expression only in nuclei within the synaptic region. Synapse-specific expression, however, does not depend upon the continuous presence of the nerve, since transcriptional activation of the delta subunit gene in subsynaptic nuclei persists after denervation. Thus, the nuclei in the synaptic region of multinucleated skeletal myofibers are transcriptionally distinct from nuclei elsewhere in the myofiber, and this spatially restricted transcription pattern is presumably imposed initially by the nerve.

Synthetic oligonucleotides recreate Drosophila fushi tarazu zebra-stripe expression.

A complex array of activator and repressor elements located within 669 bp proximal to the fushi tarazu (ftz) transcriptional start site is sufficient to generate the "zebra-stripe" expression pattern characteristic of the ftz gene. P-element-mediated transformation and ftz promoter/lacZ fusion genes were used to characterize, in detail, several of these transcriptional control elements. By reconstructing promoters with synthetic oligonucleotides containing cis-regulators of stripe expression, we show that these regulatory sites can function as independent units to direct position-specific transcription in the Drosophila embryo. In particular, we demonstrate that multiple copies of a positive regulatory site can mediate expression in both the odd- and even-numbered parasegments throughout most of the germ band and that negative regulatory sites can transform a continuous pattern of gene expression into discrete stripes. The reconstructed promoter system presented provides an effective means of studying molecular mechanisms governing spatially restricted transcription in the early embryo.

Organization of the beta-galactoside alpha 2,6-sialyltransferase gene. Evidence for the transcriptional regulation of terminal glycosylation.

Little is currently known about the mechanisms by which the cellular glycosylation machinery is regulated to produce cell type-specific glycosylation sequences on glycoprotein and glycolipid sugar chains. Previously, we have shown that one enzyme involved in terminal glycosylation, beta-galactoside alpha 2,6-sialyltransferase, is expressed in a tissue-specific fashion, with the highest enzyme activity as well as mRNA levels being found in the liver. In addition, the liver mRNA was found to be 4.3 kilobases (kb) in size as compared to a larger message of 4.7 kb in other tissues. To understand the cellular regulation of expression of this sialyltransferase, we have cloned the rat gene encoding the 4.3-kb liver mRNA and found that it spans 40 kb of genomic DNA and contains 6 exons. The gene was found to be very similar in size and exon organization to the murine beta 1,4-galactosyltransferase gene, even though this enzyme has no sequence homology to alpha 2,6-sialyltransferase. The promoter responsible for the production of the liver alpha 2,6-sialyltransferase mRNA is approximately 50-fold more active in a hepatoma cell line known to express this enzyme (HepG2) than in a cell line shown not to express this enzyme (Chinese hamster ovary) and contains consensus binding sites for the liver restricted transcription factors HNF-1 and DBP as well as the transcription factors AP-1 and AP-2. These observations are in accord with the restricted expression of the 4.3-kb mRNA, and provides evidence for the cellular regulation of glycosylation at the level of transcription.

Pseudorabies virus latency: restricted transcription

Cloned pseudorabies virus (PRV) sequences representing over 80% of the viral genome were radiolabeled and individually hybridized to nucleic acid in the trigeminal ganglia of acutely and latently infected swine. In acutely infected animals, all cloned probes hybridized to PRV RNA and DNA. In contrast, during latency transcription was found to be limited to a selected region, corresponding to the IE gene, analogous to that of two other alpha-herpesviruses. Viral DNA was not detected in latently infected neurons by in situ hybridization.

Growth restriction of negative-strand-RNA viruses in a rat 3Y1 cell line

A rat fibroblast cell line, 3Y1 is nonpermissive for infection by several negative-strand-RNA viruses including influenza virus A, Sendai virus, Newcastle disease virus and vesicular stomatitis virus (VSV), but not refractory to that of a positive-strand-RNA virus, Sindbis virus. To elucidate the mechanism of the restricted viral growth, we compared the replication pattern of VSV in 3Y1 cells and in baby hamster kidney cells, which are fully permissive for those viruses. The results indicated that the restriction was imposed predominantly on the transcription of the viral RNA. The subsequent steps such as protein synthesis and nucleocapsid assembly appeared to occur normally, although these levels remained low due to the restricted transcription. Virus attachment onto, and penetration into, 3Y1 cells were also not restricted.

Human cytomegalovirus infection of kidney glomerular visceral epithelial and tubular epithelial cells in culture.

Evidence suggests that human cytomegalovirus is resident in the kidneys of seropositive donors at the time of transplantation, and CMV has been implicated in both glomerulonephritis and interstitial nephritis. In this study we assessed the interactions of CMV with two human renal cell types in culture: glomerular visceral epithelial cells (GVE) and renal tubular epithelial (RTE) cells. GVE permitted viral adsorption, penetration, nuclear translocation, and restricted viral transcription. However, early viral protein expression was not detectable by immunofluorescence and infectious virions were not produced. In contrast, retinoic acid-treated GVE permitted early viral protein expression and supported CMV replication. RTE also permitted viral adsorption and penetration. CMV-specific early proteins were readily observed by immunofluorescence, and CMV DNA replication was observed by DNA dot blot hybridization. Assays comparing viral yield with viral DNA synthesis indicated that RTE were capable of supporting persistent and prolonged viral expression without significant cell death for at least 55 days after infection. We believe that these findings should explain chronic viruria in individuals with symptomatic and asymptomatic CMV infection. In addition, GVE could also be a potential source of CMV transmission when altered by disease or transplantation.

The Relationship and Biology of Human Retroviruses

other animal retroviruses, including long terminal repeat, group-specific polymerase, envelope, and transactivation genes. Human retroviruses discovered to date have been associated with lymphoproliferative or cytopathic disease states. Human immunodeficiency virus (HIV) shares genomic sequence, structural features, replicative mechanisms, and cytopathic features with other animal lentiviruses. Lentiviruses, such as HIV, share the common biological features of inducing fusion and death of infected host cells. Restricted transcription of viral gene products (in concert with host factors) and antigenic variation (primarily in the envelope gene) allow these viruses

The relationship and biology of human retroviruses.

other animal retroviruses, including long terminal repeat, group-specific polymerase, envelope, and transactivation genes. Human retroviruses discovered to date have been associated with lymphoproliferative or cytopathic disease states. Human immunodeficiency virus (HIV) shares genomic sequence, structural features, replicative mechanisms, and cytopathic features with other animal lentiviruses. Lentiviruses, such as HIV, share the common biological features of inducing fusion and death of infected host cells. Restricted transcription of viral gene products (in concert with host factors) and antigenic variation (primarily in the envelope gene) allow these viruses

Tissue restricted and stage specific transcription is maintained within 411 nucleotides flanking the 5' end of the chicken alpha-skeletal actin gene.

alpha-skeletal actin message levels have been shown to be tightly regulated in chicken primary myoblast cultures. To test for gene elements required for muscle cell specific expression, DNA sequences containing the 5'-flanking regions of the chicken alpha-skeletal actin, beta-cytoplasmic actin, and the histone H2b genes were linked to the coding sequences of the chloramphenicol acetyltransferase gene and transfected into myogenic and non-myogenic cells. In contrast to beta-actin CAT hybrids, the alpha-skeletal actin CAT constructions displayed restricted CAT expression in transfected non-myogenic cells. We showed that a 411 nucleotide fragment flanking the 5' end of of the alpha-skeletal actin gene was responsible for a 9-15 fold increase in CAT enzymatic activity during myoblast fusion, versus only a transient 2 fold rise for the beta-actin and histone flanking sequences. These results indicate that DNA sequences within 411 bp of the 5' terminus of the alpha-skeletal actin gene influenced its cell type and stage specific expression.

In vitro transcription by purified yeast RNA polymerase II. Coarse promoter mapping on homologous cloned genes.

Clones of the yeast Tyl element and 2 microns plasmid have been selectively transcribed in vitro by partially or completely purified yeast RNA polymerase II. Electrophoretic analysis of whole and restricted ternary transcription complexes allows the localization of the in vitro actively transcribed regions of the analyzed genes. The DNA regions that actively promote in vitro transcription correspond to the nucleotide sequence that in the Tyl element encompasses the in vivo transcription initiation sites and that in the 2 micrometer plasmid encompasses the starting codons of two oppositely oriented potential protein coding frames. The transcription assay that we describe herein may be applied to analyze rapidly the in vitro transcription of clones genes, to localize transcription initiation sites on supercoiled templates and to evaluate the differential in vitro promoter strength in RNA polymerase II served genes. Data obtained with RNA polymerase II at two different stages of purification are presented in parallel. Studies with a completely purified enzyme should certainly be preferred although the use of a partially purified RNA polymerase II may be convenient and may reveal factors which affect specificity.