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PubMed2005

Interaction of NIMIN1 with NPR1 modulates PR gene expression in Arabidopsis.

The Arabidopsis thaliana NONEXPRESSER OF PR GENES1 (NPR1, also known as NIM1) protein is an essential positive regulator of salicylic acid (SA)-induced PATHOGENESIS-RELATED (PR) gene expression and systemic acquired resistance (SAR). PR gene activity is regulated at the level of redox-dependent nuclear transport of NPR1. NPR1 interacts with members of the TGA family of transcription factors that are known to bind to SA-responsive elements in the PR-1 promoter. In an attempt to identify proteins involved in SA-mediated signal transduction, we previously described the isolation of three novel genes encoding distinct albeit structurally related proteins designated NIMIN1 (for NIM1-INTERACTING1), NIMIN2, and NIMIN3 that interact with NPR1 in the yeast two-hybrid system. Here, we show that NIMIN1 and NPR1 can be copurified from plant extracts, providing biochemical evidence for their interaction. We provide functional evidence for this interaction by describing transgenic plants constitutively expressing high amounts of NIMIN1. These plants show reduced SA-mediated PR gene induction and a compromised SAR, thus mimicking the described phenotype conferred by npr1. Moreover, they showed reduced RESISTANCE gene-mediated protection. These effects were dependent on the ability of NIMIN1 to interact with NPR1. Mutant plants with a T-DNA insertion in NIMIN1 as well as transgenic plants with reduced NIMIN1 mRNA levels showed hyperactivation of PR-1 gene expression after SA treatment but no effect on the disease resistance phenotype. Our results strongly suggest that NIMIN1 negatively regulates distinct functions of NPR1, providing a mechanism to modulate specific features of SAR.

Arabidopsis↗

PubMed1997

Involvement of AP-2 in regulation of the R-FABP gene in the developing chick retina.

Little is known regarding the molecular pathways that underlie the retinal maturation process. We are studying the regulation of the retinal fatty-acid-binding protein (R-FABP) gene, highly expressed in retinal precursor cells, to identify DNA regulatory elements and transcriptional factors involved in retinal development. Although the upstream sequence of the R-FABP gene is extremely GC rich, CpG methylation in this region is not implicated in the regulation of this gene because the 5' flanking DNA remains unmethylated with tissue differentiation when there is a dramatic decrease in R-FABP transcript levels. Using a combination of DNase I hypersensitivity experiments, gel shift assays, and DNase I footprinting, we have found three sites of DNA-protein interaction within 205 bp of 5' flanking DNA in the undifferentiated retina and four sites in the differentiated retina. DNA transfection analysis indicates that the first two footprints located within 150 bp of 5' flanking DNA are required for high levels of transcription in primary undifferentiated retinal cultures. The first footprint includes a putative TATA box and Spl binding sites while the second footprint contains a consensus AP-2 DNA binding site. Supershift experiments using antibodies to AP-2 and methylation interference experiments indicate that an AP-2-like transcription factor present in both late-proliferative-stage retina and differentiated retina binds to the upstream region of the R-FABP gene. A combination of data including the expression profile of AP-2 during retinal development and DNA transfection analysis using constructs mutated at critical residues within the AP-2 binding site suggests that AP-2 is a repressor of R-FABP transcription.

Animals↗

PubMed2004

Predicting genetic regulatory response using classification.

MOTIVATION: Studying gene regulatory mechanisms in simple model organisms through analysis of high-throughput genomic data has emerged as a central problem in computational biology. Most approaches in the literature have focused either on finding a few strong regulatory patterns or on learning descriptive models from training data. However, these approaches are not yet adequate for making accurate predictions about which genes will be up- or down-regulated in new or held-out experiments. By introducing a predictive methodology for this problem, we can use powerful tools from machine learning and assess the statistical significance of our predictions. RESULTS: We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for predicting whether a gene is up- or down-regulated in a particular experiment based on (1) the presence of binding site subsequences ('motifs') in the gene's regulatory region and (2) the expression levels of regulators such as transcription factors in the experiment ('parents'). Thus, our learning task integrates two qualitatively different data sources: genome-wide cDNA microarray data across multiple perturbation and mutant experiments along with motif profile data from regulatory sequences. We convert the regression task of predicting real-valued gene expression measurements to a classification task of predicting +1 and -1 labels, corresponding to up- and down-regulation beyond the levels of biological and measurement noise in microarray measurements. The learning algorithm employed is boosting with a margin-based generalization of decision trees, alternating decision trees. This large-margin classifier is sufficiently flexible to allow complex logical functions, yet sufficiently simple to give insight into the combinatorial mechanisms of gene regulation. We observe encouraging prediction accuracy on experiments based on the Gasch S.cerevisiae dataset, and we show that we can accurately predict up- and down-regulation on held-out experiments. We also show how to extract significant regulators, motifs and motif-regulator pairs from the learned models for various stress responses. Our method thus provides predictive hypotheses, suggests biological experiments, and provides interpretable insight into the structure of genetic regulatory networks. AVAILABILITY: The MLJava package is available upon request to the authors. Supplementary: Additional results are available from http://www.cs.columbia.edu/compbio/geneclass

Binding Sites↗

PubMed2005

Overall control of nitrogen metabolism in Lactococcus lactis by CodY, and possible models for CodY regulation in Firmicutes.

CodY, a pleiotropic transcriptional regulator conserved in low G+C species of Gram-positive bacteria, was previously described to be the central regulator of proteolysis in Lactococcus lactis. In this study, over 100 potential CodY targets were identified by DNA-microarray analysis. Complementary transcriptional analysis experiments were carried out to validate the newly defined CodY regulon. Moreover, the direct role of CodY in the regulation of several target genes was demonstrated by gel retardation experiments. Interestingly, 45 % of CodY-dependent genes encode enzymes involved in amino acid biosynthesis pathways, while most of the other genes are involved in functions related to nitrogen supply. CodY of L. lactis represents the first example of a regulator in Gram-positive bacteria that globally controls amino acid biosynthesis. This global control leads to growth inhibition in several amino-acid-limited media containing an excess of isoleucine. A conserved 15 nt palindromic sequence (AATTTTCNGAAAATT), the so-called CodY-box, located in the vicinity of the -35 box of target promoter regions was identified. Relevance of the CodY-box as an operator for CodY was demonstrated by base substitutions in gel retardation experiments. This motif is also frequently found in the promoter region of genes potentially regulated by CodY in other Gram-positive bacteria.

Bacterial Proteins↗

PubMed2006

A gene-centered C. elegans protein-DNA interaction network.

Transcription regulatory networks consist of physical and functional interactions between transcription factors (TFs) and their target genes. The systematic mapping of TF-target gene interactions has been pioneered in unicellular systems, using "TF-centered" methods (e.g., chromatin immunoprecipitation). However, metazoan systems are less amenable to such methods. Here, we used "gene-centered" high-throughput yeast one-hybrid (Y1H) assays to identify 283 interactions between 72 C. elegans digestive tract gene promoters and 117 proteins. The resulting protein-DNA interaction (PDI) network is highly connected and enriched for TFs that are expressed in the digestive tract. We provide functional annotations for approximately 10% of all worm TFs, many of which were previously uncharacterized, and find ten novel putative TFs, illustrating the power of a gene-centered approach. We provide additional in vivo evidence for multiple PDIs and illustrate how the PDI network provides insights into metazoan differential gene expression at a systems level.

Animals↗

PubMed2006

Effect of mutation on the dissociation and recombination dynamics of CO in transcriptional regulator CooA: a picosecond infrared transient absorption study.

The CO ligation process in a mutant (H77G) of CooA, the CO-sensing transcriptional regulator in Rhodospirillum rubrum, is studied with femtosecond time-resolved transient absorption spectroscopy in the mid-infrared region. Following photolyzing excitation, a transient bleach in the vibrational region of bound CO due to the CO photodissociation is detected. In contrast to the spectra of the wild-type (WT) CooA, the transient bleach spectra of H77G CooA show a bimodal shape with peaks shifting to the lower frequency during spectral evolution. The CO recombination dynamics show single-exponential behavior, and the CO escaping yield is higher than that of the WT CooA. A reorientation process of CO relative to the heme plane during recombination is revealed by anisotropy measurements. These phenomena indicate changes in the protein response to the CO ligation and suggest an alteration to the CO environment caused by the mutation. On the basis of these results, the role of His77 in the CO-dependent activation of CooA and a possible activation mechanism involving collaborative movement of the heme and the amino residues at both sides of the heme plane are discussed.

Bacterial Proteins↗

PubMed2005

MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes.

The phytohormone auxin plays critical roles during plant growth, many of which are mediated by the auxin response transcription factor (ARF) family. MicroRNAs (miRNAs), endogenous 21-nucleotide riboregulators, target several mRNAs implicated in auxin responses. miR160 targets ARF10, ARF16, and ARF17, three of the 23 Arabidopsis thaliana ARF genes. Here, we describe roles of miR160-directed ARF17 posttranscriptional regulation. Plants expressing a miRNA-resistant version of ARF17 have increased ARF17 mRNA levels and altered accumulation of auxin-inducible GH3-like mRNAs, YDK1/GH3.2, GH3.3, GH3.5, and DFL1/GH3.6, which encode auxin-conjugating proteins. These expression changes correlate with dramatic developmental defects, including embryo and emerging leaf symmetry anomalies, leaf shape defects, premature inflorescence development, altered phyllotaxy along the stem, reduced petal size, abnormal stamens, sterility, and root growth defects. These defects demonstrate the importance of miR160-directed ARF17 regulation and implicate ARF17 as a regulator of GH3-like early auxin response genes. Many of these defects resemble phenotypes previously observed in plants expressing viral suppressors of RNA silencing and plants with mutations in genes important for miRNA biogenesis or function, providing a molecular rationale for phenotypes previously associated with more general disruptions of miRNA function.

Arabidopsis↗

PubMed2005

Discriminative discovery of transcription factor binding sites from location data.

MOTIVATION: The availability of genome-wide location analyses based on chromatin immunoprecipitation (ChIP) data gives a new insight for in silico analysis of transcriptional regulations. RESULTS: We propose a novel discriminative discovery framework for precisely identifying transcriptional regulatory motifs from both positive and negative samples (sets of upstream sequences of both bound and unbound genes by a transcription factor (TF)) based on the genome-wide location data. In this framework, our goal is to find such discriminative motifs that best explain the location data in the sense that the motifs precisely discriminate the positive samples from the negative ones. First, in order to discover an initial set of discriminative substrings between positive and negative samples, we apply a decision tree learning method which produces a text-classification tree. We extract several clusters consisting of similar substrings from the internal nodes of the learned tree. Second, we start with initial profile-HMMs constructed from each cluster for representing putative motifs and iteratively refine the profile-HMMs to improve the discrimination accuracies. Our genome-wide experimental results on yeast show that our method successfully identifies the consensus sequences for known TFs in the literature and further presents significant performances for discriminating between positive and negative samples in all the TFs, while most other motif detecting methods show very poor performances on the problem of discriminations. Our learned profile-HMMs also improve false negative predictions of ChIP data.

Algorithms↗

PubMed2006

Plasticity of the cis-regulatory input function of a gene.

The transcription rate of a gene is often controlled by several regulators that bind specific sites in the gene's cis-regulatory region. The combined effect of these regulators is described by a cis-regulatory input function. What determines the form of an input function, and how variable is it with respect to mutations? To address this, we employ the well-characterized lac operon of Escherichia coli, which has an elaborate input function, intermediate between Boolean AND-gate and OR-gate logic. We mapped in detail the input function of 12 variants of the lac promoter, each with different point mutations in the regulator binding sites, by means of accurate expression measurements from living cells. We find that even a few mutations can significantly change the input function, resulting in functions that resemble Pure AND gates, OR gates, or single-input switches. Other types of gates were not found. The variant input functions can be described in a unified manner by a mathematical model. The model also lets us predict which functions cannot be reached by point mutations. The input function that we studied thus appears to be plastic, in the sense that many of the mutations do not ruin the regulation completely but rather result in new ways to integrate the inputs.

Base Sequence↗

PubMed2006

A hidden Markov model approach for determining expression from genomic tiling micro arrays.

BACKGROUND: Genomic tiling micro arrays have great potential for identifying previously undiscovered coding as well as non-coding transcription. To-date, however, analyses of these data have been performed in an ad hoc fashion. RESULTS: We present a probabilistic procedure, ExpressHMM, that adaptively models tiling data prior to predicting expression on genomic sequence. A hidden Markov model (HMM) is used to model the distributions of tiling array probe scores in expressed and non-expressed regions. The HMM is trained on sets of probes mapped to regions of annotated expression and non-expression. Subsequently, prediction of transcribed fragments is made on tiled genomic sequence. The prediction is accompanied by an expression probability curve for visual inspection of the supporting evidence. We test ExpressHMM on data from the Cheng et al. (2005) tiling array experiments on ten Human chromosomes. Results can be downloaded and viewed from our web site. CONCLUSION: The value of adaptive modelling of fluorescence scores prior to categorisation into expressed and non-expressed probes is demonstrated. Our results indicate that our adaptive approach is superior to the previous analysis in terms of nucleotide sensitivity and transfrag specificity.

Algorithms↗

PubMed2006

Comparative genomics of regulation of heavy metal resistance in Eubacteria.

BACKGROUND: Heavy metal resistance (HMR) in Eubacteria is regulated by a variety of systems including transcription factors from the MerR family (COG0789). The HMR systems are characterized by the complex signal structure (strong palindrome within a 19 or 20 bp promoter spacer), and usually consist of transporter and regulator genes. Some HMR regulons also include detoxification systems. The number of sequenced bacterial genomes is constantly increasing and even though HMR resistance regulons of the COG0789 type usually consist of few genes per genome, the computational analysis may contribute to the understanding of the cellular systems of metal detoxification. RESULTS: We studied the mercury (MerR), copper (CueR and HmrR), cadmium (CadR), lead (PbrR), and zinc (ZntR) resistance systems and demonstrated that combining protein sequence analysis and analysis of DNA regulatory signals it was possible to distinguish metal-dependent members of COG0789, assign specificity towards particular metals to uncharacterized loci, and find new genes involved in the metal resistance, in particular, multicopper oxidase and copper chaperones, candidate cytochromes from the copper regulon, new cadmium transporters and, possibly, glutathione-S-transferases. CONCLUSION: Our data indicate that the specificity of the COG0789 systems can be determined combining phylogenetic analysis and identification of DNA regulatory sites. Taking into account signal structure, we can adequately identify genes that are activated using the DNA bending-unbending mechanism. In the case of regulon members that do not reside in single loci, analysis of potential regulatory sites could be crucial for the correct annotation and prediction of the specificity.

Bacteria↗

PubMed2006

VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees.

Variable order Markov models and variable order Bayesian trees have been proposed for the recognition of transcription factor binding sites, and it could be demonstrated that they outperform traditional models, such as position weight matrices, Markov models and Bayesian trees. We develop a web server for the recognition of DNA binding sites based on variable order Markov models and variable order Bayesian trees offering the following functionality: (i) given datasets with annotated binding sites and genomic background sequences, variable order Markov models and variable order Bayesian trees can be trained; (ii) given a set of trained models, putative DNA binding sites can be predicted in a given set of genomic sequences and (iii) given a dataset with annotated binding sites and a dataset with genomic background sequences, cross-validation experiments for different model combinations with different parameter settings can be performed. Several of the offered services are computationally demanding, such as genome-wide predictions of DNA binding sites in mammalian genomes or sets of 10(4)-fold cross-validation experiments for different model combinations based on problem-specific data sets. In order to execute these jobs, and in order to serve multiple users at the same time, the web server is attached to a Linux cluster with 150 processors. VOMBAT is available at http://pdw-24.ipk-gatersleben.de:8080/VOMBAT/.

Algorithms↗

PubMed2006

The transcription factor Yin Yang 1 is an activator of BACE1 expression.

The beta-site amyloid precursor protein-cleaving enzyme 1 (BACE1) is a prerequisite for the generation of beta-amyloid peptides, the principle constituents of senile plaques in the brains of patients with Alzheimer's disease (AD). BACE1 expression and enzymatic activity are increased in the AD brain, but the regulatory mechanisms of BACE1 expression are largely unknown. Here we show that Yin Yang 1 (YY1), a highly conserved and multifunctional transcription factor, binds to its putative recognition sequence within the BACE1 promoter and stimulates BACE1 promoter activity in rat pheochromocytoma 12 (PC12) cells, rat primary neurones and astrocytes. In rat brain YY1 and BACE1 are widely expressed by neurons, but there was only a minor proportion of neurones that co-expressed YY1 and BACE1, suggesting that YY1 is not required for constitutive neuronal BACE1 expression. Resting astrocytes in the untreated rat brain did not display either YY1 or BACE1 immunoreactivity. When chronically activated, however, astrocytes expressed both YY1 and BACE1 proteins, indicating that YY1 is important for the stimulated BACE1 expression by reactive astrocytes. This is further emphasized by the expression of YY1 and BACE1 by reactive astrocytes in proximity to beta-amyloid plaques in the AD brain. Our observations suggest that interfering with expression, translocation or binding of YY1 to its BACE1 promoter-specific sequence may have therapeutic potential for treating patients with AD.

Alzheimer Disease↗

PubMed2006

On counting position weight matrix matches in a sequence, with application to discriminative motif finding.

MOTIVATION AND RESULTS: The position weight matrix (PWM) is a popular method to model transcription factor binding sites. A fundamental problem in cis-regulatory analysis is to "count" the occurrences of a PWM in a DNA sequence. We propose a novel probabilistic score to solve this problem of counting PWM occurrences. The proposed score has two important properties: (1) It gives appropriate weights to both strong and weak occurrences of the PWM, without using thresholds. (2) For any given PWM, this score can be computed while allowing for occurrences of other, a priori known PWMs, in a statistically sound framework. Additionally, the score is efficiently differentiable with respect to the PWM parameters, which has important consequences for designing search algorithms. The second problem we address is to find, ab initio, PWMs that have high counts in one set of sequences, and low counts in another. We develop a novel algorithm to solve this "discriminative motif-finding problem", using the proposed score for counting a PWM in the sequences. The algorithm is a local search technique that exploits derivative information on an objective function to enhance speed and performance. It is extensively tested on synthetic data, and shown to perform better than other discriminative as well as non-discriminative PWM finding algorithms. It is then applied to cis-regulatory modules involved in development of the fruitfly embryo, to elicit known and novel motifs. We finally use the algorithm on genes predictive of social behavior in the honey bee, and find interesting motifs. AVAILABILITY: The program is available upon request from the author.

Algorithms↗

PubMed2006

Inferring direct regulatory targets from expression and genome location analyses: a comparison of transcription factor deletion and overexpression.

BACKGROUND: Effects on gene expression due to environmental or genetic changes can be easily measured using microarrays. However, indirect effects on expression can be substantial. The indirect effects of a perturbation need to be distinguished from the direct effects if we are to understand the structure and behavior of regulatory networks. RESULTS: The most direct way to perturb a transcriptional network is to alter transcription factor activity. Here, for the first time, we compare expression changes and genomic binding in a simple regulon under conditions of both low and high transcription factor activity. Specifically, we assessed the effects on expression and binding due to deletion of the yeast LEU3 transcription factor gene and effects due to elevation of Leu3 activity. Leu3 activity was elevated through overexpression and the introduction of a mutation that renders the protein constitutively active. Genes that are bound and/or regulated by Leu3 under one or both conditions were characterized in terms of their functional annotations and their predicted potential to be bound by Leu3. We also assessed the evolutionary conservation of the predicted binding potential using a novel alignment-independent method. Both perturbations yield genes that are likely to be direct targets of Leu3, including most of the classically defined targets. Additional direct targets are identified by each of the methods. However, experimental and computational criteria suggest that most genes whose expression is affected by the Leu3 genotype are unlikely to be regulated by binding of the protein. CONCLUSION: Most genes that are differentially expressed by Leu3 are not direct targets despite the exceptional simplicity of the regulon, and the unusually direct nature of the perturbations investigated. These conclusions are reached through computational analyses that support and extend chromatin immunoprecipitation data on the identities of direct targets. These results have implications for the interpretation of expression experiments, especially in cases for which chromatin immunoprecipitation data are unavailable, incomplete, or ambiguous.

2-Isopropylmalate Synthase↗

PubMed2006

Topology of splicing and snRNP biogenesis in dinoflagellate nuclei.

BACKGROUND INFORMATION: Dinoflagellates are protists that are hypothesized to have experienced a secondary loss of histones. Amongst eukaryotes, they are unique in lacking these proteins. To date, information on the mechanisms involving remodelling, transcription and splicing of their chromatin is limited. Dinoflagellate genes lack TATA boxes and downstream polyadenylation sites and particular linear arrangements. They have an alpha-amanitin-sensitive RNA polymerase, specific transcription factors and regulators, and both transcriptional and post-transcriptional regulation of gene expression. Dinoflagellates produce either polycistronic or discrete mRNAs, and have conserved snRNAs (small nuclear RNAs), indicating that their genes are spliced. RESULTS: Five representative dinoflagellate species (Amphidinium carterae, Akashiwo sanguinea, Alexandrium lusitanicum, Alexandrium fundyense and Prorocentrum micans), which show diversity in their DNA content, nuclear organization and taxonomic position, were investigated. The nuclear distribution and ultrastructural organization of splicing and snRNP (small nuclear ribonucleoprotein) biogenesis were determined by fluorescent and electron microscopy immunolabelling with Y12 sera [recognizing the sDMA (symmetrical dimethylarginine) domain of Sm and other nuclear proteins], anti-p105-PANA [proliferation-associated nuclear antigen; a marker of IGs (interchromatin granules)] and anti-DNA antibodies. In parallel, ultrastructural analysis, including cytochemical staining for RNA, phosphorylated proteins and DNA, was carried out. Splicing factors were distributed in a diffuse perichromosomal layer containing perichromatin granules and fibrils that co-localized with the decondensed peripheral DNA loops, but not with the main chromosome body. Interchromosomal domains with IGs and Cajal-like bodies were also detected. CONCLUSIONS: Dinoflagellates are rather dissimilar to other eukaryotes in their genomes, their mechanisms of gene expression and their chromosome ultrastructure. However, they share common splicing nuclear domains and snRNP biogenesis with that of other eukaryotes.

Animals↗

PubMed2006

The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in gram-positive bacteria.

CodY is a global regulator of transcription in gram-positive bacteria. It represses during growth genes required for adaptation to nutrient limitation, including virulence genes in some human pathogens. CodY activity is regulated by GTP and branched chain amino acids, metabolites whose intracellular concentrations drop as cells enter stationary phase. Although CodY has a highly conserved sequence, it has no significant similarity to proteins of known structure. Here we report crystal structures of two fragments of CodY from Bacillus subtilis that clearly constitute its cofactor and DNA binding domains and reveal that CodY is a chimera of previously observed folding units. The N-terminal cofactor-binding fragment adopts a fold reminiscent of the GAF domains found in cyclic nucleotide phosphodiesterases and adenylate cyclases. It is a dimer stabilized by an intermolecular six alpha-helical bundle that buries an extensive apolar surface rich in residues invariant in CodY orthologues. The branched chain amino acid ligands reside in hydrophobic pockets of each monomer distal to the dimer-forming surface. The structure of the C-terminal DNA binding domain belongs to the winged helix-turn-helix family. The implications of the structure for DNA binding by CodY and its control by cofactor binding are discussed.

Adenylyl Cyclases↗

PubMed2006

Astrocyte heterogeneity revealed by expression of a GFAP-LacZ transgene.

Glial fibrillary acidic protein (GFAP) is an intermediate filament protein present primarily in astrocytes. The gene is first expressed as astrocytes mature, and in the adult is strongly upregulated in response to CNS damage. Thus, in addition to its astrocyte specificity, transcriptional regulation of the GFAP gene is of interest as a reporter of CNS signaling during development and injury. Several laboratories have shown that approximately 2 kb of 5'-flanking DNA of the human or mouse GFAP gene is sufficient to direct transgene expression to astrocytes and to confer developmental and injury-induced regulation. Enhancer regions have been identified adjacent to the basal promoter and about 1500 bp upstream of the RNA start site. Juxtaposition of these two segments yielded a 447 bp promoter, gfa28, which strongly drove reporter activity in transfected glioma cells. We report here that in mice a gfa28-lacZ transgene expresses in only certain brain regions, revealing an unexpected heterogeneity among astrocytes. The restricted pattern of expression is present early in development, is not altered by injury, and is preserved in cultured astrocytes. However, astrocytes cultured from an inactive region strongly express a transiently transfected gfa28-lacZ construct, and activity of the embedded gfa28-lacZ transgene is partially restored by treatment with a histone deacetylase inhibitor. These results indicate that the absence of gfa28-lacZ expression in specific brain regions results from a developmental failure to remodel GFAP chromatin to an open structure. Thus, expression of the gfa28-lacZ transgene appears to serendipitously mark a distinct set of astrocyte precursors.

Animals↗