bluuebunny/crossref_metadata_2025 huggingface dataset:
A unique zinc finger protein is associated preferentially with active ecdysone-responsive loci in Drosophila.
Authors: Amero S A , Elgin S C , Beyer A L
Published: June 2007

Using an immunochemical approach, we have identified a unique antigen, PEP (protein on ecdysone puffs), which is associated in third-instar larvae with the active ecdysone-regulated loci on polytene chromosomes; PEP is not associated with most intermolt puffs and is found on some, but not all, heat shock-induced puffs. The distribution pattern changes with changing puffing patterns in the developmental program. We have screened an expression library and recovered a cDNA clone encoding PEP. PEP possesses multiple potential nucleic acid- and protein- binding regions: a glycine- and asparagine-rich amino terminus, four zinc finger motifs, two very acidic segments, two short basic stretches, and an alanine- and proline-rich carboxyl terminus. The Pep gene maps by in situ hybridization to the cytological locus 74F, adjacent to the early ecdysone-responsive region; however, the gene is not regulated by ecdysone at the level of transcription. The pattern of Pep expression through development suggests that maternal Pep gene transcripts are supplied to the embryo, and that the abundance of Pep gene transcripts decreases to a lower, fairly constant level thereafter. This unusual protein may play a role in the process of gene activation, or possibly in RNA processing, for a defined set of developmentally regulated loci.
The role of branchpoint and 3'-exon sequences in the control of balanced splicing of avian retrovirus RNA.
Authors: Fu X D , Katz R A , Skalka A M , Maniatis T
Published: June 2007

We previously described an avian sarcoma-leukosis virus (ASLV) insertion mutation that causes a decrease in the ratio of unspliced to spliced RNA in vivo, resulting in a replication defect. Pseudorevertant viruses containing cis-acting suppressor mutations that restored the normal ratio were isolated. One class of the suppressor mutations consists of single-base changes or small deletions near the 3' splice site, while another consists of deletions in the 3' exon. In this paper we report results from an in vitro analysis of wild-type, mutant, and pseudorevertant pre-mRNA splicing. We find that wild-type RNA is spliced inefficiently in vitro, and that the insertion mutation and suppressors act directly at the level of splicing. Characterization of splicing intermediates reveals that the insertion mutation and suppressor mutations located within the intron alter the pattern of lariat formation. In contrast, suppressor mutations consisting of 3' exon deletions act at an earlier step in the splicing pathway. Thus, the efficiency of splicing at the env 3' splice site can be affected at the level of spliceosome assembly, lariat formation, or cleavage at the 3' splice site and exon ligation.
Two distinct destabilizing elements in the c-fos message trigger deadenylation as a first step in rapid mRNA decay.
Authors: Shyu A B , Belasco J G , Greenberg M E
Published: June 2007

The mechanisms by which c-fos mRNA is targeted for decay have been examined. Rapid removal of the poly(A) tail occurs before the transcribed portion of the c-fos message is degraded. Identification of the determinants that mediate c-fos message deadenylation reveals that they coincide directly with previously characterized determinants of c-fos mRNA instability, one in the protein-coding region and the other an AU-rich element (ARE) in the 3'-untranslated region. Insertion of either of these c-fos instability elements into the stable beta-globin message confers the property of rapid deadenylation. Mutation of the ARE indicates that this sequence controls two steps in the process of c-fos mRNA degradation: removal of the poly(A) tail, which does not require intact AUUUA pentanucleotides within the ARE, and subsequent degradation of the transcribed portion of the message, which appears to be dependent on the AUUUA pentanucleotides. These results indicate that structurally distinct instability determinants within the transcribed portion of labile messages can function by promoting rapid removal of the poly(A) tail as a first step in the decay process.
Illegitimate recombination in plants: a model for T-DNA integration.
Authors: Gheysen G , Villarroel R , Van Montagu M
Published: June 2007

Agrobacterium tumefaciens is a soil bacterium capable of transferring DNA (the T-DNA) to the genome of higher plants, where it is then stably integrated. Six T-DNA inserts and their corresponding preinsertion sites were cloned from Arabidopsis thaliana and analyzed. Two T-DNA integration events from Nicotiana tabacum were included in the analysis. Nucleotide sequence comparison of plant target sites before and after T-DNA integration showed that the T-DNA usually causes only a small (13-28 bp) deletion in the plant DNA, but larger target rearrangements can occur. Short homologies between the T-DNA ends and the target sites, as well as the presence of filler sequences at the junctions, indicate that T-DNA integration is mediated by illegitimate recombination and that these processes in plants are very analogous to events in mammalian cells. We propose a model for T-DNA integration on the basis of limited base-pairing for initial synapsis, followed by DNA repair at the junctions. Variations of the model can explain the formation of filler DNA at the junctions by polymerase slipping and template switching during DNA repair synthesis and the presence of larger plant target DNA rearrangements.
Identification of functional domains in the maize transcriptional activator C1: comparison of wild-type and dominant inhibitor proteins.
Authors: Goff S A , Cone K C , Fromm M E
Published: June 2007

Genes encoding fusions between the maize regulatory protein C1 and the yeast transcriptional activator GAL4 and mutant C1 proteins were assayed for their ability to trans-activate anthocyanin biosynthetic genes in intact maize tissues. The putative DNA-binding region of C1 fused to the transcriptional activation domain of GAL4 activated transcription of anthocyanin structural gene promoters in c1 aleurones, c1 Rscm2 embryos, and c1 r embryogenic callus. Cells receiving these constructs accumulated purple anthocyanin pigments. The C1 acidic region fused to the GAL4 DNA-binding domain activated transcription of a GAL4-regulated promoter. An internal deletion of C1 also induced pigmentation; however, frameshifts in either the amino-terminal basic or carboxy-terminal acidic region blocked trans-activation, and the latter generated a dominant inhibitory protein. Fusion constructs between the wild-type C1 cDNA and the dominant inhibitor allele C1-I cDNA were used to identify the amino acid changes in C1 responsible for the C1-I inhibitory phenotype. Results from these studies establish that amino acids within the myb-homologous domain are critical for transcriptional activation.
The human t(1;19) translocation in pre-B ALL produces multiple nuclear E2A-Pbx1 fusion proteins with differing transforming potentials.
Authors: Kamps M P , Look A T , Baltimore D
Published: June 2007

The t(1;19) translocation that characterizes 25% of pediatric pre-B cell acute lymphoblastic leukemias (pre-B ALL) produces a chimeric gene, joining 5' sequences that encode a transcriptional activator domain of E2A with 3' sequences that, in part, encode a homeo box domain of a new gene called pbx1. Two E2A-pbx1 transcripts have been cloned. They encode the putative fusion proteins, p85(E2A-Pbx1) and p77(E2A-Pbx1), which differ in Pbx1 sequences alone, containing unique carboxyl termini whose sequences diverge after the Pbx1 homeo box. In this study, an antiserum to Pbx1 was used to investigate the identity and abundance of E2A-Pbx1 fusion proteins in both the pre-B ALL cell line, 697, and in cryopreserved leukemic bone marrow cells, obtained from six children with t(1;19)-positive pre-B ALL. Five species of E2A-Pbx1 proteins were identified in all cells containing t(1;19), two of which were indistinguishable from in vitro-translated p85(E2A-Pbx1) and p77(E2A-Pbx1). To assess the biological properties of p85(E2A-Pbx1) and p77(E2A-Pbx1) in fibroblasts, the cDNAs encoding these proteins were cloned into retroviral vectors, and each was introduced into NIH-3T3 cells. Both p85(E2A-Pbx1) and p77(E2A-Pbx1) are localized in the nucleus, and expression of either resulted in malignant conversion of NIH-3T3 cells as assayed by tumor formation in nude mice. When scored by focus formation, density-independent growth, and growth in agar assays, p77(E2A-Pbx1) was a much more potent transforming protein than was p85(E2A-Pbx1). Because subtle mutations in p85(E2A-Pbx1) converted its transforming activity into that of p77(E2A-Pbx1), we suggest that a sequence within the unique carboxyl terminus of p85(E2A-Pbx1) serves to negatively regulate its biochemical activity.
AGL1-AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes.
Authors: Ma H , Yanofsky M F , Meyerowitz E M
Published: June 2007

The predicted products of floral homeotic genes, AGAMOUS (AG) from Arabidopsis thaliana and DEFICIENS A (DEF A) from Antirrhinum majus, have been shown previously to share strong sequence similarity with transcription factors from humans (SRF) and yeast (MCM1). The conserved sequence between these proteins is localized within a domain known to be necessary for the DNA binding and for the dimerization of SRF. We have isolated six new genes from A. thaliana, AGL1-AGL6, which also have this conserved sequence motif. On the basis of the sequence comparison between the AG and AGL genes, they can be assigned to two subfamilies of a large gene family. RNA dot blot analysis indicates that five of these genes (AGL1, AGL2, AGL4, AGL5, and AGL6) are preferentially expressed in flowers. In addition, in situ RNA hybridization experiments with AGL1 and AGL2 show that their mRNAs are detected in some floral organs but not in others. Our results suggest that these genes may act to control many steps of Arabidopsis floral morphogenesis. In contrast, the AGL3 gene is expressed in vegetative tissues as well as in flowers, suggesting that it functions in a broader range of tissues. We discuss possible roles of this gene family during the evolution of flowers.
Transcriptional activation of mouse retrotransposons in vivo: specific expression in steroidogenic cells in response to trophic hormones.
Authors: Schiff R , Itin A , Keshet E
Published: June 2007

Transcription of cellular retrotransposons is induced by a variety of physiological stimuli. We have used in situ hybridization analysis to determine the cell types in which mouse retrotransposons are transcriptionally activated in vivo under physiological conditions. Here, we report that VL30 retrotransposons are specifically expressed in steroidogenic cells within all four endocrine tissues engaged in synthesis of steroid hormones in response to the respective pituitary-derived trophic hormones. These tissues include ovarian steroidogenic theca cells and lutein cells of the corpus luteum, testosterone-producing Leydig cells of the testis, steroidogenic cells confined to the zona reticularis of the adrenal cortex, and progesterone-producing cells of the placenta. In the course of preovulatory follicular development and maturation, the profile of cells expressing the retrotransposon shifted in parallel to the changing profiles of the leutinizing hormone (LH)-induced steroidogenic output of the respective cells. Expression of VL30 in both male and female gonads was shown to be greatly stimulated by external administration of gonadotropins. In vitro studies using a LH-responsive Leydig cell line have confirmed that expression of the resident retrotransposons is gonadotropin dependent. Run-off transcription assays have indicated that activation is at the transcriptional level. To allow molecular access to gonadotropin-activated transcription units, the long terminal repeat (LTR) regulatory domains were cloned from VL30 cDNAs of LH-induced ovaries. Through the use of reporter gene constructs and transfection experiments it was shown that expression of these elements in steroidogenic cells is LH dependent. Furthermore, cAMP, a known mediator of trophic hormone responses, could replace the hormone for inducibility. Transfection studies have also shown that the retrotransposon LTRs may function as hormone-activated enhancers conferring a LH-dependent phenotype on a surrogate transcription unit. These studies have thus demonstrated that the transcriptional activation of resident retrotransposons in vivo is a dynamic process that can be modulated by gonadotropins and have the potential of imposing this phenotype on adjacent cellular genes.
Glucose repression of transcription of the Schizosaccharomyces pombe fbp1 gene occurs by a cAMP signaling pathway.
Authors: Hoffman C S , Winston F
Published: June 2007

Transcription of the fbp1 gene, encoding fructose-1,6-bisphosphatase, of Schizosaccharomyces pombe is subject to glucose repression. Previous work has demonstrated that several genes (git genes) are required for this repression. In this report we demonstrate that one of these genes, git2, is the same as the cyr1 gene, which encodes adenylate cyclase, and that loss-of-function mutations in git2 cause constitutive fbp1 transcription. Addition of cAMP to the growth medium suppresses the transcriptional defect in git2 mutants as well as in strains that carry mutations in any of six additional git genes. Similarly, exogenous cAMP represses fbp1 transcription in wild-type cells grown on a derepressing carbon source. Different levels of adenylate cyclase activity in different git2 mutants, coupled with the result that some git2 mutants display intragenic complementation, strongly suggest that adenylate cyclase acts as a multimer and that different git2 mutations alter distinct activities of adenylate cyclase, including catalytic activity and response to glucose. Additional experiments demonstrate that this cAMP signaling pathway is independent of the S. pombe ras1 gene and works by activation of cAMP-dependent protein kinase.
Mutations in the HML E silencer of Saccharomyces cerevisiae yield metastable inheritance of transcriptional repression.
Authors: Mahoney D J , Marquardt R , Shei G J , Rose A B , Broach J R
Published: June 2007

Mating-type genes resident in the silent cassette HML at the left arm of chromosome III are repressed by the action of four SIR gene products, mediated independently through two cis-acting sites, termed the E and I silencers. We have found that in the absence of the I silencer, deletion of any one of three distinct elements within E yields partial derepression of the mating-type genes resident at HML, whereas deletion of any two yields full derepression. These elements correspond to a binding site for the abundant DNA-binding protein RAP1, an autonomous replicating sequence (ARS), and an as yet undistinguished region. From detailed deletion analysis of the E site we conclude that the ARS element contributes to silencer function in a capacity distinct from its role as an initiator of DNA replication. In addition, we find that strains deleted for any one of these elements comprise two genetically identical but phenotypically distinct types of cells: Those with HML apparently fully derepressed, and those with HML apparently completely repressed. These results reinforce the notion that epigenetic inheritance is an intrinsic characteristic of silencer action.
Alpha-tropomyosin mutually exclusive exon selection: competition between branchpoint/polypyrimidine tracts determines default exon choice.
Authors: Mullen M P , Smith C W , Patton J G , Nadal-Ginard B
Published: June 2007

We have used exons 2 and 3 of the rat alpha-tropomyosin gene to analyze the basis of mutually exclusive exon selection. The basis of the strict mutually exclusive behavior of this exon pair is enforced by the proximity of the exon 3 branchpoint to the 5' splice site of exon 2. With the exception of smooth muscle cells, exon 3 rather than exon 2 is incorporated into mRNA in all cell types. We show here, using both in vivo and in vitro cell-free systems, that this alternative exon selection is a consequence of general principles that govern 3' splice site selection. In the absence of exon 3, exon 2 is utilized efficiently in all cells. Selection of exon 3 is therefore the default result of a competition between exons 2 and 3 for the flanking constitutive splice sites. The basis of this competition is the relative strength of the polypyrimidine tract/branchpoint elements of the two exons. The major determinant of this splice site strength is the pyrimidine content adjacent to the branchpoint, and this involves no other sequence specificity. The branchpoint elements play an important but secondary role. The functional strengths of the different polypyrimidine tract/branchpoint combinations, as determined in cis competition assays, showed a perfect correlation with their binding affinities to a spliceosome component that interacts with the pre-mRNA in an ATP-independent manner. Selection of exon 3 in most cell types therefore reflects the preferential interaction of these splice site elements with constitutive splicing factors early in spliceosome assembly. The aspects of splice site selection analyzed here are likely to be of general applicability to constitutive and alternative pre-mRNA splicing.
Analysis of the DNA-binding and activation properties of the human transcription factor AP-2.
Authors: Williams T , Tjian R
Published: June 2007

The mammalian transcription factor AP-2 is a sequence-specific DNA-binding protein expressed in neural crest lineages and regulated by retinoic acid. Here we report a structure/function analysis of the DNA-binding and transcription activation properties of the AP-2 protein. DNA contact studies indicate that AP-2 binds as a dimer to a palindromic recognition sequence. Furthermore, cross-linking and immunoprecipitation data illustrate that AP-2 exists as a dimer even in the absence of DNA. Examination of cDNA mutants reveals that the sequences responsible for DNA binding are located in the carboxy-terminal half of the protein. In addition, a domain mediating dimerization forms an integral component of this DNA-binding structure. Expression of AP-2 in mammalian cells demonstrates that transcriptional activation requires an additional amino-terminal domain that contains an unusually high concentration of proline residues. This proline-rich activation domain also functions when attached to the heterologous DNA-binding region of the GAL4 protein. This study reveals that although AP-2 shares an underlying modular organization with other transcription factors, the regions of AP-2 involved in transcriptional activation and DNA binding/dimerization have novel sequence characteristics.
Pheromone-dependent phosphorylation of the yeast STE12 protein correlates with transcriptional activation.
Authors: Song D , Dolan J W , Yuan Y L , Fields S
Published: June 2007

Haploid a and alpha cells of yeast respond to the pheromones alpha- and a-factor, respectively, by increasing the transcription of many genes whose products are essential for mating. The STE12 protein acts in this process by binding to the DNA sequence that mediates the increased transcription of pheromone-responsive genes. We show here that a hybrid protein containing STE12 fused to the DNA-binding domain of GAL4 can activate transcription of a reporter gene containing GAL4-binding sites but only after treatment of cells with pheromone. Thus, STE12 alone, when bound to DNA, is sufficient to mediate pheromone-induced transcription. By constructing hybrids of different STE12 regions with the GAL4 domain, we map the domain of STE12 necessary for this activation to the central third of the protein. Upon alpha-factor treatment, the hybrid of GAL4 with the complete STE12 sequence is rapidly phosphorylated, with kinetics consistent with the observed transcriptional induction of pheromone-responsive genes. The domain of STE12 necessary for this phosphorylation correlates with that involved in transcriptional activation. We propose that induction of pheromone-responsive genes is mediated by phosphorylation of STE12 to alter its activation function but not its DNA-binding ability.
Functional domains of the yeast transcription/replication factor MCM1.
Authors: Christ C , Tye B K
Published: June 2007

MCM1 is an essential yeast DNA-binding protein that affects both minichromosome maintenance, in a manner suggesting that it has DNA replication initiation function, and gene expression. It activates alpha-specific genes together with MAT alpha 1, and represses a-specific genes together with MAT alpha 2. Alone, MCM1 can activate transcription. To determine whether different domains of the protein mediate these diverse functions, we constructed and analyzed several mcm1 mutants. The gene expression and minichromosome maintenance phenotypes of these mutants suggest that the role of MCM1 in DNA replication initiation may not involve transcriptional activation. However, both transcription and replication activities require only the 80-amino-acid fragment of MCM1 homologous to the DNA-binding domain of the serum response factor (SRF). This small fragment is also sufficient for cell viability and repression of a-specific genes. A polyacidic amino acid stretch immediately adjacent to the SRF homologous domain of MCM1 was found to be important for activation of alpha-specific genes in alpha cells. Mutants lacking the acidic stretch confer higher expression from an alpha-specific UAS in a cells in addition to lower expression in alpha cells, suggesting that negative regulation at this site occurs in a cells, in addition to the well-documented positive regulation in alpha cells.
Rev is necessary for translation but not cytoplasmic accumulation of HIV-1 vif, vpr, and env/vpu 2 RNAs.
Authors: Arrigo S J , Chen I S
Published: June 2007

The effect of Rev on cytoplasmic accumulation of the singly spliced human immunodeficiency virus type 1 (HIV-1) vif, vpr, and env/vpu RNAs was examined by using a quantitative RNA polymerase chain reaction (PCR) analysis following transfection of complete proviral molecular clones into lymphoid cells. Previously published studies using subgenomic env constructs in nonlymphoid cell types concluded that Rev was necessary for cytoplasmic accumulation of high levels of unspliced env RNA and that, by analogy, Rev must be necessary for the cytoplasmic accumulation of all HIV-1 RNAs that contain the Rev-responsive element (RRE). We confirm those results in COS cells. Unexpectedly, in lymphoid cells, we find that although Rev acts somewhat to increase the cytoplasmic level of full-length HIV-1 RNA, Rev has little or no effect on cytoplasmic accumulation of singly spliced HIV-1 RNAs. However, Env protein expression was greatly reduced in the absence of Rev. Analysis of the cytoplasmic RNA revealed that in the absence of Rev or the RRE, the cytoplasmic vif, vpr, and env/vpu 2 RNAs were not associated with polysomes but with a complex of 40S-80S in size. Consequently, efficient expression of the Vif, Vpr, Vpu, and Env proteins from these RNAs is dependent on Rev. These results exclude a mechanism whereby the sole function of Rev is simply to export RNAs from nucleus to cytoplasm. We discuss other models to take into account the dependence on Rev for efficient translation of cytoplasmic HIV-1 RNAs.
Transcriptional regulation of a pair-rule stripe in Drosophila.
Authors: Small S , Kraut R , Hoey T , Warrior R , Levine M
Published: June 2007

The periodic, seven-stripe pattern of the primary pair-rule gene even-skipped (eve) is initiated by crude, overlapping gradients of maternal and gap gene proteins in the early Drosophila embryo. Previous genetic studies suggest that one of the stripes, stripe 2, is initiated by the maternal morphogen bicoid (bcd) and the gap protein hunchback (hb), while the borders of the stripe are formed by selective repression, involving the gap protein giant (gt) in anterior regions and the Krüppel (Kr) protein in posterior regions. Here, we present several lines of evidence that are consistent with this model for stripe 2 expression, including in vitro DNA-binding experiments and transient cotransfection assays in cultured cells. These experiments suggest that repression involves a competition or short-range quenching mechanism, whereby the binding of gt and Kr interferes with the binding or activity of bcd and hb activators at overlapping or neighboring sites within the eve stripe 2 promoter element. Such short-range repression could reflect a general property of promoters composed of multiple, but autonomous regulatory elements.
The crooked neck gene of Drosophila contains a motif found in a family of yeast cell cycle genes.
Authors: Zhang K , Smouse D , Perrimon N
Published: June 2007

The crooked neck (crn) gene of Drosophila encodes a protein of 702 amino acids and contains 16 tandemly arranged copies of a 34-amino-acid repeat that is similar to the tetratrico peptide repeat (TPR). Multiple copies of the TPR motif have also been found in a family of yeast genes, including several members that are necessary for cell division. TPR-containing proteins encoded by the yeast genes CDC16, CDC23, and nuc2+ are required for progression through the G2/M transition of the cell cycle. Loss of zygotic expression of crn causes defects in the proliferation of brain neuroblasts and results in the absence of identified neuronal lineages in the central and peripheral nervous systems. The sequence similarity and mutant phenotypes are consistent with a cell cycle requirement for the crn gene product.
Chromatin differences between active and inactive X chromosomes revealed by genomic footprinting of permeabilized cells using DNase I and ligation-mediated PCR.
Authors: Pfeifer G P , Riggs A D
Published: June 2007

Ligation-mediated polymerase chain reaction (LMPCR) provides adequate sensitivity for nucleotide-level analysis of single-copy genes. Here, we report that chromatin structure can be studied by enzyme treatment of permeabilized cells followed by LMPCR. DNase I treatment of lysolecithin-permeabilized cells was found to give very clear footprints and to show differences between active and inactive X chromosomes (Xa and Xi, respectively) at the human X-linked phosphoglycerate kinase (PGK-1) locus. Beginning 380 bp upstream and continuing 70 bp downstream of the major transcription start site of PGK-1, we analyzed both strands of this promoter and CpG island and discovered the following: (1) The transcriptionally active Xa in permeabilized cells has several upstream regions that are almost completely protected on both strands from DNase I nicking. (2) Nuclei isolated in polyamine-containing buffers lack these footprints, suggesting that data from isolated nuclei can be flawed; other buffers are less disruptive. (3) The Xa has no detectable footprints at the transcription start and HIP1 consensus sequence. (4) The heterochromatic and transcriptionally inactive Xi has no footprints but has two regions showing increased DNase I sensitivity at 10-bp intervals, suggesting that the DNA is wrapped on the surface of a particle; one nucleosome-sized particle seems to be positioned over the transcription start site and another is centered approximately 260 bp upstream. (5) Potassium permanganate and micrococcal nuclease (MNase) studies indicate no melted or otherwise unusual DNA structures in the region analyzed, and MNase, unlike restriction endonuclease MspI, does cut within the positioned particles on the Xi. Results are discussed in the context of X chromosome inactivation and the maintenance of protein and DNA methylation differences between euchromatin and facultative heterochromatin at CpG islands.
Functional analysis and in vivo footprinting implicate the erythroid transcription factor GATA-1 as a positive regulator of its own promoter.
Authors: Tsai S F , Strauss E , Orkin S H
Published: June 2007

Transcription of erythroid-expressed genes and normal erythroid development in vivo are dependent on a regulatory protein (GATA-1) that recognizes a consensus GATA motif. GATA-1 expression is itself restricted to erythroid progenitors and to two related hematopoietic lineages, megakaryocytes and mast cells. During cellular maturation the levels of GATA-1 RNA and protein increase progressively. In an effort to delineate mechanisms by which this pivotal transcription factor is itself regulated we have characterized the mouse GATA-1 gene and cis-elements within its promoter. We find that the isolated promoter retains cell specificity exhibited by the intact gene. Full promoter activity requires the presence of proximal CACCC box sequences and an upstream, double GATA motif that binds a single GATA-1 molecule in an asymmetric fashion. Using in vivo footprinting of mouse erythroleukemic cells we detect protein binding in vivo to both cis-elements. On the basis of these findings we propose that a positive feedback loop mediated through GATA-1 serves two complementary functions: maintenance of the differentiated state by locking the promoter into an "on" state, and programming the progressive increase in protein content throughout cellular maturation.
Mcm2 and Mcm3, two proteins important for ARS activity, are related in structure and function.
Authors: Yan H , Gibson S , Tye B K
Published: June 2007

MCM2 and MCM3 are essential genes believed to play important roles in the initiation of DNA replication in Saccharomyces cerevisiae. Mutants defective in Mcm2 or Mcm3 are remarkably similar in phenotype. They both show an autonomously replicating sequence (ARS)-specific minichromosome maintenance defect, although their ARS specificities are not identical. In addition, these mutants exhibit a premitotic cell cycle arrest and an increase in chromosome loss and recombination. Genetic studies suggest that the two MCM gene products play interacting or complementary roles in DNA replication. Double mutants of mcm2-1 and mcm3-1 are inviable at the permissive growth temperature (23 degrees C) for each of the single mutants. Furthermore, overproduction of Mcm3 accentuates the deleterious effect of the mcm2-1 mutation, whereas overproduction of Mcm2 partially complements the mcm3-1 mutation. MCM2 encodes a protein of 890 amino acids containing a putative zinc-finger domain that is essential for Mcm2 function. Mcm2 shows striking homology to Mcm3 and three other proteins, Cdc46 of S. cerevisiae, and Nda4 and Cdc21 of Schizosaccharomyces pombe. The phenotypes of mutants defective in these proteins suggest that they belong to a protein family involved in the early steps of DNA replication.
A group of interacting yeast DNA replication genes.
Authors: Hennessy K M , Lee A , Chen E , Botstein D
Published: June 2007

Mutations in the cell-division-cycle genes CDC46 and CDC47 were originally isolated as suppressors of mutations in two other cell-division-cycle genes (CDC45 and CDC54). We found several combinations of mutations in these genes that result in allele-specific suppression and synthetic lethality, confirming that this set of genes forms a group of genetically interacting components. Here, we show that the other genes, like CDC46, are all involved in an early step of DNA replication, possibly initiation of DNA synthesis. Mutants defective in each of the four genes exhibit high rates of mitotic chromosome loss and recombination. The mutants appear also to accumulate chromosome damage that can be detected by a novel chromosome electrophoresis assay. Conditional mutants in this group, under fully nonpermissive conditions, show cell-cycle arrest at the beginning of DNA synthesis; under less stringent conditions, some arrest later, in S-phase. The DNA sequence of the CDC46 gene indicates that the protein is a member of a new family of genes apparently required for DNA initiation, with family members now identified in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and mouse cells.
Ablation of Drosophila photoreceptor cells by conditional expression of a toxin gene.
Authors: Kunes S , Steller H
Published: June 2007

We have used toxin-mediated ablation to study some aspects of visual system development in Drosophila melanogaster. To devise a method that permits the conditional expression of a cellular toxin, we introduced an amber mutation into the diphtheria toxin-A-chain gene. In transgenic animals, this toxin gene can be activated by providing the gene for an amber suppressor tRNA. By coupling this toxin gene to the photoreceptor cell-specific promoter of the chaoptic gene, photoreceptor cells could be specifically ablated during development. Photoreceptor cell-specific markers normally activated during pupal development failed to appear after midpupation. Photoreceptor cells were absent from the retinas of adult flies at eclosion. We have assessed the consequences of photoreceptor cell ablation for eye and optic lobe development. We suggest that the larval photoreceptor nerve is not essential, in the late larval stages, for retinula photoreceptor cell axons to achieve their proper projection pattern in the brain. Moreover, while retinula photoreceptor innervation is initially required for the development of normal optic ganglia, the ablation of these cells in midpupation has no discernible effect. This approach to cell-specific ablation should be generally applicable to the study of cellular functions in development and behavior.
Purkinje cell protein-2 regulatory regions and transgene expression in cerebellar compartments.
Authors: Vandaele S , Nordquist D T , Feddersen R M , Tretjakoff I , Peterson A C , Orr H T
Published: June 2007

The Purkinje cell protein 2 (Pcp-2) is expressed in cerebellar Purkinje cells and retinal bipolar neurons. To illuminate how Pcp-2 expression is restricted to only two neuronal types and to derive tools to express heterologous genes in these neuronal subpopulations, genomic sequences of the mouse Pcp-2 gene have been cloned and flanking sequences have been evaluated as a source of neuron-specific regulatory elements. An upstream region with homology to other genes expressed in neurons was identified and a hybrid gene containing this sequence was constructed by ligating 0.4 kb of upstream and 0.3 kb of downstream Pcp-2-flanking DNA to lacZ. Transgenic mice bearing this construct exhibited beta-galactosidase in a wide array of neuron types, suggesting that this sequence may play an important role in specifying neuronal expression. Addition of a further 3.1 kb of Pcp-2 upstream sequences restricted expression of beta-galactosidase to a small number of neuron types and most notably to Purkinje cells within parasagitally oriented cerebellar compartments. The presence of elements lying within the 3.1-kb upstream region and acting to specifically restrict Pcp-2 expression is therefore suggested. Moreover, as beta-galactosidase was not expressed in the bipolar cells of these transgenic mice, retinal expression of the endogenous Pcp-2 gene must involve elements in addition to those conferring expression within Purkinje cells.
Rodletless, a new Aspergillus developmental mutant induced by directed gene inactivation.
Authors: Stringer M A , Dean R A , Sewall T C , Timberlake W E
Published: June 2007

The Aspergillus nidulans CAN41 transcription unit is activated by the brlA regulatory gene early during development of the asexual reproductive apparatus, the conidiophore. Disruption of CAN41 results in a novel mutant phenotype in which conidiophore cells and spores lack an external wall layer, the rodlet layer, making them less hydrophobic than in the wild type and leading to inefficient spore dispersal. The rodletless mutation defines a new locus on chromosome III, rodA. rodA encodes a small, moderately hydrophobic polypeptide containing 8 cysteines arranged in a pattern similar to that observed in three hydrophobic cell wall proteins from the Holobasidiomycete Schizophyllum commune. We propose that the Aspergillus and Schizophyllum 8-cysteine polypeptides define a class of secreted, hydrophobic, fungal cell wall proteins that are important in the formation and function of aerial structures such as conidiophores and mushrooms.
cop1: a regulatory locus involved in light-controlled development and gene expression in Arabidopsis.
Authors: Deng X W , Caspar T , Quail P H
Published: June 2007

Light signals from the environment are perceived by specific regulatory photoreceptors in plants and are transduced by unknown mechanisms to genes that control growth and development. We have identified a genetic locus in Arabidopsis thaliana, which appears to play a central role in this transduction process. Mutations in this locus, designated cop1 (constitutively photomorphogenic), result in dark-grown seedlings with the morphology of wild-type seedlings grown in the light. In addition, these mutations lead to constitutive expression of an array of normally light-regulated genes in dark-grown seedlings and in light-grown adult plants placed in darkness. Promoter-reporter fusion constructs of some of these genes are constitutively expressed in dark-grown transgenic cop1 seedlings, indicating that the aberrant behavior of these genes results primarily from aberrant modulation of their promoter activities in the mutant. In contrast, light control of seed germination and diurnal control of cab gene expression is normal in the cop1 mutants. Because these mutations are recessive, we conclude that in seedlings and adult plants, the wild-type cop1 gene product normally acts in darkness to repress the expression of genes involved in the dark-adaptive developmental and that regulatory photoreceptors act to reverse this action upon exposure to light. However, photocontrol of seed germination and diurnal rhythms is apparently exerted via one or more separate pathways not involving the cop1 product. one or more separate pathways not involving the cop1 product.
Domains of the adenovirus E1A protein required for oncogenic activity are also required for dissociation of E2F transcription factor complexes.
Authors: Raychaudhuri P , Bagchi S , Devoto S H , Kraus V B , Moran E , Nevins J R
Published: June 2007

Recent experiments have shown that the cellular E2F transcription factor is found in complexes with cellular proteins and that one such complex contains the cyclin-A protein. Isolation of a cellular activity, which we term E2F-BF, can reconstitute the E2F-cyclin-A complex and has permitted a more detailed analysis of the mechanism of E1A dissociation. Through the analysis of a series of E1A mutants, we find that sequences in conserved region 1 (CR1) and conserved region 2 (CR2) are important for dissociation of the E2F complex, whereas amino-terminal sequences are not required. In contrast to the requirements for dissociation, only the CR1 sequences are required to block formation of the complex if E1A is added when the components are combined. We have also identified an activity, termed E2F-I, that inhibits E2F binding to DNA, again apparently through the formation of a complex with E2F. This inhibitory activity is also blocked by E1A, dependent on the same elements of the E1A protein that disrupt the interaction with E2F-BF. Because the E1A sequences that are important for releasing E2F from these interactions are also sequences necessary for oncogenesis, we suggest that this activity may be a critical component of the transforming activity of E1A.
Alternative splicing of fosB transcripts results in differentially expressed mRNAs encoding functionally antagonistic proteins.
Authors: Mumberg D , Lucibello F C , Schuermann M , Müller R
Published: June 2007

We show that serum-stimulated fibroblasts transiently express two different forms of fosB mRNA, which are generated by alternative splicing of the transcript from a single gene. In addition to the known long form (fosB-L), encoding a protein of 338 amino acids (FosB-L), a second shorter form (fosB-S) with a deletion of 140 bp was detected. This deletion creates a stop codon 3' to the leucine repeat, giving rise to a protein of 237 amino acids (FosB-S) lacking the carboxyl terminus of FosB-L. Only the long FosB form efficiently induces transformation in mouse and rat fibroblast cell lines and trans-represses the c-fos promoter. Both of these functions are suppressed by coexpressed FosB-S. Upon serum stimulation, maximum expression of the oncogenic fosB-L form precedes the expression of the antagonistic fosB-S form, indicating a new mechanisms regulating the action of members of the Fos family. However, FosB-L and FosB-S do not differ in all trans-regulatory properties: Trans-activation of a 5x TRE-CAT reporter construct in HeLa and NIH-3T3 cells was found with both FosB forms. These observations suggest a correlation between fosB-induced transformation and trans-repression, thus pointing to different mechanisms involved in transformation by fosB and c-fos/v-fos.
Characterization and molecular cloning of polypyrimidine tract-binding protein: a component of a complex necessary for pre-mRNA splicing.
Authors: Patton J G , Mayer S A , Tempst P , Nadal-Ginard B
Published: June 2007

alpha-Tropomyosin exons 2 and 3 are spliced in a mutually exclusive manner. Exon 3 is included as the default exon in the mRNA of most cell types, whereas exon 2 is only included in the mRNA of smooth muscle cells. The primary determinant for the default selection of exon 3 is the branchpoint/polypyrimidine tract. This element upstream of exon 3 clearly and effectively outcompetes the corresponding element upstream of exon 2. To identify trans-acting factors that bind to this important cis element, we used UV cross-linking to identify a 57-kD protein whose binding characteristics directly correlate with 3'-splice-site selection in cis-competition splicing assays. This protein appears to be identical to polypyrimidine tract-binding protein. In this report we have used oligonucleotides derived from peptide sequences to isolate and sequence cDNA clones encoding this 57.2-kD protein. The primary sequence reveals a novel protein with significant homology to other RNA-binding proteins. Expression of the mRNA is detected in all tissues and cells examined, although its levels exhibit tissue-specific and developmental regulation. Using a biochemical complementation assay, we have found that this protein, along with a 100-kD protein, exists as part of a large complex that is required to rescue splicing from depleted nuclear extracts.
Importance of globin gene order for correct developmental expression.
Authors: Hanscombe O , Whyatt D , Fraser P , Yannoutsos N , Greaves D , Dillon N , Grosveld F
Published: June 2007

We have used transgenic mice to study the influence of position of the human globin genes relative to the locus control region (LCR) on their expression pattern during development. The LCR, which is located 5' of the globin gene cluster, is normally required for the activation of all the genes. When the human beta-globin gene is linked as a single gene to the LCR it is activated prematurely in the embryonic yolk sac. We show that the correct timing of beta gene activation is restored when it is placed farther from the LCR than a competing human gamma- or alpha-globin gene. Correct timing is not restored when beta is the globin gene closest to the LCR. Similarly, the human gamma-globin gene is silenced earlier when present farthest from the LCR. On the basis of this result, we propose a model of developmental gene control based on stage-specific elements immediately flanking the genes and on polarity in the locus. We suggest that the difference in relative distance to the LCR, which is a consequence of the ordered arrangement of the genes, results in nonreciprocal competition between the genes for activation by the LCR.
Inactivation of a sperm motility gene by insertion of an epidermal growth factor receptor transgene whose product is overexpressed and compartmentalized during spermatogenesis.
Authors: Merlino G T , Stahle C , Jhappan C , Linton R , Mahon K A , Willingham M C
Published: June 2007

Transgenic mice were generated with a human epidermal growth factor (EGF) receptor cDNA driven by the chicken beta-actin gene promoter. One line (AE24) that exhibited a unique expression pattern in which dramatically elevated levels of EGF receptor RNA were found only in the testis was established, suggesting that the beta-actin promoter was being influenced by an adjacent testis-specific enhancer. EGF receptor RNA was detected in primary spermatocytes, whereas the synthesis of receptor protein was restricted to elongate spermatids, indicating that transgene expression was under translational control. At spermiation, the EGF receptor was sequestered in residual bodies and excluded from mature sperm by a compartmentalization mechanism. About half of AE24 homozygous males were sterile because of sperm paralysis, whereas heterozygous males and females of either genotype were completely fertile. Electron microscopic analysis of sperm flagella from sterile AE24 homozygotes revealed an aberrant axonemal structure in which outer doublet microtubules were missing from the middle piece, resembling changes observed in the sperm of some infertile humans. Flagellar axonemal disassembly was observed in the vas deferens and epididymis but not in the testis, suggesting that outer doublets were assembled in a grossly normal manner but possessed a latent instability. These results demonstrate that in the AE24 mouse line the EGF receptor transgene was integrated into and inactivated an endogenous autosomal gene, causing sperm flagellar axonemal disruption and male sterility.
Alternative splicing in the neural cell adhesion molecule pre-mRNA: regulation of exon 18 skipping depends on the 5'-splice site.
Authors: Tacke R , Goridis C
Published: June 2007

Two isoforms of the neural cell adhesion molecule (NCAM), termed NCAM-180 and NCAM-140, derive from a single gene via inclusion or exclusion of the penultimate exon 18 (E18). This alternative splicing event is tissue-specific and regulated during differentiation. To explore its structural basis, we have analyzed the pattern of spliced mRNA generated from transiently transfected minigenes construct containing this exon and portions of the adjacent introns and exons faithfully reproduces the differentiation state-dependent alternative splicing of the endogenous pre-mRNA. By systematic deletion and replacement analysis, we scanned the minigene for the presence of functionally important cis-elements. We identified two sequences that affected differentiation state-dependent regulation. One, the central part of E18, does not seem to contain a specific cis-element essential for proper splice site choice, because extending the deletion restored correctly regulated expression of the splicing products. In contrast, the 5'-splice site is an important element for regulation. Replacing it with a corresponding sequence from the alpha-globin gene resulted in constitutive use of the optional exon. When placed in the alpha-globin gene it did not promote alternative splicing. Instead, we observed a strongly decreased efficiency of splicing of the downstream intron in undifferentiated cells. This block of splicing was partially relieved after differentiation. The results are consistent with a model in which skipping of E18 is controlled in part at the associated 5'-splice site by trans-acting factors that undergo quantitative or qualitative changes during differentiation of N2a cells.