Intron-mediated regulation of gene expression.

Introns can significantly affect gene expression in plants and many other eukaryotes in a variety of ways. Several types of gene regulation, both positive and negative, that involve plant introns are reviewed in this chapter. Some introns contain enhancer elements or alternative promoters, while many others elevate mRNA accumulation by a different process that has been named intron-mediated enhancement (IME). The introns involved in IME must be within transcribed sequences near the start of a gene and in their natural orientation to increase expression. The intron sequences involved are still poorly defined, and the mechanism of IME remains mysterious. A model of IME is presented in which introns increase transcript elongation.

Tumores germinales malignos extracerebrales en niños y adolescentes: resultados del protocolo tgm 95 en una institución / Extra cerebral malignant germ gelf tumors in children and adolescents: results of the protocol tgm 95 in our institution

Objetivos: Evaluación de las características clínicas y los resultados terapéuticos de los tumores germinales malignos (TGM) extra cerebrales tratados según los lineamientos del protocolo TGM 95 de la Sociedad Francesa de Oncología Pediátrica (SFOP) en una sola institución. Pacientes y Métodos: Entre septiembre de 1995 y septiembre de 2005, 110 pacientes (pts) nuevos consecutivos con tumores germinales extra cerebrales fueron registrados en nuestra institución, 62 de los cuales eran malignos, todos ellos fueron evaluados. El primer gesto diagnóstico terapéutico fue la gonadectomía inicial o la detección de niveles elevados de marcadores tumorales. Los pacientes fueron tratados según los lineamientos del Protocolo TGM 95 de la SFOP. Para la enfermedad estadio I-II completamente resecada y con marcadores positivos, se utilizó una estrategia de expectación y seguimiento. Para los casos avanzados de diseminación hemátogena o niveles de alfa fetoproteína superiores a 15.000 ng/ml se empleó el régimen "VIP" (Etopósido, ifosfamida y cisplatino) 4-6 ciclos. El resto de los casos fue tratado con el regimén VBP (vinblastina, bleomicina y cisplatino) 3-5 ciclos. Resultados: La mediana edad para el grupo fue 12.1 (r: 0-17) años. Varones: 30; mujeres:32 (V/M: 0.94). La signo sintomatología clínica varió según la localización y la extensión tumoral. Hubo 13 (21) pacientes en estadio I y 9 (14,5) en estadio II (35,5). En estadio III y 18 (29) en estadío IV. Ocho (12,9) fueron tumores puros del saco vitelino. Cincuenta (80.6) fueron TGM mixtos con variadas combinaciones de componentes malignos teratomatosos. Dos (3,2) fueron teratomas inmaduros de alto grado. Veintiseis (41,9) fueron de origen ovárico, 25 (40,3) testiculares., 6 (9,7) sacrococcigeos, 3 (4,8) mediastinales y 2 (3,2) de otra localización. Catorce pacientes en estadio I-II y enfermedad inicialmente resecada en forma completa, no recibieron quimioterapia luego del a cirugía.

Occurrence of seizure clusters and status epilepticus during inpatient video-EEG monitoring.

OBJECTIVE: To investigate the occurrence of status epilepticus and seizure clusters, and the duration until first seizure at epilepsy monitoring units in the United States. METHODS: The authors examined the inpatient video-EEG monitoring reports of 514 consecutive patients admitted to five comprehensive epilepsy centers during the year 2000. Time to first seizure, seizure clustering, and seizure duration were ascertained from reports and entered into a database. RESULTS: In 169 admissions with complex partial seizures (CPSs) or secondarily generalized tonic-clonic (2GTC) seizures, there were 5 (3.0%) patients with status epilepticus, 30 (17.8%) with 4-hour seizure clusters, and 82 (48.5%) with 24-hour seizure clusters. There were no statistically significant differences between centers, except that seizure clusters were observed to be less common at the one center with a formal drug withdrawal protocol. The average time to CPS or 2GTC seizure was 2.1 days; the average number of days to nonepileptic event was 1.2 days (p = 0.001). CONCLUSIONS: Although status epilepticus is uncommon at epilepsy monitoring units, clusters of seizures are common. Intensive monitoring with drug withdrawal must be performed in a highly supervised, hospitalized setting. Inpatient video-EEG monitoring is efficient, with recording of the first epileptic or nonepileptic events in 2 days or less.

Intron-mediated enhancement of gene expression independent of unique intron sequences and splicing.

Either of the first two introns of the Arabidopsis tryptophan pathway gene PAT1 elevates mRNA accumulation from a PAT1:beta-glucuronidase (GUS) fusion roughly 5-fold without affecting the rate of PAT1:GUS transcription. To further explore the mechanism of this intron-mediated enhancement of gene expression, we wanted to determine whether splicing or specific intron sequences were necessary. In-frame derivatives of PAT1 intron 1, whose splicing was prevented by a point mutation or large deletions, were able to increase mRNA accumulation from a PAT1:GUS fusion, demonstrating that splicing per se is not required. Furthermore, each of a series of introns containing overlapping deletions that together span PAT1 intron 1 increased PAT1:GUS mRNA accumulation as much as the full-length intron did, indicating that all intron sequences are individually dispensable for this phenomenon. These results eliminate the simple idea that this intron stimulates mRNA accumulation via a unique RNA-stabilizing sequence or through the completed act of splicing. However, they are consistent with a possible role for redundant intron sequence elements or an association of the pre-mRNA with the spliceosome.

Childhood acute promyelocytic leukemia: no benefit of all-trans-retinoic acid administered in a short-course schedule.

From January 1990 to August 1997, 29 consecutive patients were treated with newly diagnosed primary acute promyelocytic leukemia (APL) at the authors' Institution. Of these, 27 (16 boys and 11 girls) were evaluable. Median age at diagnosis was 6.3 (range: 1.9-15.7) years. This population was treated with two consecutive protocols: 13 patients were included in the AML-HPG-90 protocol and 14 in the AML-HPG-95. The initial treatment was the same for both protocols: an induction 8-day phase with cytarabine, idarubicin, and etoposide was followed by a consolidation with cyclophosphamide, cytarabine, 6-mercaptopurine, vincristine, doxorubicin, and prednisone. Two courses of intensification with high-dose (HD) cytarabine and etoposide were given in the first study. Only one intensification course was administered in the second study, with HD cytarabine plus idarubicin or etoposide decided by randomization. Complete remission was achieved in 67% (18/27) of cases. Mortality on induction was quite high, 30% (8/27) mainly due to hemorrhages from disseminated intravascular coagulation (DIC). The event-free survival estimate for all patients was 0.47 (SE: 0.1). From April 1994, all-trans-retinoic acid (ATRA) was administered just during the first days of the induction phase (median: 9, range: 2-27) to stop or prevent DIC. Eighteen patients received ATRA and 9 did not. Three patients developed signs of ATRA syndrome during the first days of administration but no one died due to this toxicity. The impact of a short course of ATRA on early control of DIC was studied by analyzing the number of platelet, cryoprecipitate, and fresh frozen plasma transfusions during the induction phase in both groups. No statistical differences in complete remission rate, early mortality, need of transfusion of blood components for DIC, and survival estimates could be established between patients who received ATRA and those who did not. ATRA used in a short-course schedule during induction of APL did not stop early mortality due to DIC. Moreover, survival results did not improve with this method of ATRA usage. Longer periods of ATRA administration during APL therapy are strongly recommended.

Adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum. site-directed mutagenesis at putative phosphoryl-accepting and ATP P-loop residues.

The properties of Penicillium chrysogenum adenosine 5'-phosphosulfate (APS) kinase mutated at Ser-107 were examined. Ser-107 is analogous to a serine of the E. coli enzyme that has been shown to serve as an intermediate acceptor in the transfer of a phosphoryl group from ATP to APS. Replacement of Ser-107 with alanine yielded an active enzyme with kinetic characteristics similar to those of wild-type APS kinase. Another mutant form of the enzyme in which Ser-107 was replaced by cysteine was also active. Covalent modification of Cys-107 eliminated catalytic activity, and substrates protected against modification. Mutation of Ser-97, of Ser-99, of Thr-103, of Ser-104 to alanine, or of Tyr-109 to phenylalanine also yielded an active enzyme. The cumulative results indicate that Ser-107 may reside in the substrate binding pocket of fungal APS kinase, but neither it nor any nearby hydroxy amino acid serves as an obligatory phophoryl acceptor in the 3'-phosphoadenylylsulfate synthesis reaction. The results also indicate that the absence of a serine at position 478 in the APS kinase-like C-terminal region of fungal ATP sulfurylase does not account for the lack of APS kinase activity in that enzyme. However, mutating the ATP P-loop residues in APS kinase to those found in the analogous C-terminal region of fungal ATP sulfurylase eliminated enzyme activity.

Introns act post-transcriptionally to increase expression of the Arabidopsis thaliana tryptophan pathway gene PAT1.

The expression of the Arabidopsis thaliana PAT1 gene, which encodes the tryptophan biosynthetic enzyme phosphoribosylanthranilate transferase, was investigated using translational fusions of the PAT1 promoter to the GUS reporter gene. Independent stably transformed A. thaliana lines containing a single copy of a fusion that includes the entire plastid transit peptide and the first two introns of PAT1 had on average 30 times more GUS enzyme activity than plants transformed with a construct in which GUS was fused a short distance downstream of the PAT1 start codon. Plants containing the construct without introns or leader peptide accumulated undetectable amounts of PAT1-GUS fusion protein and mRNA, even though the transcriptional rate of both fusion constructs was comparable. Fusions containing the entire transit peptide and either of the first two introns yield as much GUS activity as constructs containing both introns, but constructs containing the transit peptide but no introns give rise to much lower levels. Therefore, introns greatly enhance the expression of PAT1-GUS fusions, and they act post-transcriptionally to increase the steady-state level of mRNA.

Hyperactivation of the silencing proteins, Sir2p and Sir3p, causes chromosome loss.

The SIRgene products maintain transcriptional repression at the silent mating type loci and telomeres in Saccharomyces cerevisiae, although no enzymatic or structural activity has been assigned to any of the Sir proteins nor has the role of any of these proteins in transcriptional silencing been clearly defined. We have investigated the functions and interactions of the Sir2, Sir3, and Sir4 proteins by overexpressing them in yeast cells. We find that Sir2p and Sir3p are toxic when overexpressed, while high Sir4p levels have no toxic effect. Epistasis experiments indicate that Sir2p-induced toxicity is diminished in strains lacking the SIR3 gene, while both Sir2p and Sir4p are required for Sir3p to manifest its full toxic effect. In addition, the effects of Sir2 or Sir3 overexpression are exacerbated by specific mutations in the N-terminus of the histone H4 gene. These results are consistent with a model in which Sir2p, Sir3p and Sir4p function as a complex and interact with histones to modify chromatin structure. We find no evidence that toxicity from high levels of the Sir proteins results from widespread repression of transcription. Instead, we find that high levels of Sir2p and/or Sir3p cause a profound decrease in chromosome stability. These results can be appreciated in the context of the effects of Sir2p in histone acetylation and of chromatin structure on chromosome stability.

An allelic series of blue fluorescent trp1 mutants of Arabidopsis thaliana.

Nine blue fluorescent mutants of the flowering plant Arabidopsis thaliana were isolated by genetic selections and fluorescence screens. Each was shown to contain a recessive allele of trp1, a previously described locus that encodes the tryptophan biosynthetic enzyme phosphoribosylanthranilate transferase (PAT, called trpD in bacteria). The trp1 mutants consist of two groups, tryptophan auxotrophs and prototrophs, that differ significantly in growth rate, morphology, and fertility. The trp1 alleles cause plants to accumulate varying amounts of blue fluorescent anthranilate compounds, and only the two least severely affected of the prototrophs have any detectable PAT enzyme activity. All four of the trp1 mutations that were sequenced are G to A or C to T transitions that cause an amino acid change, but in only three of these is the affected residue phylogenetically conserved. There is an unusually high degree of sequence divergence in the single-copy gene encoding PAT from the wild-type Columbia and Landsberg erecta ecotypes of Arabidopsis.

Arabidopsis phosphoribosylanthranilate isomerase: molecular genetic analysis of triplicate tryptophan pathway genes.

Phosphoribosylanthranilate isomerase (PAI) catalyzes the third step of the tryptophan biosynthetic pathway. Arabidopsis PAI cDNAs were cloned from a cDNA expression library by complementation of an Escherichia coli trpC- PAI deficiency mutation. Genomic DNA blot hybridization analysis detected three nonallelic genes encoding PAI in the Arabidopsis genome. DNA sequence analysis of cDNA and genomic clones indicated that the PAI1 and PAI2. All three PAI polypeptides possess an N-terminal putative plastid target sequence, suggesting that these enzymes all function in plastids. The PAI1 gene is flanked by nearly identical direct repeats of approximately 350 nucleotides. Our results indicate that, in contrast to most microorganisms, the Arabidopsis PAI protein is not fused with indole-3-glycerolphosphate synthase, which catalyzes the next step in the pathway. Yeast artificial chromosome hybridization studies indicated that the PAI2 gene is tightly linked to the anthranilate synthase alpha subunit 1 (ASA1) gene on chromosome 5. PAI1 was mapped to the top of chromosome 1 using recombinant inbred lines, and PAI3 is loosely linked to PAI1. cDNA restriction mapping and sequencing and RNA gel blot hybridization analysis indicated that all three genes are transcribed in wild-type plants. The expression of antisense PAI1 RNA significantly reduced the immunologically observable PAI protein and enzyme activity in transgenic plants. The plants expressing antisense RNA also showed two phenotypes consistent with a block early in the pathway: blue fluorescence under UV light and resistance to the anthranilate analog 6-methylanthranilate. The extreme nucleotide conservation between the unlinked PAI1 and PAI2 loci suggests that this gene family is actively evolving.

Transcriptional silencing in yeast is associated with reduced nucleosome acetylation.

Two classes of sequences in the yeast Saccharomyces cerevisiae are subject to transcriptional silencing: the silent mating-type cassettes and telomeres. In this report we demonstrate that the silencing of these regions is strictly associated with acetylation of the epsilon-amino groups of lysines in the amino-terminal domains of three of the four core histones. Both the silent mating-type cassettes and the Y domains of telomeres are packaged in nucleosomes in vivo that are hypoacetylated relative to those packaging active genes. This difference in acetylation is eliminated by genetic inactivation of silencing: The silent cassettes from sir2, sir3, or sir4 cells show the same level of acetylation as other active genes. The correspondence of silencing and hypoacetylation of the mating-type cassettes is observed even for an allele lacking a promoter, indicating that silencing per se, rather than the absence of transcription, is correlated with hypoacetylation. Finally, overexpression of Sir2p, a protein required for transcriptional silencing in yeast, yields substantial histone deacetylation in vivo. These studies fortify the hypothesis that silencing in yeast results from heterochromatin formation and argue that the silencing proteins participate in this formation.

A Phosphoribosylanthranilate Transferase Gene Is Defective in Blue Fluorescent Arabidopsis thaliana Tryptophan Mutants.

An Arabidopsis thaliana gene encoding phosphoribosylanthranilate transferase is shown to be the gene that is defective in blue fluorescent trp1 mutant plants. This gene, named PAT1, was isolated using an A. thaliana cDNA clone that suppressed an Escherichia coli trpD(-) mutation. The PAT1 coding region is homologous to those for the phosphoribosylanthranilate transferases from many microorganisms. Unlike other genes involved in aromatic amino acid biosynthesis in A. thaliana, PAT1 appears to be a single-copy gene. PAT1 was demonstrated to be the gene that is defective in blue fluorescent trp1 mutants by two methods: genetic complementation in transgenic plants and genetic mapping studies. This is the first report of cloning a plant phosphoribosylanthranilate transferase gene. The PAT1 gene should prove useful as a selectable marker for transformation or a visible reporter of gene expression when used in conjunction with trp1 plants.

Mutations in the HML E silencer of Saccharomyces cerevisiae yield metastable inheritance of transcriptional repression.

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.

Transposable element sequences involved in the enhancement of yeast gene expression.

The his4-917 mutation of yeast results from the insertion of a Ty element, Ty917, into the 5' regulatory region of the HIS4 gene. Ty917 prevents HIS4 transcription, thus rendering the cell histidine requiring. Recombination between Ty917 and a Ty element elsewhere in the yeast genome can result in the replacement of part or all of the Ty917 element by sequences from the Ty element. Recombinant derivatives display a variety of phenotypes including His-, weakly His+, and strongly His+. In most of the His+ derivatives, the expression of HIS4 is controlled by genes at the mating type locus. To identify the Ty sequences important in controlling the expression of an adjacent gene, we used Ty elements that have different effects on gene expression to construct hybrid Ty elements in vitro. The effects of these hybrid elements on HIS4 expression were examined. These experiments indicate that the critical sequence differences between Ty elements that permit HIS4 expression and those that prevent its expression lie in the rightmost (HIS4-proximal) 730 base pairs of the element. The DNA sequence of this region was determined for three elements: Ty917, which prevents HIS4 expression; Ty917(467), which confers a weak His+ phenotype; and Ty917(480), which confers a strong His+ phenotype. Within this region, Ty917(467) differs from Ty917 by a single base-pair change that is in the internal (epsilon) region of the Ty element. Ty917(480) differs from Ty917 by this same base-pair change and by 10 changes in the terminal delta sequence. The sequence change common to Ty917(467) and Ty917(480) lies in a region of the Ty element that is homologous to the simian virus 40 enhancer of transcription.