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PubMed2000

Transcription and proper splicing of a mammalian gene in yeast.

The house mouse strain C57BL/6 harbours 64 copies of the multicopy gene Sp100-rs. Three of these are contained in the yeast artificial chromosome (YAC) clone yMm75. Four Sp100-rs transcripts of 3.0, 2.6, 1.6 and 1.3kb were detected by Northern hybridization in the yMm75-harbouring line of Saccharomyces cerevisiae. Additional and less abundant transcripts were detected by RT-PCR. With one exception, the YAC-derived Sp100-rs transcripts were a subset of those found in the C57BL/6 mouse. This indicates transcription and proper splicing of murine pre-mRNAs in yeast. Analysis of the splice sites shows that the yeast splicing machinery accepts splice sites that deviate from the standard yeast consensus sequences. It may be feasible, therefore, at least in a fair proportion of cases, to exploit the mammalian mRNAs present in transgenic yeast for gene recognition of YAC-inserts.

Amino Acid Sequence↗
PubMed2006

Effects of L1 retrotransposon insertion on transcript processing, localization and accumulation: lessons from the retinal degeneration 7 mouse and implications for the genomic ecology of L1 elements.

The retinal degeneration 7 (rd7) mouse is a naturally occurring model of enhanced S-cone syndrome, Goldman-Favre syndrome and clumped pigmentary retinopathy in humans, allelic disorders caused by inactivation of a photoreceptor-specific nuclear hormone receptor, NR2E3. We show here that the rd7 mutation arose from the antisense insertion of a long interspersed nuclear element (LINE-1) (or L1) into exon 5 of the mouse Nr2e3 gene. L1 insertion blocks splicing of Nr2e3 intron 5 by separating an inefficient splice donor from essential splicing enhancers within exon 5, with the result that incompletely spliced transcripts accumulate to high levels at the mutant Nr2e3 locus in photoreceptor nuclei. The high efficiency of transcription through the 7 kb L1 was unexpected and led us to compare the effect on transcript abundance of sense or antisense L1 insertions in transfected cells. In a variety of sequence contexts antisense L1 insertions had little or no effect on transcript levels or the production of full-length transcripts, whereas sense L1 insertions reduced transcript levels from several-fold to more than 10-fold. A bioinformatic analysis of all mouse L1s shows a approximately 2-fold under-representation of L1s in introns when compared with bulk genomic DNA, and, within introns, a further approximately 2-fold under-representation of sense when compared with antisense L1s. Interestingly, there is no evidence for orientation-specific positive or negative selection within any subregions of the L1 element. These data suggest that L1s have evolved to present the host transcriptional machinery with a minimally disruptive profile in the antisense orientation such that antisense intronic L1s often escape purifying negative selection.

Animals↗
PubMed1990

Latent transcripts of Marek's disease virus are clustered in the short and long repeat regions.

Marek's disease herpesvirus (MDV) induces tumors in chickens, and lymphoblastoid cells derived from such tumors contain the viral genome in a latent state and do not produce infectious virus. Poly(A)+ RNAs extracted from MDV-induced kidney lymphoma cells and from MKT-1 cells, a nonproducing lymphoblastoid cell line derived from a tumor induced by MDV, were electrophoretically separated under denaturing conditions, transferred to a solid substrate, and hybridized with labeled DNA probes representing approximately 95% of the virus genome. These analyses revealed 29 viral RNA transcripts in the kidney lymphoma and 32 viral RNAs in MKT-1 cells. In both instances, the transcripts hybridized to a restricted region comprising approximately 20% of the MDV genome located in the repeats flanking the long and short unique sequences and in the adjacent unique sequences. The sizes of the transcripts derived from kidney lymphoma and MKT-1 cells and the distributions of the homologous regions in the viral genome were very similar. The most abundant transcripts were homologous to the BamHI I2 fragment. The results suggest that expression of the MDV genome in MKT-1 cells closely reflects the expression of the MDV genome in tumors. The gene expression over extended regions of the genome is in concordance with that observed in latent gammaherpesviruses rather than that observed in latent alphaherpesviruses.

Cell Line↗
PubMed1994

Developmentally regulated, low abundance Tec element transcripts in Euplotes crassus--implications for DNA elimination and transposition.

During macromolecular development in the ciliated protozoan, Euplotes crassus, > 105 Tec elements are precisely eliminated from the genome in a 2-4 h time interval, generating extrachromosomal circular forms of the elements. Various models have proposed a transposition-based mechanism for this excision. We have tested this hypothesis by determining the abundance of transcripts of Tec element open reading frames (ORFs) and the timing of their appearance. Transcripts are very low in abundance and are only detected by PCR amplification techniques. Thus, the low levels of transcripts argue against the participation of element-encoded functions in the Tec element elimination process. The element transcripts are only detected in RNA samples from mated cells, indicating that the micronucleus and/or developing macronucleus are transcriptionally active during the sexual phase of the life cycle. The transcription detected could allow a low level of germline-specific transposition for these elements.

Animals↗
PubMed1993

The predominant mRNA class in HPV16-infected genital neoplasias does not encode the E6 or the E7 protein.

Human papillomavirus (HPV) type 16 is strongly implicated in the development of progressive neoplasias of the uterine cervix. Its oncogenic potential is decisively determined by the activity of the early gene products E6 and E7. To look for changes in the expression of these genes during tumour progression we cloned subgenomic fragments of HPV16 into RNA expression vectors, which allowed the generation of 35S-labelled riboprobes specific for distinct mRNA classes. Four constructs were made to differentiate between transcripts starting upstream of the E6 ORF or the E1 ORF, and one probe was specific for unspliced E6/E7 region transcripts. Five other constructs were used to identify transcripts covering the E1, E2, E4, L1 and L2 regions. With the help of these constructs, we analyzed by in situ hybridization 2 low-grade intraepithelial neoplasias of the vulva, 1 high-grade neoplasia of the cervix as well as 4 vulvar and 3 cervical carcinomas. Transcripts from the E1, E2, E4, L1 and L2 region that were consistently detected in the differentiated layers of benign lesions were variably expressed in precancers and carcinomas. None of the investigated cases revealed detectable amounts of unspliced E6/E7 transcripts with a coding potential for a full-length E6 protein. In benign lesions, the E7 transcripts were confined to isolated nuclei of differentiated cells, whereas high-grade lesions and invasive cancers showed elevated levels of equally distributed E7-specific signals in the cytoplasm of all tumour cells. The most abundant transcripts observed in intraepithelial neoplasias and in invasive cancers appear to initiate within ORF E7 and therefore have no coding potential for full-length E6 and E7 proteins. Our data show that the actual level of E7-specific transcripts in cancers is lower than anticipated from earlier studies using an ORF E6/E7-specific probe that hybridizes with the 5'-ends of the abundant mRNA class.

Base Sequence↗
PubMed1994

Cloning and regulation of rat tissue inhibitor of metalloproteinases-2 in osteoblastic cells.

Rat tissue inhibitor of metalloproteinases-2 (TIMP-2) was cloned from a UMR 106-01 rat osteoblastic osteosarcoma cDNA library. The 969-bp full-length clone demonstrates 98 and 86% sequence identity to human TIMP-2 at the amino acid and nucleic acid levels, respectively. Parathyroid hormone (PTH), at 10(-8) M, stimulates an approximately twofold increase in both the 4.2- and 1.0-kb transcripts over basal levels in UMR cells after 24 h of exposure. The PTH stimulation of TIMP-2 transcripts was not affected by the inhibitor of protein synthesis, cycloheximide (10(-5) M), suggesting a primary effect of the hormone. This is in contradistinction to regulation of interstitial collagenase (matrix metalloproteinase-1) by PTH in these same cells. Nuclear run-on assays demonstrate that PTH causes an increase in TIMP-2 transcription that parallels the increase in message levels. Parathyroid hormone, in its stimulation of TIMP-2 mRNA, appears to act through a signal transduction pathway involving protein kinase A (PKA) since the increase in TIMP-2 mRNA is reproduced by treatment with the cAMP analogue, 8-bromo-cAMP (5 x 10(-3) M). The protein kinase C and calcium pathways do not appear to be involved due to the lack of effect of phorbol 12-myristate 13-acetate (2.6 x 10(-6) M) and the calcium ionophore, ionomycin (10(-7) M), on TIMP-2 transcript abundance. In this respect, regulation of TIMP-2 and collagenase in osteoblastic cells by PTH are similar. However, we conclude that since stimulation of TIMP-2 transcription is a primary event, the PKA pathway must be responsible for a direct increase in transcription of this gene.

8-Bromo Cyclic Adenosine Monophosphate↗
PubMed2004

Crustacean retinoid-X receptor isoforms: distinctive DNA binding and receptor-receptor interaction with a cognate ecdysteroid receptor.

We have identified cDNA clones that encode homologs of the ecdysteroid receptor (EcR) and retinoid-X receptor (RXR)/USP classes of nuclear receptors from the fiddler crab Uca pugilator (UpEcR and UpRXR). Several UpRXR cDNA splicing variants were found in coding regions that could potentially influence function. A five-amino acid (aa) insertion/deletion is located in the "T" box in the hinge region. Another 33-aa insertion/deletion is found inside the ligand-binding domain (LBD), between helix 1 and helix 3. Ribonuclease protection assays (RPA) showed that four UpRXR transcripts [UpRXR(+5+33), UpRXR(-5+33), UpRXR(+5-33) and UpRXR(-5-33)] were present in regenerating limb buds. UpRXR(-5+33) was the most abundant transcript present in regenerating limb buds in both early blastema and late premolt growth stages. Expression vectors for these UpRXR variants and UpEcR were constructed, and the proteins expressed in E. coli and in vitro expression systems. The expressed crab nuclear receptors were then characterized by electrophoretic mobility shift assay (EMSA) and glutathione S-transferase (GST) pull down experiments. EMSA results showed that UpEcR/UpRXR(-5+33) heterocomplexes bound with a series of hormone response elements (HREs) including eip28/29, IRper-1, DR-4, and IRhsp-1 with appreciable affinity. Competition EMSA also showed that the affinity decreased as sequence composition deviated from a perfect consensus element. Binding to IRper-1 HREs occurred only if the heterodimer partner UpRXR contained the 33-aa LBD insertion. UpRXR lacking both the 5-aa and 33-aa insertion bound to a DR-1G HRE in the absence of UpEcR. The results of GST-pull down experiments showed that UpEcR interacted only with UpRXR variants containing the 33-aa insertion, and not with those lacking the 33-aa insertion. These in vitro receptor protein-DNA and receptor protein-protein interactions occurred in the absence of hormone (20-hydroxyecdysone and 9-cis retinoid acid, 9-cis RA). Transactivation studies using a hybrid UpEcR ligand-binding domain construct and UpRXR (+/-33) ligand-binding domain constructs also showed that the 33-aa insertion was indispensable in mediating ecdysteroid stimulated transactivation.

Alternative Splicing↗
PubMed1982

The biogenesis and regulation of yeast mitochondria RNA polymerase.

Yeast mitochondrial RNA polymerase is a nuclear-coded protein of approximately 90,000 daltons comprised of two 45,000-dalton subunits of pI 6.9 to 7.0. To investigate the nature of the initial translation product of the RNA polymerase, we have analyzed those products of a cell-free translation system directed by yeast RNA that are immunoreactive with antibodies to the 45,000-dalton peptide of polymerase. A precursor of one or more of the subunits of the polymerase, 2,000 daltons later than the mature product, has been characterized using immunoreaction, immunocompetition, and peptide digestion. The role of transcription of the polymerase gene in catabolite repression of mitochondrial development has been investigated by analyzing the changes in cell-free synthesis of the RNA polymerase precursor during glucose and raffinose growth. The results indicate an increase in precursor synthesis and probably in the corresponding transcript abundance during glucose derepression. In contrast, the precursor is present at high levels until stationary phase during raffinose growth. These data indicate the involvement of increased transcription of the polymerase gene in the process of derepression.

Cell Nucleus↗
PubMed1986

Regulation of c-myc transcription and mRNA abundance by serum growth factors and cell contact.

We describe effects of serum insufficiency and cell contact on the transcription and abundance of the c-myc proto-oncogene mRNA in BALB/c 3T3 fibroblasts. In exponentially growing cells, withdrawal of serum caused a 10-fold decline in c-myc mRNA within 90 min. At least part of this decline was due to a decrease in the level of myc gene transcription. These cells became quiescent at subconfluence after 36-40 h. Cells made quiescent at subconfluence or confluence contained low levels of c-myc mRNA which rose more than 20-fold 2 h after stimulation of growth by fresh serum. Thereafter, the mRNA level declined. In subconfluent cells, it declined to the level in exponentially growing cells, i.e. nearly 10-fold over the level in quiescent cells. In confluent cells, by contrast, the mRNA returned to near-quiescent levels within 18 h (by mid-S phase). However, c-myc gene transcription was regulated identically in subconfluent and confluent cultures; quiescent cells transcribed c-myc at detectable levels, and stimulation by serum caused a 5-fold increase in 1 h, followed by a decline to about 2-fold over the quiescent level within 18 h. Thus, confluence affected steady state mRNA levels without affecting the level of transcription. Our results suggest that extracellular conditions that modulate cell proliferation (serum and cell contact) exert strong and rapid control over c-myc mRNA by post-transcriptional and transcriptional mechanisms.

Actins↗
PubMed1985

The detection of Jonah gene transcripts in Drosophila by in situ hybridization.

The Jonah genes constitute a family of approximately 20 genes expressed at two periods during the development of Drosophila melanogaster. They are expressed only in the midgut, where they yield very abundant transcripts of approximately 900 bases. The function of their products is not known. We have used in situ hybridization to show that transcripts homologous to two members of the Jonah family have quite different distributions within the midgut. Transcripts closely homologous to Jon65Aiv are expressed throughout most of the anterior midgut and in the posterior section of the middle midgut. Transcripts closely homologous to Jon99C beta are expressed only in the anterior region of the posterior midgut.

Animals↗
PubMed1985

In situ hybridization: a routine method for parallel localization of DNA sequences and of their transcripts in consecutive paraffin sections with the use of 3H-labelled nick translated cloned DNA probes.

A routine in situ hybridization method is described and discussed, which allows parallel detection of repeated DNA sequences and of their abundant transcripts in consecutive tissue sections of a same biological sample with a unique probe. The protocol, based on the use of classical 3H-labelled nick translated cloned DNA probes and of conventional paraffin sections of ethanol-acetic acid-fixed tissues, consists of a simple combination of procedures in current use for separate detection of either RNA or DNA. Different treatments recommended in other methods are omitted or simplified, making the protocol suitable for routine use. The method is successfully applied here to a test-system where ribosomal sequences are sought in the ovarian follicles of the Lepidopteran Ephestia kühniella, by using a recombinant plasmid containing a Drosophila melanogaster rDNA repeating unit as a probe. Specific and reproducible results are obtained. Sensitivity is sufficient though moderate specific activities are used. Background level is very low. The regionalized distribution of sequences of both types in the chosen model allows to demonstrate that specific detection of RNA requires the systematic removal of DNA from the tissue sections prior to hybridization.

Animals↗
PubMed1999

Posttranscriptional regulation of US11 in cells infected with a herpes simplex virus 1 recombinant lacking both 222-bp domains containing S-component origins of DNA synthesis.

The US11 gene of herpes simplex virus 1 maps in the unique sequences of the short component of the HSV-1(F) genome approximately 775 bp from the center of the DNA replication origin (OriS) and encodes a virion protein which binds RNA in sequence- and conformation-specific fashion, negatively regulates the accumulation of a prematurely terminated transcript of UL34, associates in the infected cell with the 60S ribosomal subunit, and, late in infection, accumulates in nucleoli. We report the following: (i) Deletion of a 222-bp sequence including OriS (DeltaOriS) negatively affected the accumulation of the US11 protein without decreasing the accumulation of the US11 transcript. (ii) The defect, observed at all times after infection, was multiplicity independent, was unrelated to US11 protein stability, and apparently resulted from a cis-acting element since a coinfecting virus was unable to complement the DeltaOriS virus. (iii) Transcription from the US11 promoter initiated from three sites on the DeltaOriS virus. Transcripts initiated from two of the three initation sites accumulated similarly in cells infected with the DeltaOriS virus or wild-type parent virus. The low-abundance transcript initiating from the third site was apparently unique to the DeltaOriS virus but was not expected to alter the coding capacity of the mRNA. (iv) Infected cells accumulated RNA derived by antisense transcription of the genome domain containing the US11 gene. One transcript accumulated in larger amounts in cells infected with the DeltaOriS virus than in cells infected with parent or repaired virus.

Autoradiography↗
PubMed1984

Mapping of polyadenylated transcripts of a monkey lymphotropic papova virus.

Polyadenylated transcripts of a monkey lymphotropic papovavirus (LPV), which can be propagated in monkey and human lymphoblastoid cell lines, were identified and mapped. Polyadenylated RNA was purified from cells of the human line BJA/B infected with LPV, and was hybridized with various LPV DNA fragments. The hybrids were treated with S1 endonuclease and analyzed by alkaline gel electrophoresis. This analysis revealed two groups of RNA molecules encoded in two regions of the LPV genome. One group includes four colinear transcripts of 2.3, 2.1, 1.85, and 1.2 kb, whose polyadenylated termini map at a single site on the LPV DNA. The second group includes two less-abundant transcripts of 1.8 and 1.95 kb. The polarities of the LPV transcripts were determined by hybridizing cDNA complementary to their 3' termini with LPV DNA fragments. The two groups were found to have opposite polarities. It is shown that the four major transcripts can be aligned with, and may be functionally related to, SV40 and polyoma virus "late" mRNAs. It is also inferred that the 1.8- and 1.95-kb RNA species may be functionally related to the "early" transcripts of these papovaviruses.

Animals↗
PubMed2006

Genetics of global gene expression.

A new field of genetic analysis of global gene expression has emerged in recent years, driven by the realization that traditional techniques of linkage and association analysis can be applied to thousands of transcript levels measured by microarrays. Genetic dissection of transcript abundance has shed light on the architecture of quantitative traits, provided a new approach for connecting DNA sequence variation with phenotypic variation, and improved our understanding of transcriptional regulation and regulatory variation.

Amino Acid Sequence↗
PubMed2004

Gene expression profile of the nucleus accumbens of human cocaine abusers: evidence for dysregulation of myelin.

Chronic cocaine abuse induces long-term neural adaptations as a consequence of alterations in gene expression. This study was undertaken to identify those transcripts differentially regulated in the nucleus accumbens of human cocaine abusers. Affymetrix microarrays were used to measure transcript abundance in 10 cocaine abusers and 10 control subjects matched for age, race, sex, and brain pH. As expected, gene expression of cocaine- and amphetamine-regulated transcript (CART) was increased in the nucleus accumbens of cocaine abusers. The most robust and consistent finding, however, was a decrease in the expression of a number of myelin-related genes, including myelin basic protein (MBP), proteolipid protein (PLP), and myelin-associated oligodendrocyte basic protein (MOBP). The differential expression seen by microarray for CART as well as MBP, MOBP, and PLP was verified by RT-PCR. In addition, immunohistochemical experiments revealed a decrease in the number of MBP-immunoreactive oligodendrocytes present in the nucleus accumbens and surrounding white matter of cocaine abusers. These findings suggest a dysregulation of myelin in human cocaine abusers.

Adult↗
PubMed2000

Nutrient regulation of gene expression by the sterol regulatory element binding proteins: increased recruitment of gene-specific coregulatory factors and selective hyperacetylation of histone H3 in vivo.

We have evaluated the mechanism for sterol-regulated gene expression by the sterol regulatory element binding proteins (SREBPs) in intact cells. We show that activation of SREBPs by sterol depletion results in the increased binding of Sp1 to a site adjacent to SREBP in the promoter for the low density lipoprotein (LDL) receptor gene in vivo. Similarly, sterol depletion resulted in the increased recruitment of two distinct SREBP coregulatory factors, NF-Y and CREB, to the promoter for hydroxymethyl glutaryl CoA reductase, another key gene of intracellular cholesterol homeostasis. Furthermore, increased acetylation of histone H3 but not H4 was also detected in chromatin from both promoters on SREBP activation. Thus, SREBP activation results in the similar selective recruitment of different coregulatory generic transcription factors to two separate cholesterol-regulated promoters. These studies demonstrate the utility of the chromatin immunoprecipitation technique for analyzing the differential action of low-abundance transcription factors in fundamental regulatory events in intact cells. Our results also provide key in vivo support for the mechanism proposed from cell-free experiments, where SREBP increased the binding of Sp1 to the LDL receptor promoter. Finally, our findings also indicate that subtle differences in the pattern of core histone acetylation play a role in selective gene activation.

Acetylation↗
PubMed1991

Chloroplast RNA Stability in Chlamydomonas: Rapid Degradation of psbB and psbC Transcripts in Two Nuclear Mutants.

Toward understanding regulation of chloroplast transcript abundance, we have isolated and analyzed nuclear mutant strains of Chlamydomonas reinhardtii that lack chloroplast-encoded mRNAs for photosystem II proteins. Mutant 6.2z5 accumulates no transcripts of the psbC locus for the 43-kilodalton chlorophyll-binding protein. In mutant GE2.10, transcripts of psbB, encoding the 47-kilodalton chlorophyll-binding protein, cannot be detected [Jensen, K.H., Herrin, D.L., Plumley, F.G., and Schmidt, G.W. (1986). J. Cell Biol. 103, 1315-1325]. Also, GE2.10 does not accumulate several low molecular weight transcripts from a region of the chloroplast genome proximal to psbB. The levels of mRNAs from other chloroplast genes are not affected in either mutant. Chloroplast transcription was analyzed in permeabilized cells and by in vivo pulse labeling. Although 5[prime] ribonuclease was found as an artifactual activity of permeabilized cells, the results from both assays demonstrated that wild-type levels of psbC transcription occur in mutant 6.2z5 and that chloroplasts of GE2.10 transcribe psbB and adjacent genes. Thus, it appears that the nuclear genes that are mutated in 6.2z5 and GE2.10 encode products that, respectively, confer stability to transcripts from the psbC and the psbB regions of the chloroplast genome.

Journal Article↗
PubMed1982

Assembly of the mitochondrial membrane system. Processing of the apocytochrome b precursor RNAs in Saccharomyces cerevisiae D273-10B.

The DNA sequence of the apocytochrome b gene in Saccharomyces cerevisiae D273-10B contains two intervening sequences (Nobrega, F. G., and Tzagoloff, A. (1980) J. Biol. Chem. 255, 9828-9837). The exon-intron boundaries of the gene have been determined in this study from the sequence of the DNA which was copied from the mRNA. A protein of 385 amino acid residues is predicted from the 1155-nucleotide long coding regions. Northern blot analysis of total mitochondrial RNA, probed with restriction fragments from both exon and intron regions of the gene, reveals a 4.3-kilobase (kb) transcript containing both introns and two partially spliced intermediates, one (2.9 kb) lacking the first intron and the other (3.6 kb) lacking the second intron. The most abundant transcript (2.1 kb) hybridizes only to exon probes and is presumed to the fully spliced mRNA. S1 nuclease mapping of the purified mRNA indicates existence of two separate RNAs with identical 3' termini but differing by approximately 217 nucleotides at their 5' ends. The larger transcript has a 950-nucleotide nontranslated leader. Analyses of the RNA species present in various rho- and mit- mutants indicate that: 1) exon mutants process both introns, albeit not as efficiently as wild type, 2) intron mutants blocked in the excision of the first or second intron are capable of processing the alternate intron, suggesting a non-obligatory order of excision of the two intervening sequences, and 3) excision of the second intron occurs in rho- mutants and therefore does not require a mitochondrial translation product.

Base Sequence↗