Control of gene expression in P2-related coliphages: the in vitro transcription pattern of coliphage 186.

Bacillus subtilis employs five purine riboswitches for the control of purine de novo synthesis and transport at the transcription level. All of them are formed by a structurally conserved aptamer, and a variable expression platform harboring a rho-independent transcription terminator. In this study, we characterized all five purine riboswitches under the context of active gene expression processes both in vitro and in vivo. We identified transcription pause sites located in the expression platform upstream of the terminator of each riboswitch. Moreover, we defined a correlation between in vitro transcription readthrough and in vivo gene expression. Our in vitro assay demonstrated that the riboswitches operate in the micromolar range of concentration for the cognate metabolite. Our in vivo assay showed the dynamics of control of gene expression by each riboswitch. This study deepens the knowledge of the regulatory mechanism of purine riboswitches.

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Ligand-dependent, Pit-1/growth hormone factor-1 (GHF-1)-independent transcriptional stimulation of rat growth hormone gene expression by thyroid hormone receptors in vitro

Molecular and Cellular Biology ◽

10.1128/mcb.13.3.1719-1727.1993 ◽

1993 ◽

Vol 13 (3) ◽

pp. 1719-1727

Author(s):

C S Suen ◽

W W Chin

Keyword(s):

Gene Expression ◽

Growth Hormone ◽

Thyroid Hormone ◽

Promoter Activity ◽

Hormone Receptors ◽

Nuclear Extract ◽

In Vitro Transcription ◽

Stimulation Of ◽

Transcriptional Stimulation

The expression of the rat growth hormone (rGH) gene in the anterior pituitary gland is modulated by Pit-1/GHF-1, a pituitary-specific transcription factor, and by other more widely distributed factors, such as the thyroid hormone receptors (TRs), Sp1, and the glucocorticoid receptor. Thyroid hormone (T3)-mediated transcriptional stimulation of rGH gene expression has been extensively studied in vivo and in vitro including the measurements of (i) rGH mRNA by blot hybridization, (ii) transcriptional rate of rGH gene by nuclear run-on, and (iii) reporter gene expression in which a chimeric plasmid containing 5'-flanking sequences of the rGH gene linked to a reporter gene has been transfected either stably or transiently into pituitary and/or nonpituitary cells. From these studies, it has been suggested that the Pit-1/GHF-1 binding site is necessary for full T3 action. We developed a cell-free in vitro transcription system to examine further the roles of the TRs and Pit-1/GHF-1 in rGH gene activation. Using GH3 nuclear extract as a source of TRs and Pit-1/GHF-1, this in vitro transcription assay showed that T3 stimulation of rGH promoter activity is dependent on the addition of T3 to the GH3 nuclear extract. This transcriptional stimulation was augmented with increasing concentrations of ligand and was T3, but not T4 or reverse T3, specific. T3-mediated stimulation of rGH promoter activity was completely abolished by preincubation of the nuclear extract with rGH-thyroid hormone response element (-200 to -160) but not with Pit-1/GHF-1 (-137 to -65) oligonucleotides. Further, neither deletion of both Pit-1/GHF-1 binding sites nor mutation of the proximal Pit-1/GHF-1 binding site from the rGH promoter abrogated the T3 effect. These results provide evidence that T3-stimulated rGH promoter activity is independent of Pit-1/GHF-1 and raise the possibility that the stimulation of rGH gene expression by T3 might involve direct interaction of TRs with the general transcriptional apparatus.

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Regulation of protamine gene expression in an in vitro homologous system.

Acta Biochimica Polonica ◽

10.18388/abp.1996_4506 ◽

1996 ◽

Vol 43 (2) ◽

pp. 369-377 ◽

Cited By ~ 1

Author(s):

J M Jankowski ◽

P D Cannon ◽

F Van der Hoorn ◽

L D Wasilewska ◽

N C Wong ◽

...

Keyword(s):

Gene Expression ◽

Regulatory Elements ◽

In Vitro Transcription ◽

Tata Box ◽

Transcription System ◽

Proposed Model ◽

Binding Factor ◽

Gc Box ◽

Responsive Element

An in vitro transcription system from the trout testis nuclei was developed to study trout protamine gene expression. The protamine promoter contains, among others, two regulatory elements: 1) a cAMP-responsive element or CRE element (TGACGTCA) which is present in position 5' to TATA box, and 2) GC box (CCGCCC) which is present in position 3' to TATA box. The removal of the CRE-binding protein by titration (by the addition of appropriate oligonucleotides to the incubation mixture) resulted in a decrease in transcription of the protamine gene. These results were confirmed by experiments in which the pure CRE-binding factor (TPBP1) was used, as well as by those where a stimulatory effect of cAMP on protamine promoter transcription was observed. On the other hand, addition of oligonucleotides containing the GC-box sequence enhanced the protamine gene transcription indicating that the protein (Sp1 like) which binds to this sequence acts as a repressor of protamine gene expression. These results confirm the previously proposed model which suggested that the GC box played a role in negative regulation of the protamine gene expression. Involvement of some other factors in this process was also discussed.

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The GAGA factor is required in the early Drosophila embryo not only for transcriptional regulation but also for nuclear division

Development ◽

10.1242/dev.122.4.1113 ◽

1996 ◽

Vol 122 (4) ◽

pp. 1113-1124 ◽

Cited By ~ 1

Author(s):

K.M. Bhat ◽

G. Farkas ◽

F. Karch ◽

H. Gyurkovics ◽

J. Gausz ◽

...

Keyword(s):

Gene Expression ◽

Chromatin Remodeling ◽

In Vitro Transcription ◽

Drosophila Embryo ◽

Gaga Factor ◽

Early Drosophila Embryo ◽

Hypersensitive Sites ◽

And Function ◽

Stimulatory Factor

The GAGA protein of Drosophila was first identified as a stimulatory factor in in vitro transcription assays using the engrailed and Ultrabithorax promoters. Subsequent studies have suggested that the GAGA factor promotes transcription by blocking the repressive effects of histones; moreover, it has been shown to function in chromatin remodeling, acting together with other factors in the formation of nuclease hypersensitive sites in vitro. The GAGA factor is encoded by the Trithorax-like locus and in the studies reported here we have used the maternal effect allele Trl13C to examine the functions of the protein during embryogenesis. We find that GAGA is required for the proper expression of a variety of developmental loci that contain GAGA binding sites in their upstream regulatory regions. The observed disruptions in gene expression are consistent with those expected for a factor involved in chromatin remodeling. In addition to facilitating gene expression, the GAGA factor appears to have a more global role in chromosome structure and function. This is suggested by the spectrum of nuclear cleavage cycle defects observed in Trl13C embryos. These defects include asynchrony in the cleavage cycles, failure in chromosome condensation, abnormal chromosome segregation and chromosome fragmentation. These defects are likely to be related to the association of the GAGA protein with heterochromatic satellite sequences which is observed throughout the cell cycle.

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The Mycobacterium tuberculosis sRNA F6 regulates expression of groEL/S

10.1101/2020.07.15.204107 ◽

2020 ◽

Author(s):

Joanna Houghton ◽

Angela Rodgers ◽

Graham Rose ◽

Kristine B. Arnvig

Keyword(s):

Gene Expression ◽

Mycobacterium Tuberculosis ◽

Small Rnas ◽

Transcriptional Control ◽

Cold Shock ◽

Control Of Gene Expression ◽

Rna Biology ◽

Mouse Model Of Infection

ABSTRACTAlmost 140 years after the identification of Mycobacterium tuberculosis as the etiological agent of tuberculosis, important aspects of its biology remain poorly described. Little is known about the role of post-transcriptional control of gene expression and RNA biology, including the role of most of the small RNAs (sRNAs) identified to date. We have carried out a detailed investigation of the M. tuberculosis sRNA, F6, and show it to be dependent on SigF for expression and significantly induced during in vitro starvation and in a mouse model of infection. However, we found no evidence of attenuation of a ΔF6 strain within the first 20 weeks of infection. A further exploration of F6 using in vitro models of infection suggests a role for F6 as a highly specific regulator of the heat shock repressor, HrcA. Our results point towards a role for F6 during periods of low metabolic activity similar to cold shock and associated with nutrient starvation such as that found in human granulomas in later stages of infection.

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DEFECTIVE STEROIDAL SYNTHESIS BY ADRENAL TISSUE: THE CONTROL OF GENE EXPRESSION CAUSING LOSS OF ACTIVE STEROIDOGENIC ENZYMES

Acta Endocrinologica ◽

10.1530/acta.0.0770325 ◽

1974 ◽

Vol 77 (2) ◽

pp. 325-336

Author(s):

K. Williams

Keyword(s):

Gene Expression ◽

Adrenal Glands ◽

Hydroxysteroid Dehydrogenase ◽

Ascites Cell ◽

Control Of Gene Expression ◽

Adrenocortical Hyperplasia ◽

Normal Human ◽

Adrenocortical Tumour

ABSTRACT RNA was isolated from normal human adrenal glands and found to cause the formation of Δ5-3β-hydroxysteroid dehydrogenase-isomerase and steroid 21-hydroxylase activities by a Krebs II ascites cell-free protein synthesising system. Although no functional steroid 21-hydroxylase in vivo or in vitro was found in a gland from a patient with virilism due to congenital adrenocortical hyperplasia the RNA would still give steroid 21-hydroxylase-like activity in the protein synthesising system which suggests that the inherited defect was not in the structural gene. Activity could not be induced by RNA from a 'non-functioning' adrenocortical tumour or rat liver.

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Cell-specific posttranscriptional regulation of CFTR gene expression via influence of MAPK cascades on 3′UTR part of transcripts

AJP Cell Physiology ◽

10.1152/ajpcell.00595.2004 ◽

2005 ◽

Vol 289 (5) ◽

pp. C1240-C1250 ◽

Cited By ~ 26

Author(s):

Maryvonne Baudouin-Legros ◽

Alexandre Hinzpeter ◽

Amandine Jaulmes ◽

Franck Brouillard ◽

Bruno Costes ◽

...

Keyword(s):

Gene Expression ◽

Cell Lines ◽

Posttranscriptional Regulation ◽

P38 Map Kinase ◽

Cftr Gene ◽

Control Of Gene Expression ◽

Cytosolic Proteins ◽

Tnf Α ◽

Ht 29

Expression of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene, which contains the mutations responsible for CF, is regulated by cytokines (TNF-α and IL-1β) in a cell-specific manner. TNF-α decreases CFTR mRNA in human colon cell lines (HT-29), but not in pulmonary cell lines (Calu-3), and IL-1β increases it only in Calu-3 cells. We looked for the cytokine-induced posttranscriptional regulation of CFTR gene expression and studied the modulation of CFTR mRNA stability linked to its 3′ untranslated sequence (3′UTR) in HT-29 and Calu-3 cells. The stability of CFTR mRNA was analyzed by Northern blot after in vitro incubation of total RNAs from CFTR-expressing cells with cytosolic proteins extracted from control or cytokine-treated HT-29 and Calu-3 cells. CFTR mRNA was degraded only by extracts of TNF-α-treated HT-29 cells and not by cytosolic proteins from untreated or IL-1β-treated HT-29 cells. In contrast, extracts of untreated Calu-3 cells enhanced CFTR mRNA degradation, and IL-1β treatment inhibited this; TNF-α had no significant effect. The 3′UTR part of CFTR mRNA was found to be required for this posttranscriptional regulation. The 5′ part of the 3′UTR (the 217 first bases), which contains two AUUUA sequences, was implicated in CFTR mRNA destabilization and the following 136 bases, containing several C-repeats in U-rich environment, in its protection. The proteins, which reacted with the U- and C-repeats of CFTR mRNA 3′UTR, were mainly controlled by stimulation of the p42/p44 and p38 MAP kinase cascades with interaction between these pathways. This posttranscriptional control of gene expression is a common feature of CFTR and many proteins of inflammation.

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In Vitro Transcription Amplification and Labeling Methods Contribute to the Variability of Gene Expression Profiling with DNA Microarrays

Journal of Molecular Diagnostics ◽

10.2353/jmoldx.2006.050077 ◽

2006 ◽

Vol 8 (2) ◽

pp. 183-192 ◽

Cited By ~ 20

Author(s):

Changqing Ma ◽

Maureen Lyons-Weiler ◽

Wenjing Liang ◽

William LaFramboise ◽

John R. Gilbertson ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Dna Microarrays ◽

In Vitro Transcription

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Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0900028106 ◽

2009 ◽

Vol 106 (17) ◽

pp. 7028-7033 ◽

Cited By ~ 356

Author(s):

Zhe Ji ◽

Ju Youn Lee ◽

Zhenhua Pan ◽

Bingjun Jiang ◽

Bin Tian

Keyword(s):

Gene Expression ◽

Embryonic Development ◽

Posttranscriptional Regulation ◽

Regulation Of Gene Expression ◽

Alternative Polyadenylation ◽

Untranslated Regions ◽

C2c12 Myoblast ◽

Control Of Gene Expression ◽

Differentiation And Proliferation

The 3′ untranslated regions (3′ UTRs) of mRNAs containcis-acting elements for posttranscriptional regulation of gene expression. Here, we report that mouse genes tend to express mRNAs with longer 3′ UTRs as embryonic development progresses. This global regulation is controlled by alternative polyadenylation and coordinates with initiation of organogenesis and aspects of embryonic development, including morphogenesis, differentiation, and proliferation. Using myogenesis of C2C12 myoblast cells as a model, we recapitulated this process in vitro and found that 3′ UTR lengthening is likely caused by weakening of mRNA polyadenylation activity. Because alternative 3′ UTR sequences are typically longer and have higher AU content than constitutive ones, our results suggest that lengthening of 3′ UTR can significantly augment posttranscriptional control of gene expression during embryonic development, such as microRNA-mediated regulation.

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Intrusion of a DNA Repair Protein in the RNome World: Is This the Beginning of a New Era?

Molecular and Cellular Biology ◽

10.1128/mcb.01174-09 ◽

2009 ◽

Vol 30 (2) ◽

pp. 366-371 ◽

Cited By ~ 65

Author(s):

Gianluca Tell ◽

David M. Wilson ◽

Chow H. Lee

Keyword(s):

Gene Expression ◽

Dna Repair ◽

Mrna Level ◽

Rna Metabolism ◽

Coding Region ◽

Control Of Gene Expression ◽

Dna And Rna ◽

New Findings

ABSTRACT Apurinic/apyrimidinic endonuclease 1 (APE1), an essential protein in mammals, is known to be involved in base excision DNA repair, acting as the major abasic endonuclease; the protein also functions as a redox coactivator of several transcription factors that regulate gene expression. Recent findings highlight a novel role for APE1 in RNA metabolism. The new findings are as follows: (i) APE1 interacts with rRNA and ribosome processing protein NPM1 within the nucleolus; (ii) APE1 interacts with proteins involved in ribosome assembly (i.e., RLA0, RSSA) and RNA maturation (i.e., PRP19, MEP50) within the cytoplasm; (iii) APE1 cleaves abasic RNA; and (iv) APE1 cleaves a specific coding region of c-myc mRNA in vitro and influences c-myc mRNA level and half-life in cells. Such findings on the role of APE1 in the posttranscriptional control of gene expression could explain its ability to influence diverse biological processes and its relocalization to cytoplasmic compartments in some tissues and tumors. In addition, we propose that APE1 serves as a “cleansing” factor for oxidatively damaged abasic RNA, establishing a novel connection between DNA and RNA surveillance mechanisms. In this review, we introduce questions and speculations concerning the role of APE1 in RNA metabolism and discuss the implications of these findings in a broader evolutionary context.

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