scholarly journals Codon choice and gene expression: synonymous codons differ in their ability to direct aminoacylated-transfer RNA binding to ribosomes in vitro.

1988 ◽  
Vol 85 (12) ◽  
pp. 4242-4246 ◽  
Author(s):  
L. K. Thomas ◽  
D. B. Dix ◽  
R. C. Thompson
Keyword(s):  
Gene Expression ◽  
Rna Binding ◽  
Transfer Rna ◽  
Synonymous Codons

scholarly journals General and Target-Specific RNA Binding Properties of Epstein-Barr Virus SM Posttranscriptional Regulatory Protein

2009 ◽  
Vol 83 (22) ◽  
pp. 11635-11644 ◽  
Author(s):  
Zhao Han ◽  
Dinesh Verma ◽  
Chelsey Hilscher ◽  
Dirk P. Dittmer ◽  
Sankar Swaminathan
Keyword(s):  
Gene Expression ◽  
Nuclear Export ◽  
Epstein Barr Virus ◽  
Rna Binding ◽  
Regulatory Protein ◽  
Lytic Cycle ◽  
Binding Properties ◽  
Barr Virus ◽  
Epstein Barr

ABSTRACT Epstein-Barr virus (EBV) SM protein is an essential nuclear shuttling protein expressed by EBV early during the lytic phase of replication. SM acts to increase EBV lytic gene expression by binding EBV mRNAs and enhancing accumulation of the majority of EBV lytic cycle mRNAs. SM increases target mRNA stability and nuclear export, in addition to modulating RNA splicing. SM and its homologs in other herpesvirus have been hypothesized to function in part by binding viral RNAs and recruiting cellular export factors. Although activation of gene expression by SM is gene specific, it is unknown whether SM binds to mRNA in a specific manner or whether its RNA binding is target independent. SM-mRNA complexes were isolated from EBV-infected B-lymphocyte cell lines induced to permit lytic EBV replication, and a quantitative measurement of mRNAs corresponding to all known EBV open reading frames was performed by real-time quantitative reverse transcription-PCR. The results showed that although SM has broad RNA binding properties, there is a clear hierarchy of affinities among EBV mRNAs with respect to SM complex formation. In vitro binding assays with two of the most highly SM-associated transcripts suggested that SM binds preferentially to specific sequences or structures present in noncoding regions of some EBV mRNAs. Furthermore, the presence of these sequences conferred responsiveness to SM. These data are consistent with a mechanism of action similar to that of hnRNPs, which exert sequence-specific effects on gene expression despite having multiple degenerate consensus binding sites common to a large number of RNAs.

scholarly journals RNA interactions with CTCF are essential for its proper function

2019 ◽  
Author(s):  
Ricardo Saldaña-Meyer ◽  
Javier Rodriguez-Hernaez ◽  
Mayilaadumveettil Nishana ◽  
Karina Jácome-López ◽  
Elphege P. Nora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Binding ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Ctcf Binding ◽  
Proper Function ◽  
List Type ◽  
Transcriptional Inhibition ◽  
Local Insulation

SummaryThe function of the CCCTC-binding factor (CTCF) in the organization of the genome has become an important area of investigation, but the mechanisms of how CTCF dynamically contributes to genome organization is not clear. We previously discovered that CTCF binds to large numbers of endogenous RNAs; promoting its oligomerization. Here we found that inhibition of transcription or interfering with CTCF ability to bind RNA through mutations of two of its 11 zinc fingers that are not involved with CTCF binding to its cognate site in vitro, zinc finger-1 (ZF1) or −10 (ZF10), disrupt CTCF association to chromatin. These mutations alter gene expression profiles as CTCF mutants lose their ability to promote local insulation. Our results highlight the importance of RNA as a structural component of the genome, in part by affecting the association of CTCF with chromatin and likely its interaction with other factors.Transcriptional inhibition disrupts CTCF binding to chromatinRNA-binding regions (RBR) in CTCF are found within ZF1 and ZF10Local insulation is markedly decreased in ZF1∆ and ZF10∆ mutant rescuesGene expression and chromatin organization are disrupted by RBR mutants

scholarly journals The RNA-binding protein HuR regulates intestinal epithelial restitution by modulating Caveolin-1 gene expression

2020 ◽  
Author(s):  
Shan Cao ◽  
Lan Xiao ◽  
Junyao Wang ◽  
Guodong Chen ◽  
Yulan Liu
Keyword(s):  
Gene Expression ◽  
Posttranscriptional Regulation ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Mrna Levels ◽  
Epithelial Repair ◽  
Caveolin 1 ◽  
Protein Levels ◽  
Ectopic Overexpression

The integrity of the intestinal mucosal barrier protects hosts against pathological conditions. Early mucosal restitution after wounding refers to epithelial cell migration into a defect. The RNA-binding protein HuR plays an important role in the posttranscriptional regulation of gene expression and is involved in many aspects of cellular physiology. In the present study, we investigated the role of HuR in the regulation of cell migration through the posttranscriptional regulation of Caveolin-1 (Cav-1). Online software was used to identify Cav-1 mRNA as a potential target of HuR. The interaction of HuR with Cav-1 mRNA was investigated via ribonucleoprotein immunoprecipitation (RNP IP) assays and biotin pulldown analysis. HuR was found to bind specifically to the Cav-1 3’-UTR rather than the coding region or 5’-UTR. Transfection of cells with siHuR decreased both HuR protein levels and Cav-1 protein levels; conversely, ectopic overexpression of HuR via infection of cells with an adenoviral vector containing HuR cDNA (AdHuR) increased Cav-1 protein levels without disturbing Cav-1 mRNA levels. Thus, HuR enhanced Cav-1 expression in vitro by stimulating Cav-1 translation. Intestinal epithelium–specific HuR knockout in mice decreased Cav-1 protein levels without changing Cav-1 mRNA levels, consistent with the in vitro results. Decreasing the levels of HuR via siHuR transfection inhibited early epithelial repair, but this effect was reversed by ectopic overexpression of GFP-tagged Cav-1. These results indicate that posttranscriptional regulation of Cav-1 gene expression by HuR plays a critical role in the regulation of rapid epithelial repair after wounding.

scholarly journals Gle1 Regulates RNA Binding of the DEAD-Box Helicase Ded1 in Its Complex Role in Translation Initiation

2017 ◽  
Vol 37 (21) ◽  
Author(s):  
Peyman P. Aryanpur ◽  
Chelsea A. Regan ◽  
John M. Collins ◽  
Telsa M. Mittelmeier ◽  
David M. Renner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Binding ◽  
Mrna Export ◽  
Binding Assays ◽  
Cellular Mechanisms ◽  
Ribonucleoprotein Complexes ◽  
Dead Box

ABSTRACT DEAD-box proteins (DBPs) are required in gene expression to facilitate changes to ribonucleoprotein complexes, but the cellular mechanisms and regulation of DBPs are not fully defined. Gle1 is a multifunctional regulator of DBPs with roles in mRNA export and translation. In translation, Gle1 modulates Ded1, a DBP required for initiation. However, DED1 overexpression causes defects, suggesting that Ded1 can promote or repress translation in different contexts. Here we show that GLE1 expression suppresses the repressive effects of DED1 in vivo and Gle1 counteracts Ded1 in translation assays in vitro. Furthermore, both Ded1 and Gle1 affect the assembly of preinitiation complexes. Through mutation analysis and binding assays, we show that Gle1 inhibits Ded1 by reducing its affinity for RNA. Our results are consistent with a model wherein active Ded1 promotes translation but inactive or excess Ded1 leads to translation repression. Gle1 can inhibit either role of Ded1, positioning it as a gatekeeper to optimize Ded1 activity to the appropriate level for translation. This study suggests a paradigm for finely controlling the activity of DEAD-box proteins to optimize their function in RNA-based processes. It also positions the versatile regulator Gle1 as a potential node for the coordination of different steps of gene expression.

scholarly journals Coordination of mRNA and tRNA methylations by TRMT10A

2020 ◽  
Vol 117 (14) ◽  
pp. 7782-7791 ◽  
Author(s):  
R. Jordan Ontiveros ◽  
Hui Shen ◽  
Julian Stoute ◽  
Amber Yanas ◽  
Yixiao Cui ◽  
...  
Keyword(s):  
Gene Expression ◽  
Messenger Rna ◽  
High Throughput Sequencing ◽  
Transfer Rna ◽  
Decay Rates ◽  
Cross Linking ◽  
Additional Layer ◽  
Trna Methyltransferase ◽  
Regulatory Complexity

The posttranscriptional modification of messenger RNA (mRNA) and transfer RNA (tRNA) provides an additional layer of regulatory complexity during gene expression. Here, we show that a tRNA methyltransferase, TRMT10A, interacts with an mRNA demethylase FTO (ALKBH9), both in vitro and inside cells. TRMT10A installsN1-methylguanosine (m1G) in tRNA, and FTO performs demethylation onN6-methyladenosine (m6A) andN6,2′-O-dimethyladenosine (m6Am) in mRNA. We show that TRMT10A ablation not only leads to decreased m1G in tRNA but also significantly increases m6A levels in mRNA. Cross-linking and immunoprecipitation, followed by high-throughput sequencing results show that TRMT10A shares a significant overlap of associated mRNAs with FTO, and these mRNAs have accelerated decay rates potentially through the regulation by a specific m6A reader, YTHDF2. Furthermore, transcripts with increased m6A upon TRMT10A ablation contain an overrepresentation of m1G9-containing tRNAs codons read by tRNAGln(TTG), tRNAArg(CCG), and tRNAThr(CGT). These findings collectively reveal the presence of coordinated mRNA and tRNA methylations and demonstrate a mechanism for regulating gene expression through the interactions between mRNA and tRNA modifying enzymes.

scholarly journals Casein Kinase II Phosphorylates the Fragile X Mental Retardation Protein and Modulates Its Biological Properties

2002 ◽  
Vol 22 (24) ◽  
pp. 8438-8447 ◽  
Author(s):  
Mikiko C. Siomi ◽  
Kyoko Higashijima ◽  
Akira Ishizuka ◽  
Haruhiko Siomi
Keyword(s):  
Gene Expression ◽  
Rna Binding ◽  
Fragile X ◽  
Regulation Of Gene Expression ◽  
Phosphorylation Site ◽  
Casein Kinase Ii ◽  
Biological Properties ◽  
Casein Kinase

ABSTRACT Fragile X syndrome is caused by loss of FMR1 protein expression. FMR1 binds RNA and associates with polysomes in the cytoplasm; thus, it has been proposed to function as a regulator of gene expression at the posttranscriptional level. Posttranslational modification of FMR1 had previously been suggested to regulate its activity, but no experimental support for this model has been reported to date. Here we report that FMR1 in Drosophila melanogaster (dFMR1) is phosphorylated in vivo and that the homomer formation and the RNA-binding activities of dFMR1 are modulated by phosphorylation in vitro. Identification of a protein phosphorylating dFMR1 showed it to be Drosophila casein kinase II (dCKII). dCKII directly interacts with and phosphorylates dFMR1 in vitro. The phosphorylation site in dFMR1 was identified as Ser406, which is highly conserved among FMR1 family members from several species. Using mass spectrometry, we established that Ser406 of dFMR1 is indeed phosphorylated in vivo. Furthermore, human FMR1 (hFMR1) is also phosphorylated in vivo, and alteration of the conserved Ser500 in hFMR1 abolishes phosphorylation by CKII in vitro. These studies support the model that the biological functions of FMR1, such as regulation of gene expression, are likely regulated by its phosphorylation.

Effect of moderate hypothermia on gene expression by THP-1 cells: a DNA microarray study

2006 ◽  
Vol 26 (1) ◽  
pp. 91-98 ◽  
Author(s):  
Larry A. Sonna ◽  
Matthew M. Kuhlmeier ◽  
Heather C. Carter ◽  
Jeffrey D. Hasday ◽  
Craig M. Lilly ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Binding ◽  
Geometric Mean ◽  
Acute Monocytic Leukemia ◽  
Moderate Hypothermia ◽  
Binding Motif ◽  
Monocytic Leukemia ◽  
Paired Samples

The mechanisms by which moderate hypothermia (32°C for 12–72 h) affect human cellular function are unclear. We tested the hypothesis that it produces broad changes in mRNA expression in vitro. Acute monocytic leukemia (THP-1) cells were incubated under control conditions (37°C) or moderate hypothermia (32°C) for 24 h. RNA was extracted, and the hypothermic response was confirmed by examining the expression of the cold-induced RNA-binding protein (CIRBP) gene by RT-PCR. Gene expression analysis was performed on seven sets of paired samples with Affymetrix U133A chips using established statistical methods. Sequences were considered affected by cold if they showed statistically significant changes in expression and also met published post hoc filter criteria (changes in geometric mean expression of ≥2-fold and expression calls of “present” or “marginal” in at least half of the experiments). Changes in the expression of selected sequences were further confirmed by PCR. Sixty-seven sequences met the criteria for increased expression (including cold-inducible genes CIRBP and RNA binding motif 3), and 100 sequences showed decreased expression as a result of hypothermia. Functional categories affected by hypothermia included genes involved in immune responses; cell growth, proliferation, and differentiation; and metabolism and biosynthesis. Several heat shock proteins (HSPs) showed decreases in expression. Moderate hypothermia produces substantial changes in gene expression, in categories potentially of systemic importance. Cold exposure without rewarming decreased the expression of several HSPs. These in vitro findings suggest that prolonged hypothermia in vivo might be capable of producing physiologically relevant changes in gene expression by circulating leukocytes.

scholarly journals Cold-Inducible RNA-binding protein (CIRBP) adjusts clock gene expression and REM sleep recovery following sleep deprivation

2018 ◽  
Author(s):  
Marieke MB Hoekstra ◽  
Yann Emmenegger ◽  
Paul Franken
Keyword(s):  
Gene Expression ◽  
Sleep Deprivation ◽  
Rem Sleep ◽  
Clock Gene ◽  
Rna Binding ◽  
High Amplitude ◽  
Knock Out ◽  
Clock Gene Expression ◽  
Sleep Homeostasis

AbstractSleep depriving mice affects clock gene expression, suggesting that these genes partake in sleep homeostasis. The mechanisms linking wakefulness to clock gene expression are, however, not well understood. We propose CIRBP because its rhythmic expression is i) sleep-wake driven and ii) necessary for high-amplitude clock gene expression in vitro. We therefore expect Cirbp knock-out (KO) mice to exhibit attenuated sleep-deprivation (SD) induced changes in clock gene expression, and consequently to differ in their sleep homeostatic regulation. Lack of CIRBP indeed blunted the SD-incurred changes in cortical expression of the clock gene Rev-erbα whereas it amplified the changes in Per2 and Clock. Concerning sleep homeostasis, KO mice accrued only half the extra REM sleep wild-type (WT) littermates obtained during recovery. Unexpectedly, KO mice were more active during lights-off which was accompanied by an acceleration of theta oscillations. Thus, CIRBP adjusts cortical clock gene expression after SD and expedites REM sleep recovery.

scholarly journals Cold-inducible RNA-binding protein (CIRBP) adjusts clock-gene expression and REM-sleep recovery following sleep deprivation

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Marieke MB Hoekstra ◽  
Yann Emmenegger ◽  
Jeffrey Hubbard ◽  
Paul Franken
Keyword(s):  
Gene Expression ◽  
Sleep Deprivation ◽  
Rem Sleep ◽  
Clock Gene ◽  
Rna Binding ◽  
High Amplitude ◽  
Knock Out ◽  
Clock Gene Expression ◽  
Sleep Homeostasis

Sleep depriving mice affects clock-gene expression, suggesting that these genes contribute to sleep homeostasis. The mechanisms linking extended wakefulness to clock-gene expression are, however, not well understood. We propose CIRBP to play a role because its rhythmic expression is i) sleep-wake driven and ii) necessary for high-amplitude clock-gene expression in vitro. We therefore expect Cirbp knock-out (KO) mice to exhibit attenuated sleep-deprivation-induced changes in clock-gene expression, and consequently to differ in their sleep homeostatic regulation. Lack of CIRBP indeed blunted the sleep-deprivation incurred changes in cortical expression of Nr1d1, whereas it amplified the changes in Per2 and Clock. Concerning sleep homeostasis, KO mice accrued only half the extra REM sleep wild-type (WT) littermates obtained during recovery. Unexpectedly, KO mice were more active during lights-off which was accompanied with faster theta oscillations compared to WT mice. Thus, CIRBP adjusts cortical clock-gene expression after sleep deprivation and expedites REM-sleep recovery.

Changes of taxane production and gene expression during the development of in vitro Taxus plant cultures

Planta Medica ◽  
2011 ◽  
Vol 77 (12) ◽  
Author(s):  
M Onrubia ◽  
A Gallego ◽  
K Ramírez ◽  
HR Vidal Limon ◽  
RM Cusidó ◽  
...  
Keyword(s):  
Gene Expression
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