scholarly journals Buffering of transcription rate by mRNA half-life is a conserved feature of Rett syndrome models

2021 ◽  
Author(s):  
Deivid Carvalho Rodrigues ◽  
Marat Mufteev ◽  
Kyoko E Yuki ◽  
Ashrut Narula ◽  
Wei Wei ◽  
...  
Keyword(s):  
Rett Syndrome ◽  
Half Life ◽  
Rna Binding ◽  
Neurodevelopmental Disorder ◽  
Rna Binding Protein ◽  
Transcription Rate ◽  
Mrna Levels ◽  
Life Changes ◽  
Limited Evidence ◽  
Mrna Half Life

Models of MECP2 dysfunction in Rett syndrome (RTT) assume that transcription rate changes directly correlate with altered steady-state mRNA levels. However, limited evidence suggests that transcription rate changes are buffered by poorly understood compensatory post-transcriptional mechanisms. Here we measure transcription rate and mRNA half-life changes in RTT patient neurons using RATE-seq, and reinterpret nuclear and whole-cell RNAseq from Mecp2 mice. Genes are dysregulated by changing transcription rate only or half-life only and are buffered when both are changed. We utilized classifier models to understand the direction of transcription rate changes based on gene-body DNA sequence, and combined frequencies of three dinucleotides were better predictors than contributions by CA and CG. MicroRNA and RNA-Binding Protein (RBP) motifs were enriched in 3ʹUTRs of genes with half-life changes. Motifs for nuclear localized RBPs were enriched on buffered genes with increased transcription rate. Our findings identify post-transcriptional mechanisms in humans and mice that alter half-life only or buffer transcription rate changes when a transcriptional modulator gene is mutated in a neurodevelopmental disorder.

The KH-type splicing regulatory protein (KSRP) regulates type III interferon expression post-transcriptionally

2019 ◽  
Vol 476 (2) ◽  
pp. 333-352 ◽  
Author(s):  
Lisa Schmidtke ◽  
Katharina Schrick ◽  
Sabrina Saurin ◽  
Rudolf Käfer ◽  
Fabian Gather ◽  
...  
Keyword(s):  
Half Life ◽  
Rna Binding ◽  
Binding Protein ◽  
Regulatory Protein ◽  
Rna Binding Protein ◽  
Luciferase Reporter ◽  
Regulatory Function ◽  
Type Iii ◽  
Type Iii Ifn ◽  
Mrna Half Life

Abstract Type III interferons (IFNs) are the latest members of the IFN family. They play an important role in immune defense mechanisms, especially in antiviral responses at mucosal sites. Moreover, they control inflammatory reactions by modulating neutrophil and dendritic cell functions. Therefore, it is important to identify cellular mechanisms involved in the control of type III IFN expression. All IFN family members contain AU-rich elements (AREs) in the 3′-untranslated regions (3′-UTR) of their mRNAs that determine mRNA half-life and consequently the expressional level of these cytokines. mRNA stability is controlled by different proteins binding to these AREs leading to either stabilization or destabilization of the respective target mRNA. The KH-type splicing regulatory protein KSRP (also named KHSRP) is an important negative regulator of ARE-containing mRNAs. Here, we identify the interferon lambda 3 (IFNL3) mRNA as a new KSRP target by pull-down and immunoprecipitation experiments, as well as luciferase reporter gene assays. We characterize the KSRP-binding site in the IFNL3 3′-UTR and demonstrate that KSRP regulates the mRNA half-life of the IFNL3 transcript. In addition, we detect enhanced expression of IFNL3 mRNA in KSRP−/− mice, establishing a negative regulatory function of KSRP in type III IFN expression also in vivo. Besides KSRP the RNA-binding protein AUF1 (AU-rich element RNA-binding protein 1) also seems to be involved in the regulation of type III IFN mRNA expression.

Regulation of c-myc mRNA Half-Life by an RNA-Binding Protein

Tumor Biology ◽  
1996 ◽  
pp. 257-272
Author(s):  
Jeffrey Ross ◽  
Philip Bernstein ◽  
Rebecca D. Prokipcak ◽  
David J. Herrick
Keyword(s):  
Half Life ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Mrna Half Life

scholarly journals Identification and characterization of a 44 kDa protein that binds specifically to the 3′-untranslated region of CYP2a5 mRNA: inducibility, subcellular distribution and possible role in mRNA stabilization

1996 ◽  
Vol 313 (3) ◽  
pp. 1029-1037 ◽  
Author(s):  
Olivier GENESTE ◽  
Françoise RAFFALLI ◽  
Matti A. LANG
Keyword(s):  
Half Life ◽  
Untranslated Region ◽  
Translational Regulation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Blocking Agent ◽  
Subcellular Fractionation ◽  
Mrna Stabilization ◽  
Nuclear Extracts

Stabilization of mRNA is important in the regulation of CYP2a5 expression but the factors involved in the process are not known [Aida and Negishi (1991) Biochemistry 30, 8041–8045]. In this paper, we describe, for the first time, a protein that binds specifically to the 3′-untranslated region of CYP2a5 mRNA and which is inducible by pyrazole, a compound known to increase the half-life of CYP2a5 mRNA. We also demonstrate that pyrazole treatment causes an elongation of the CYP2a5 mRNA poly(A) tail, and that phenobarbital, which is transcriptional activator of the CYP2a5 gene that does not affect the mRNA half-life, neither induces the RNA-binding protein nor affects the poly(A) tail size. SDS/PAGE of the UV-cross-linked RNA–protein complex demonstrated that the RNA-binding protein has an apparent molecular mass of 44 kDa. The protein-binding site was localized to a 70-nucleotide region between bases 1585 and 1655. Treatment of cytoplasmic extracts with an SH-oxidizing agent, diamide, an SH-blocking agent, N-ethylmaleimide or potato acid phosphatase abolished complex-formation, suggesting that the CYP2a5 mRNA-binding protein is subject to post-translational regulation. Subcellular fractionation showed that the 44 kDa protein is present in polyribosomes and nuclei, and that its apparent induction is much stronger in polyribosomes than in nuclear extracts. We propose that this 44 kDA RNA-binding protein is involved in the stabilization of CYP2a5 mRNA by controlling the length of the poly(A) tail.

Depression of nuclear transcription and extension of mRNA half-life under anoxia in Artemia franciscana embryos

2000 ◽  
Vol 203 (7) ◽  
pp. 1123-1130 ◽  
Author(s):  
F. van Breukelen ◽  
R. Maier ◽  
S.C. Hand
Keyword(s):  
Half Life ◽  
Mammalian Cells ◽  
Transcriptional Activity ◽  
Artemia Franciscana ◽  
Mrna Levels ◽  
Compensatory Mechanisms ◽  
Depressed State ◽  
Initiation Of Transcription ◽  
Mrna Half Life

Transcriptional activity, as assessed by nuclear run-on assays, was constant during 10 h of normoxic development for embryos of the brine shrimp Artemia franciscana. Exposure of embryos to only 4 h of anoxia resulted in a 79.3+/−1 % decrease in levels of in-vivo-initiated transcripts, and transcription was depressed by 88. 2+/−0.7 % compared with normoxic controls after 24 h of anoxia (means +/− s.e.m., N=3). Initiation of transcription was fully restored after 1 h of normoxic recovery. Artificially lowering the intracellular pH of aerobic embryos to the value reflective of anoxia (pH 6.7) showed that acidification alone explained over half the transcriptional arrest. Initiation of transcription was not rescued by application of 80 % carbon monoxide under anoxia, which suggests that heme-based oxygen sensing is not involved in this global arrest. When these transcriptional data are combined with the finding that mRNA levels are unchanged for at least 6 h of anoxia, it is clear that the half-life of mRNA is extended at least 8.5-fold compared with that in aerobic embryos. In contrast to the activation of compensatory mechanisms to cope with anoxia that occurs in mammalian cells, A. franciscana embryos enter a metabolically depressed state in which gene expression and mRNA turnover are cellular costs apparently not compatible with survival and in which extended tolerance supercedes the requirement for continued metabolic function.

scholarly journals Regulation of thrombospondin-1 expression through AU-rich elements in the 3′UTR of the mRNA

2011 ◽  
Vol 16 (1) ◽  
Author(s):  
Asa Mcgray ◽  
Timothy Gingerich ◽  
James Petrik ◽  
Jonathan Lamarre
Keyword(s):  
Gene Expression ◽  
Mrna Stability ◽  
Half Life ◽  
Rna Binding ◽  
Binding Protein ◽  
Site Directed Mutagenesis ◽  
Hek293 Cells ◽  
Luciferase Reporter ◽  
Thrombospondin 1 ◽  
Mrna Half Life

AbstractThrombospondin-1 (TSP-1) is a matricellular protein that participates in numerous normal and pathological tissue processes and is rapidly modulated by different stimuli. The presence of 8 highly-conserved AU rich elements (AREs) within the 3′-untranslated region (3′UTR) of the TSP-1 mRNA suggests that post-transcriptional regulation is likely to represent one mechanism by which TSP-1 gene expression is regulated. We investigated the roles of these AREs, and proteins which bind to them, in the control of TSP-1 mRNA stability. The endogenous TSP-1 mRNA half-life is approximately 2.0 hours in HEK293 cells. Luciferase reporter mRNAs containing the TSP-1 3′UTR show a similar rate of decay, suggesting that the 3′UTR influences the decay rate. Site-directed mutagenesis of individual and adjacent AREs prolonged reporter mRNA halflife to between 2.2 and 4.4 hours. Mutation of all AREs increased mRNA half life to 8.8 hours, suggesting that all AREs have some effect, but that specific AREs may have key roles in stability regulation. A labeled RNA oligonucleotide derived from the most influential ARE was utilized to purify TSP-1 AREbinding proteins. The AU-binding protein AUF1 was shown to associate with this motif. These studies reveal that AREs in the 3′UTR control TSP-1 mRNA stability and that the RNA binding protein AUF1 participates in this control. These studies suggest that ARE-dependent control of TSP-1 mRNA stability may represent an important component in the control of TSP-1 gene expression.

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 Differential regulation of the expression of fast-type sarcoplasmic-reticulum Ca2+-ATPase by thyroid hormone and insulin-like growth factor-I in the L6 muscle cell line

1994 ◽  
Vol 303 (2) ◽  
pp. 467-474 ◽  
Author(s):  
M H M Thelen ◽  
A Muller ◽  
M J Zuidwijk ◽  
G C van der Linden ◽  
W S Simonides ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Growth Factor ◽  
Thyroid Hormone ◽  
Sarcoplasmic Reticulum ◽  
Mrna Stability ◽  
Half Life ◽  
Mrna Levels ◽  
Factor I ◽  
Igf I ◽  
Mrna Half Life

The aim of this study was to investigate the mechanism(s) underlying the thyroid-hormone (L-tri-iodothyronine, T3)-induced elevation of fast-type sarcoplasmic-reticulum Ca(2+)-ATPase (SERCA1) levels in L6 myotubes and the potentiating effect of insulin-like growth factor-I (IGF-I) [Muller, van Hardeveld, Simonides and van Rijn (1991) Biochem. J. 275, 35-40]. T3 increased the SERCA1 protein level (per microgram of DNA) by 160%. The concomitant increase in the SERCA1 mRNA level was somewhat higher (240%). IGF-I also increased SERCA1 protein (110%) and mRNA levels (50%), whereas IGF-I + T3 increased SERCA1 protein and mRNA levels by 410% and 380% respectively. These SERCA1 mRNA analyses show that the more-than-additive action of T3 and IGF-I on SERCA1 expression is, at least in part, pre-translational in nature. Further studies showed that the half-life of SERCA1 protein in L6 cells (17.5 h) was not altered by T3. In contrast, IGF-I prolonged the half-life of SERCA1 protein 1.5-1.9-fold, which may contribute to the disproportional increase in SERCA1 protein content compared with mRNA by IGF-I. Measurements of SERCA1 mRNA half-life (as determined by actinomycin D chase) showed no difference from the control values (15.5 h) in the presence of T3 or IGF-I alone. When T3 and IGF-I were both present, the SERCA1 mRNA half-life was prolonged 2-fold. No significant effects of T3 and IGF-I were observed on the half-life of total protein (37.4 h) and total RNA (37.0 h). The absence of an effect of T3 on SERCA1 protein and mRNA stability, when it was present alone, suggested transcriptional regulation, which was confirmed by nuclear run-on experiments, showing a 3-fold increase in transcription frequency of the SERCA1 gene by T3. We conclude that the synergistic stimulating effects of T3 and IGF-I on SERCA1 expression are the result of both transcriptional and post-transcriptional regulation. T3 acts primarily at the transcriptional level by increasing the transcription frequency of the SERCA1 gene, whereas IGF-I seems to act predominantly at post-transcriptional levels by enhancing SERCA1 protein and mRNA stability, the latter, however, only in the presence of T3.

Mechanism of all trans-retinoic acid and glucocorticoid regulation of surfactant protein mRNA

1998 ◽  
Vol 274 (4) ◽  
pp. L560-L566 ◽  
Author(s):  
Thomas N. George ◽  
Olga L. Miakotina ◽  
Kelli L. Goss ◽  
Jeanne M. Snyder
Keyword(s):  
Gene Expression ◽  
Retinoic Acid ◽  
Gene Transcription ◽  
Mrna Stability ◽  
Half Life ◽  
Normal Function ◽  
Mrna Levels ◽  
Trans Retinoic Acid ◽  
All Trans Retinoic Acid ◽  
Mrna Half Life

The surfactant proteins (SPs) are required for the normal function of pulmonary surfactant, a lipoprotein substance that prevents alveolar collapse at end expiration. We characterized the effects of cortisol and all trans-retinoic acid (RA) on SP-A and SP-B gene expression in H441 cells, a human pulmonary adenocarcinoma cell line. Cortisol, at 10−6M, caused a significant inhibition of SP-A mRNA to levels that were 60–70% of controls and a five- to sixfold increase in the levels of SP-B mRNA. RA alone (10−6M) had no effect on SP-A mRNA levels and modestly reduced the inhibitory effect of cortisol. RA alone and the combination of cortisol and RA both significantly increased SP-B mRNA levels. RA had no effect on the rate of SP-A gene transcription or on SP-A mRNA stability. Cortisol alone and the combination of cortisol and RA significantly inhibited the rate of SP-A gene transcription but had no effect on SP-A mRNA half-life. RA at 10−6 M had no effect on the rate of SP-B gene transcription but prolonged SP-B mRNA half-life. Cortisol alone and the combination of cortisol and RA caused a significant increase in the rate of SP-B gene transcription and also caused a significant increase in SP-B mRNA stability. We conclude that RA has no effect on SP-A gene expression and increases SP-B mRNA levels by an effect on SP-B mRNA stability and not on the rate of SP-B gene transcription. In addition, the effects of the combination of RA and cortisol were generally similar to those of cortisol alone.

scholarly journals Human La protein: a stabilizer of histone mRNA.

1997 ◽  
Vol 17 (6) ◽  
pp. 3028-3036 ◽  
Author(s):  
R S McLaren ◽  
N Caruccio ◽  
J Ross
Keyword(s):  
Half Life ◽  
Mrna Decay ◽  
Rna Binding ◽  
S Phase ◽  
Coding Region ◽  
Histone Mrna ◽  
Histone Proteins ◽  
Unbound Fraction ◽  
Mrna Half Life

Histone mRNA is destabilized at the end of S phase and in cell-free mRNA decay reaction mixtures supplemented with histone proteins, indicating that histones might autoregulate the histone mRNA half-life. Histone mRNA destabilization in vitro requires three components: polysomes, histones, and postpolysomal supernatant (S130). Polysomes are the source of the mRNA and mRNA-degrading enzymes. To investigate the role of the S130 in autoregulation, crude S130 was fractionated by histone-agarose affinity chromatography. Two separate activities affecting the histone mRNA half-life were detected. The histone-agarose-bound fraction contained a histone mRNA destabilizer that was activated by histone proteins; the unbound fraction contained a histone mRNA stabilizer. Further chromatographic fractionation of unbound material revealed only a single protein stabilizer, which was purified to homogeneity, partially sequenced, and found to be La, a well-characterized RNA-binding protein. When purified La was added to reaction mixtures containing polysomes, a histone mRNA decay intermediate was stabilized. This intermediate corresponded to histone mRNA lacking 12 nucleotides from its 3' end and containing an intact coding region. Anti-La antibody blocked the stabilization effect. La had little or no effect on several other cell cycle-regulated mRNAs. We suggest that La prolongs the histone mRNA half-life during S phase and thereby increases histone protein production.

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