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ARED 2.0 buildup strategy. A schematic chart showing the stages of theARED 2.0 buildup. Programs and *computational derivation of ARE motif used in this study has been previously described (2). Programs are either PERL scripts or part of the GCG (Wisconsin Bioinformatics Package). Numbers on the right column indicate number of sequences.
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The Adenylate Uridylate (AU)-Rich Element Database, ARED-mRNA version 2.0, contains information not present in the previous ARED. This includes additional data entries, new information and links to Unigene, LocusLink, RefSeq records and mouse homologue data. An ARE consensus sequence specific to the 3'UTR is the basis of ARED that demonstrated two...
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Context 1
... avoid the above inconsistencies, we first comprehensively extract all possible records as shown in Figure 1 and followed by exclusion of records that distinguish molecule type or mRNA region such as words like introns, HTG, PAC (Fig. 1). Subsequently, computational extraction of 3 0 UTR and removal of redundancy was performed. ...
Context 2
... avoid the above inconsistencies, we first comprehensively extract all possible records as shown in Figure 1 and followed by exclusion of records that distinguish molecule type or mRNA region such as words like introns, HTG, PAC (Fig. 1). Subsequently, computational extraction of 3 0 UTR and removal of redundancy was performed. Redundancy was further refined by consolidation with UniGene and RefSeq databases. The 3 0 UTRs were searched for the 13-bp pattern WWWUAUUUAUWW with mismatch ¼ À1 which was computationally derived as previously described (2). The pattern was ...
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Heparanase up-regulation was documented in an increasing number of human carcinomas, associated with poor prognosis. The purpose of the current study was to identify mechanisms responsible for heparanase induction. We provide evidence that heparanase expression is regulated at the post-transcriptional level by sequences at the 3' untranslated regio...
Citations
... RBPs are major components of SGs and important regulators of gene expression. Among them, AU-rich element binding proteins (AUBPs) govern the mRNA stability and translation of 5 to 8% of the transcriptomes by binding to AU-rich elements present in the 3′UTR of target mRNAs [116][117][118][119]. AUBPs usually regulate the fate of target mRNAs by recruiting them within either P-bodies or SGs. ...
Stress granules (SGs) are small membrane-free cytosolic liquid-phase ordered entities in which mRNAs are protected and translationally silenced during cellular adaptation to harmful conditions (e.g., hypoxia, oxidative stress). This function is achieved by structural and functional SG components such as scaffold proteins and RNA-binding proteins controlling the fate of mRNAs. Increasing evidence indicates that the capacity of cells to assemble/disassemble functional SGs may significantly impact the onset and the development of metabolic and inflammatory diseases, as well as cancers. In the liver, the abnormal expression of SG components and formation of SG occur with chronic liver diseases, hepatocellular carcinoma (HCC), and selective hepatic resistance to anti-cancer drugs. Although, the role of SG in these diseases is still debated, the modulation of SG assembly/disassembly or targeting the expression/activity of specific SG components may represent appealing strategies to treat hepatic disorders and potentially cancer. In this review, we discuss our current knowledge about pathophysiological functions of SGs in HCC as well as available molecular tools and drugs capable of modulating SG formation and functions for therapeutic purposes.
... Type I contains several scattered AUUUA motifs in U-rich regions [122]. Class II contains at least two repeated UUAUUUA (U/A) (U/A) sequences [123]. Class III belongs to the U-rich region, without typical features and the AUUUA motif [124]. ...
Zinc-finger proteins, a superfamily of proteins with a typical structural domain that coordinates a zinc ion and binds nucleic acids, participate in the regulation of growth, development, and stress adaptation in plants. Most zinc fingers are C2H2-type or CCCC-type, named after the configuration of cysteine (C) and histidine (H); the less-common CCCH zinc-finger proteins are important in the regulation of plant stress responses. In this review, we introduce the domain structures, classification, and subcellular localization of CCCH zinc-finger proteins in plants and discuss their functions in transcriptional and post-transcriptional regulation via interactions with DNA, RNA, and other proteins. We describe the functions of CCCH zinc-finger proteins in plant development and tolerance to abiotic stresses such as salt, drought, flooding, cold temperatures and oxidative stress. Finally, we summarize the signal transduction pathways and regulatory networks of CCCH zinc-finger proteins in their responses to abiotic stress. CCCH zinc-finger proteins regulate the adaptation of plants to abiotic stress in various ways, but the specific molecular mechanisms need to be further explored, along with other mechanisms such as cytoplasm-to-nucleus shuttling and post-transcriptional regulation. Unraveling the molecular mechanisms by which CCCH zinc-finger proteins improve stress tolerance will facilitate the breeding and genetic engineering of crops with improved traits.
... HnRNP D is one of the RBPs which interact with AREs to regulate mRNA degradation [13]. An estimated 8% of the human genome codes for mRNAs which contain AREs, suggesting that hnRNP D plays a major regulatory role in gene expression and ARE-directed mRNA decay [8]. The effect of hnRNP D binding on mRNA stability has been found to be both cell-type specific [13,215] and isoform dependent [121]. ...
Dysregulated RNA metabolism is emerging as a crucially important mechanism underpinning the pathogenesis of frontotemporal dementia (FTD) and the clinically, genetically and pathologically overlapping disorder of amyotrophic lateral sclerosis (ALS). Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RNA-binding proteins with diverse, multi-functional roles across all aspects of mRNA processing. The role of these proteins in neurodegeneration is far from understood. Here, we review some of the unifying mechanisms by which hnRNPs have been directly or indirectly linked with FTD/ALS pathogenesis, including their incorporation into pathological inclusions and their best-known roles in pre-mRNA splicing regulation. We also discuss the broader functionalities of hnRNPs including their roles in cryptic exon repression, stress granule assembly and in co-ordinating the DNA damage response, which are all emerging pathogenic themes in both diseases. We then present an integrated model that depicts how a broad-ranging network of pathogenic events can arise from declining levels of functional hnRNPs that are inadequately compensated for by autoregulatory means. Finally, we provide a comprehensive overview of the most functionally relevant cellular roles, in the context of FTD/ALS pathogenesis, for hnRNPs A1-U.
... In most cases, AREs have been reported to destabilize mRNAs, although in some cellular contexts certain AREs and ARE-binding proteins have been shown to stabilize mRNAs [6,7]. Subsequent analyses of the human genome concluded that as many as 58% of human genes code for mRNAs that contain AREs [8,9,10], suggesting that these elements play a major role in regulating expression of a large group of genes. ...
... Non-AUUUA AREs had a U-rich region and other unknown features, and the relationship of these sequences to AUUUA-containing AREs remains poorly understood. Subsequent studies based on analyses of a set of 4884 AUUUA-containing AREs led to a new classification based primarily on the number of overlapping AUUUA-repeats [8,9,10]. This classification system, with five clusters distinguished by the number of repeats, was used to identify AUUUA-containing AREs in the human genome. ...
AU-rich elements (AREs) are 3' UTR cis-regulatory elements that regulate the stability of mRNAs. Consensus ARE motifs have been determined, but little is known about how differences in 3' UTR sequences that conform to these motifs affect their function. Here we use functional annotation of sequences from 3' UTRs (fast-UTR), a massively parallel reporter assay (MPRA), to investigate the effects of 41,288 3' UTR sequence fragments from 4,653 transcripts on gene expression and mRNA stability. The library included 9,142 AREs, and incorporated a set of fragments bearing mutations in each ARE. Our analyses demonstrate that the length of an ARE and its registration (the first and last nucleotides of the repeating ARE motif) have significant effects on gene expression and stability. Based on this finding, we propose improved ARE classification and concomitant methods to categorize and predict the effect of AREs on gene expression and stability. Our new approach explains 64+/-13% of the contribution of AREs to the stability of human 3' UTRs in Jurkat cells and predicts ARE activity in an unrelated cell type. Finally, to investigate the advantages of our general experimental design for annotating 3' UTR elements we examine other motifs including constitutive decay elements (CDEs), where we show that the length of the CDE stem-loop has a significant impact on steady-state expression and mRNA stability. We conclude that fast-UTR, in conjunction with our analytical approach, can produce improved yet simple sequence-based rules for predicting the activity of human 3' UTRs containing functional motifs.
... Among them, ARE and ARE-binding proteins have attracted the most attention. Up to 8%-10% of the genes in the human genome contain at least one putative ARE in their 3′-UTR [84]. AREs are found in the tightly regulated mRNAs that encode proto-oncogene proteins (e.g., c-Fos and c-Myc) and inflammatory mediators (e.g., CXCL2 and IL-1β). ...
Poly(ADP-ribosyl)ation (PARylation) is an important post-translational modification in which an ADP-ribose group is transferred to the target protein by poly(ADP-riboses) polymerases (PARPs). Since the discovery of poly-ADP-ribose (PAR) 50 years ago, its roles in cellular processes have been extensively explored. Although research initially focused on the functions of PAR and PARPs in DNA damage detection and repair, our understanding of the roles of PARPs in various nuclear and cytoplasmic processes, particularly in gene expression, has increased significantly. In this review, we discuss the current advances in understanding the roles of PARylation with a particular emphasis in gene expression through RNA biogenesis and processing. In addition to updating PARP’s significance in transcriptional regulation, we specifically focus on how PARPs and PARylation affect gene expression, especially inflammation-related genes, at the post-transcriptional levels by modulating RNA processing and degrading. Increasing evidence suggests that PARP inhibition is a promising treatment for inflammation-related diseases besides conventional chemotherapy for cancer.
... The reporter assay showed that the CCL3 39-UTR had a very strong downregulatory effect in all eight cell types (10 6 5% relative to BTV) ( Fig. 2A). Using ARED (39) and TargetScan (42), we found a predicted ARE and a predicted let-7 target in the CCL3 39-UTR. Both of these predicted elements are evolutionarily conserved (Fig. 5A). ...
Chemokines are a large family of chemotactic cytokines that play critical roles in inflammation, development, and diseases. Chemokine expression is highly regulated during development and in response to environmental stimuli. The 3' untranslated regions (3'-UTRs) of mRNA are believed to be important in the control of chemokine gene expression. However, the regulatory effects of most chemokine 3'-UTRs have not been characterized previously. In this work, we systematically studied the effects of 43 CC and CXC chemokine 3'-UTRs on gene expression in eight human cell lines and two types of human primary cells. We found that chemokine 3'-UTRs had a wide spectrum of regulatory effects on mRNA abundance and protein production that were tightly correlated with the effects on mRNA stability. In general, 3'-UTRs had remarkably similar effects across all cell types studied. The presence of AU-rich elements, microRNA targets, and Pumilio binding sites were associated with chemokine 3'-UTR activity but did not fully account for all 3'-UTR activity detected using the reporter assay. Mutational analysis illustrated how specific cis-regulatory elements contributed to the regulatory effect of chemokine 3'-UTRs. These findings bring new insights into the mechanisms by which chemokine expression is regulated by 3'-UTRs.
... Thus, ARE and GRE can regulate pre-mRNA splicing, translation, and/or mRNA deadenylation or decay depending on the repertoire of proteins they interact with in different intracellular settings. The classification of AREs and GREs has been described in multiple manuscripts [74][75][76][77], and an overview is shown in Table 1. Single nucleotide polymorphism studies in humans demonstrated that SNPs in ARE and GRE sites are associated with higher risk of human diseases that involve adaptive immune response; mutations in these conserved cisacting elements resulted in changes in RNA stability and binding preferences for RNA-BPs (reviewed in ref. [44,63,78,79]). ...
... The identification of AREs was originally experimentally associated with a small number of interferons and cytokines, and then, over the years, we have bioinformatically expanded it to nearly 4000 mRNAs with a wide range of cellular roles such as cell proliferation, RNA metabolism, transcriptional regulation, signaling, and response to stress and microbes [10,16,17]. The canonical site and functional attributes of AREs are in the 3′UTR; however, their presence in other parts of the genome, such as introns, has not been systematically investigated. ...
Adenylate-uridylate (AU)-rich elements (AREs) are sequence instability elements that are known to be located in the 3' untranslated regions (UTR) in thousands of human transcripts. AREs regulate the expression of many genes at the post-transcriptional level, and they are essential for many normal cellular functions. We conducted a transcriptome-wide screen for AREs and found that they are most abundant in introns, with up to 25% of introns containing AREs corresponding to 58% of human genes. Clustering studies of ARE size, complexity, and distribution revealed that, in introns, longer AREs with two or more overlapping repeats are more abundant than in the 3'UTR, and only introns can contain very long AREs with 6-14 overlapping AUUUA pentamers. We found that intronic sites of the ARE binding proteins HuR/ELAVL1, ZFP36/TTP, AUF1, and BRF1/ZFP36L1 overlap with the intronic AREs with HuR being most abundant. Accordingly, RNA-IP experiments demonstrated a specific association of HuR with reporter and endogenous pre-mRNAs that contain intronic AREs. Moreover, HuR knockdown led to a significant general reduction in the mRNA levels of genes that contain intronic AREs and to a specific reduction in the expression of ARE-intronic reporters. The data represent bioinformatics analysis for key RNA-binding proteins interactions with intronic AREs and provide experimental evidence for HuR binding to AREs. The widespread distribution of intronic AREs and their particular association with HuR and HuR binding sites indicates that more than half of human genes can be regulated post-transcriptionally by AREs.
... Comme évoqué en fin de partie I, notre équipe a également montré que l'expression de NPM-ALK entraînait la surexpression de la protéine anti-apoptotique Mcl-1, en réprimant l'expression de miR- Uridine (ARE) ont initialement été qualifiés de motifs de « déstabilisation", après avoir observé la dégradation de l'ARNm de la -Globine de lapin suite à sa fusion à l'ARE de l'ARNm codant la cytokine Granulocyte Macrophage Colony Stimulating Factor (GM-CSF) 108 . La dégradation médiée par les motifs ARE (AMD) consiste, comme l'interférence à l'ARN, en une étape de déadénylation et de décoiffage, On sait aujourd'hui que 5 à 8% des ARNm portent ce type de motifs, le plus souvent au niveau de leur extrémité 3' Non Traduite (3' NT), et qu'il s'agit pour la plupart d'ARNm issus de gènes dits « adaptatifs » ou « environnementaux », c'est-à-dire des gènes devant être exprimés de façon transitoire tels que les gènes codant les cytokines, les facteurs de croissance, les facteurs de transcription, de gènes impliqués dans les processus de réponses au stress ou encore certaines 50 51 enzymes du métabolisme 113,114 . Les séquences ARE sont également fréquemment retrouvées sur des transcrits issus d'oncogènes tels que c-fos, c-myc ou c-jun 115 . ...
Les lymphomes anaplasiques à grandes cellules (LAGC) sont des lymphomes non-hodgkiniens dits de type T ou nul, représentant la majorité des lymphomes T pédiatriques (20 à 30%). Dans plus de 80% des cas, une translocation chromosomique réciproque aboutissant à l'expression anormale de protéines chimères de type X-ALK qui arborent constitutivement et de manière anormale l'activité tyrosine-kinase ALK (Anaplastic Lymphoma Kinase) est le moteur de la tumorigenèse (LAGC dits "ALK+ "). L'une des particularités de ces lymphomes, mise en évidence par mon équipe, est le fait que B-Cell Lymphoma-2 (BCL-2) demeure indétectable dans les cas ALK+ contrairement aux cas ALK-. Ce point est d'autant plus surprenant que BCL-2, oncogène largement établi comme prototype de protéines anti-apoptotiques ainsi que régulateur clé de l'autophagie, est fortement surexprimé dans la majorité des lymphomes. A l'inverse, Human Antigen R (HuR) est surexprimée dans les LAGC (comme dans la plupart des cancers). Il a été démontré que cette protéine de liaison aux ARN participait au maintien du phénotype tumoral, et que sa localisation subcellulaire et ses fonctions dépendaient étroitement de son statut de phosphorylation, lequel est régulé par ALK dans les LAGC ALK+. Au niveau du cytoplasme, HuR permet de stabiliser et d'augmenter la traduction d'ARNm possédant, dans leur région 3'-UTR, des séquences riches en adénine et uridine (AU-rich elements, "ARE"). De manière plus générale, HuR a la capacité de dialoguer avec les microARNs (miARN), soit en empêchant leur action par compétition, soit à l'inverse en coopérant avec ces derniers et en promouvant ainsi leur fonction de régulateur négatif sur certains transcrits cibles communs. Le transcrit Bcl-2, dont l'expression est réprimée dans les LAGC ALK+, fait partie des cibles potentielles de HuR. Au cours de ma thèse, j'ai ainsi cherché à comprendre les mécanismes moléculaires mis en jeu dans la répression de l'expression de Bcl-2, en me focalisant sur le rôle de HuR et de miARN "partenaires" dans ce processus. Mes données semblent indiquer que ce mécanisme implique le recrutement par HuR du miR-34a sur l'ARNm Bcl-2, conduisant à la mise en silence de ce dernier. A l'inverse, quand l'activité tyrosine- kinase de ALK est inhibée, l'interaction entre HuR et le transcrit Bcl-2 diminue, ce qui limite le recrutement de miR-34a et conduit à une restauration de l'expression de cette oncogène majeur dans les cellules lymphomateuses. Dans le contexte des essais cliniques d'inhibiteurs ciblant l'activité tyrosine kinase de ALK tels que le Crizotinib, la question de cette ré-expression de BCL-2 éclaire d'une lumière nouvelle certains échecs thérapeutiques subis par cette molécule pourtant prometteuse. Je me suis donc également consacré, pendant ma thèse, à l'étude des conséquences de cette ré-expression de BCL-2 sur les LAGC ALK+ traités par le Crizotinib. Les résultats que j'ai obtenus in vitro et in vivo montrent que contrecarrer, par interférence à l'ARN, l'élévation du taux de BCL-2 consécutive au traitement par le Crizotinib, permet de potentialiser les effets de la drogue : cela se traduit en particulier par une potentialisation de la mort par apoptose induite par le traitement mais aussi, de manière fascinante, par une conversion de la réponse autophagique initialement cytoprotectrice et pro-tumorale en une autophagie incontrôlée et délétère, qui participe alors à l'effet thérapeutique accru de la drogue. De manière globale, ce travail permet d'envisager de nouvelles combinaisons et alternatives thérapeutiques pour les patients souffrants de LAGC ALK+, et illustre la complexité des régulations croisées entre processus apoptotiques et autophagiques.
... The best-studied instability elements in mammalian mRNA are the AREs 33 . Up to 8% of the genes in the human genome contain at least one putative ARE in their 3 0 -UTR 34 . The stability of ARE-containing mRNAs is mediated by ARE-binding proteins. ...
Poly(ADP-ribosyl)ation (PARylation) is mainly catalysed by poly-ADP-ribose polymerase 1 (PARP1), whose role in gene transcription modulation has been well established. Here we show that, in response to LPS exposure, PARP1 interacts with the adenylateuridylate-rich element-binding protein embryonic lethal abnormal vision-like 1 (Elavl1)/human antigen R (HuR), resulting in its PARylation, primarily at site D226. PARP inhibition and the D226 mutation impair HuR’s PARylation, nucleocytoplasmic shuttling and mRNA binding. Increases in mRNA level or stability of pro-inflammatory cytokines/chemokines are abolished by PARP1 ablation or inhibition, or blocked in D226A HuR-expressing cells. The present study demonstrates a mechanism to regulate gene expression at the post-transcriptional level, and suggests that blocking the interaction of PARP1 with HuR could be a strategy to treat inflammation-related diseases that involve increased mRNA stability.
