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Integrative AUF1 PAR-CLIP analysis uncovers AUF1 roles in translation and genome integrity (RNA-Seq 2)

ABSTRACT: We report that AUF1 modulates global mRNA stability and translation, in turn promoting the maintenance of DNA integrity. Please see individual series. In short, for AUF1 PAR-CLIP, the four isoforms of AUF1 (p37, p40, p42, and p45) tagged with a Flag epitope were expressed in HEK293 cells. For total RNA-Seq HEK293 cells were transfected with Control siRNA, AUF1 siRNA, Empty Vector, Flag-AUF1 p37, p40, p42, or p45 as well as WI-38 cells were collected at PDL 15 and 55 and also transfected with Control siRNA, AUF1 siRNA, HuR siRNA. For Ribo-Seq HeLa cells were transfected with Control siRNA, AUF1 siRNA, or HuR siRNA.

ORGANISM(S): Homo sapiens

SUBMITTER: Kevin Becker

PROVIDER: E-GEOD-52975 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Integrative AUF1 PAR-CLIP analysis uncovers AUF1 roles in translation and genome integrity (Ribosome)

Project description:We report that AUF1 modulates global mRNA stability and translation, in turn promoting the maintenance of DNA integrity. Please see individual series. In short, For AUF1 PAR-CLIP, the four isoforms of AUF1 (p37, p40, p42, and p45) tagged with a Flag epitope were expressed in HEK293 cells. For total RNA-Seq HEK293 cells were transfected with Control siRNA, AUF1 siRNA, Empty Vector, Flag-AUF1 p37, p40, p42, or p45 as well as WI-38 cells were collected at PDL 15 and 55 and also transfected with Control siRNA, AUF1 siRNA, HuR siRNA. For Ribo-Seq HeLa cells were transfected with Control siRNA, AUF1 siRNA, or HuR siRNA.

2014-11-04 | E-GEOD-52976 | biostudies-arrayexpress

Integrative AUF1 PAR-CLIP analysis uncovers AUF1 roles in translation and genome integrity (RNA-Seq 1)

Project description:We report that AUF1 modulates global mRNA stability and translation, in turn promoting the maintenance of DNA integrity. Please see individual series. For AUF1 PAR-CLIP, the four isoforms of AUF1 (p37, p40, p42, and p45) tagged with a Flag epitope were expressed in HEK293 cells. For total RNA-Seq HEK293 cells were transfected with Control siRNA, AUF1 siRNA, Empty Vector, Flag-AUF1 p37, p40, p42, or p45 as well as WI-38 cells were collected at PDL 15 and 55 and also transfected with Control siRNA, AUF1 siRNA, HuR siRNA. For Ribo-Seq HeLa cells were transfected with Control siRNA, AUF1 siRNA, or HuR siRNA.

2014-11-04 | E-GEOD-52973 | biostudies-arrayexpress

Integrative AUF1 PAR-CLIP analysis uncovers AUF1 roles in translation and genome integrity (PAR-CLIP)

Project description:We report that AUF1 modulates global mRNA stability and translation, in turn promoting the maintenance of DNA integrity. Please see individual series. In short, for AUF1 PAR-CLIP, the four isoforms of AUF1 (p37, p40, p42, and p45) tagged with a Flag epitope were expressed in HEK293 cells. For total RNA-Seq HEK293 cells were transfected with Control siRNA, AUF1 siRNA, Empty Vector, Flag-AUF1 p37, p40, p42, or p45 as well as WI-38 cells were collected at PDL 15 and 55 and also transfected with Control siRNA, AUF1 siRNA, HuR siRNA. For Ribo-Seq HeLa cells were transfected with Control siRNA, AUF1 siRNA, or HuR siRNA.

2014-11-05 | E-GEOD-52971 | biostudies-arrayexpress

Concurrent Versus Individual Binding of HuR and AUF1 to Common Labile Target mRNAs

Project description:RNA was isolated from material that had been immunoprecipitated (IP) from Hela cells using antibodies recognizing RNA-binding proteins HuR or AUF1, as well as using a control IgG1 antibody. RNA was reverse-transcribed in the presence of [alpha-33P]dCTP and the radiolabeled product used to hybridize human cDNA arrays. The experiment was repeated using three independent sample sets. The samples were numbered HuR-1, HuR-2, HuR-3, AUF1-1, AUF1-2, AUF1-3, IgG1-1, IgG1-2, IgG1-3. HuR represents RNA from IP reactions using an anti-HuR antibody, AUF1 represents RNA from IP reactions using an anti-AUF1 antibody and, IgG1 represents RNA from IP reactions using an anti-IgG1 antibody. The numbers 1, 2 and 3 correspond to the three independent experimental datasets. Keywords = RNa-binding protein Keywords = mRNA stability Keywords = exosome Keywords = polysome Keywords = RNA motif Keywords: ordered

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Concurrent Versus Individual Binding of HuR and AUF1 to Common Labile Target mRNAs

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Identification of AUF1 target mRNAs

Project description:Regulation of mRNA stability by RNA-protein interactions contributes significantly to quantitative aspects of gene expression. We have identified potential mRNA targets of the AU-rich element binding protein AUF1. Myc-tagged AUF1 p42 was induced in mouse NIH-3T3 cells and RNA-protein complexes isolated using anti-myc tag antibody beads. Bound mRNAs were analyzed with Affymetrix microarrays. We have identified 508 potential target mRNAs that were at least 3-fold enriched compared to control cells without myc-AUF1. 22.3% of the enriched mRNAs had an AU-rich cluster in the ARED Organism database, against 16.3% of non-enriched control mRNAs. The enrichment towards AU-rich elements was also visible by AREScore with an average value of 5.2 in the enriched mRNAs versus 4.2 in the control group. Yet, many mRNAs were enriched without a high ARE score suggesting that AUF1 has a broader binding spectrum than standard AUUUA repeats. AUF1 did not preferentially bind to unstable mRNAs. Still, some enriched mRNAs were highly unstable, as those of TNFSF11 (known as RANKL), KLF10, HES1, CCNT2, SMAD6, and BCL6. We have mapped some of the instability determinants. HES1 mRNA appeared to have a coding region determinant. Detailed analysis of the RANKL and BCL6 3’UTR revealed for both that full instability required two elements, which are conserved in evolution. In RANKL mRNA both elements are AU-rich and separated by 30 bases, while in BCL6 mRNA one is AU-rich and 60 bases from a non AU-rich element that potentially forms a stem-loop structure.

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RNA-seq for HepG2 cell line with AUF1 knockdown.

Project description:Although several studies indicate that ARE-specific RNA binding proteins (ARE-BPs) contribute to the development of cancer, the detailed functions and mechanisms of ARE-BPs have not been fully elucidated. By using a bioinformatics analysis of two well-established hepatocellular carcinoma (HCC) datasets, we identified the AU-rich binding factor 1(AUF1), one of the well-known ARE-BPs, was abnormally highly expressed in HCC and the high expression of AUF1 was correlated with poor prognosis of HCC patients. The prognostic value of AUF1 expression was also confirmed in our HBV-related HCC cohorts. Gain and loss of function analyses demonstrated that AUF1 promoted HCC tumorigenesis both in vitro and in vivo. Mechanistically, we found that aldoketo reductase family 1 member B 10(AKR1B10) was a critical target of AUF1 and was essential for sustaining the AUF1-induced proliferation of HCC cells. AUF1 stabilized AKR1B10 mRNA by binding to the 3'UTR region of AKR1B10. Additionally, we confirmed that E2F1 enhanced AUF1 expression in HCC through the transcription level, and in HBV-related HCC, HBx could up-regulate E2F1 expression and promote the expression of AUF1. Our study reveals a novel role of AUF1 in promoting hepatocarcinogenesis via the post-transcriptional regulation of AKR1B10 expression and proposes that the HBx/E2F1/AUF1/AKR1B10 pathway may serve as a potential therapeutic target in HCC.

2021-05-01 | GSE162706 | GEO

WT and AUF1 KO satellite cell RNA-sequencing

Project description:Following skeletal muscle injury, muscle stem cells (satellite cells) are activated, proliferate, and differentiate to form myofibers. We show that mRNA decay protein AUF1 regulates satellite cell function through targeted degradation of specific mRNAs. AUF1 targets certain mRNAs containing 3 AU-rich elements (AREs) for rapid decay. Auf1-/- (KO) mice undergo accelerated skeletal muscle wasting with age and impaired muscle repair following injury. Satellite cell mRNA analysis and regeneration studies demonstrate that auf1-/- satellite cell self-renewal is impaired due to increased stability and overexpression of ARE-mRNAs. Control of ARE-mRNA decay by AUF1 and potentially other ARE-binding proteins represents a mechanism for adult stem cell regulation and is implicated in human muscle wasting diseases. We report the RNA transcript expression profiles from sorted satellite cells isolated from wild type (WT) and AUF1-null (KO) mice hindlimb muscles

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RNA-binding protein AUF1 promotes myogenesis by regulating MEF2C expression levels

Project description:The mammalian RNA-binding protein AUF1 (AU-binding factor 1, also known as heterogeneous nuclear ribonucleoprotein D, hnRNP D) binds to numerous mRNAs and influences their post-transcriptional fate. Given that many AUF1 target mRNAs encode muscle-specific factors, we investigated the function of AUF1 in skeletal muscle differentiation. In mouse C2C12 myocytes, where AUF1 levels rise at the onset of myogenesis and remain elevated throughout myocyte differentiation into myotubes, RIP (RNP immunoprecipitation) analysis indicated that AUF1 binds prominently to Mef2c (myocyte enhancer factor 2c) mRNA, which encodes the key myogenic transcription factor Mef2c. By performing mRNA half-life measurements and polysome distribution analysis, we found that AUF1 associated with the 3’UTR of Mef2c mRNA and promoted Mef2c translation without affecting Mef2c mRNA stability. In addition, AUF1 promoted Mef2c gene transcription via a lesser-known role of AUF1 in transcriptional regulation. Importantly, lowering AUF1 delayed myogenesis, while ectopically restoring Mef2c expression levels partially rescued the impairment of myogenesis seen after reducing AUF1 levels. We propose that Mef2c is a key effector of the myogenesis program promoted by AUF1. Keywords: ribonucleoprotein complex; post-transcriptional gene regulation; muscle cell differentiation; myocytes; mRNA translation; mRNA stability; post-transcriptional gene regulation; transcriptome

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