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Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.

ABSTRACT: The degradation of TNFα mRNA is critical for restricting TNFα synthesis and involves a constitutive decay element (CDE) in the 3’ untranslated region of the mRNA. We demonstrate that the active CDE is a stem-loop RNA motif that is recognized by the RNA-binding protein Roquin. Deep sequencing of Roquin-associated mRNAs identified CDE-containing mRNAs as the primary targets of Roquin on a transcriptome-wide scale.

ORGANISM(S): Mus musculus

PROVIDER: GSE44775 | GEO | 2013/05/15

SECONDARY ACCESSION(S): PRJNA191615

REPOSITORIES: GEO

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Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.

Project description:The degradation of TNFM-NM-1 mRNA is critical for restricting TNFM-NM-1 synthesis and involves a constitutive decay element (CDE) in the 3M-bM-^@M-^Y untranslated region of the mRNA. We demonstrate that the active CDE is a stem-loop RNA motif that is recognized by the RNA-binding protein Roquin. Deep sequencing of Roquin-associated mRNAs identified CDE-containing mRNAs as the primary targets of Roquin on a transcriptome-wide scale. Expression profiles of LPS treated Raw264.7 cells (input), after Roquin IP or control IP were generated by deep sequencing, in three biological replicates, using Illumina HiSeq 2000.

2013-05-15 | E-GEOD-44775 | biostudies-arrayexpress

Analysis of Roquin targetome during HCMV infection

Project description:To investigate how Roquin regulates cellular transcripts during Human cytomegalovirus (HCMV) infection, we examined the levels of cellular transcripts in cells treated control or Roquin-targeting siRNA during HCMV replication. Also, we performed Roquin crosslinking and immunoprecipitation followed by high-throughput sequencing (Roquin CLIP-seq) in HCMV-infected cells to identify which transcripts are directly bound by Roquin.

2019-08-15 | GSE132081 | GEO

RNA-binding preference of the Roquin-1 CCCH-type zinc finger

Project description:Zinc finger (ZnF) domains are widespread RNA-binding domains, recognizing single stranded and double stranded RNAs. Together with other RNA-binding domains, ZnFs enhance the affinity and specificity of RNA-binding proteins (RBPs). The ZnF-containing RBP Roquin controls mRNA decay by recognizing stem-loop elements in the 3'-UTR of its target mRNAs. Stem-loop elements are bound in a shape-specific manner by the unique ROQ domain with nanomolar affinity. The ZnF was suggested to play an essential role in RNA decay by Roquin. However, its RNA motif preference was not investigated so far. Here, we use RBNS to elucidate the RNA binding preference of the isolated Roquin-1 ZnF domain. We find that the ZnF preferentially recognizes single-stranded AU-rich elements (ARE).

2024-03-21 | GSE253536 | GEO

Structure of human Roquin-2 and its complex with constitutive-decay element RNA.

Project description:Roquin mediates mRNA degradation by recognizing the constitutive-decay element (CDE) in the 3' untranslated region of the target gene followed by recruitment of the deadenylation machinery. Deficiency or dysfunction of Roquin has been associated with autoimmunity and inflammation. To establish the structural basis for the recognition of CDE RNA by Roquin, the crystal structure of the ROQ domain of human Roquin-2 was determined in ligand-free and CDE-derived RNA-bound forms. The ROQ domain of Roquin-2 folded into a winged-helix structure in which the wing region showed structural flexibility and acted as a lid for RNA binding. The CDE RNA, forming a stem-loop structure, bound to the positively charged surface of the ROQ domain and was mainly recognized via direct interactions with the phosphate backbone in the 5' half of the stem-loop and its triloop and via indirect water-mediated interactions. Structural comparison with Roquin-1 revealed conserved features of the RNA-binding mode. Therefore, it is suggested that the Roquin proteins function redundantly in mRNA degradation.

| S-EPMC4528940 | biostudies-literature

Effect of ROQUIN2(Y691F) expression on mRNA levels upon BCR stimulation

Project description:Roquin2, and its paralog Roquin1, are key regulator of mRNA decay. Roquin proteins recognize mRNAs containing a 3’-UTR stem-loop motif, called constitutive decay element (CDE), through the ROQ domain. Upon target engagement, Roquin proteins recruit the CCR4-CAF1-NOT complex, mediating mRNA deadenylation and destabilization. To study the effect of Roquin2 stabilization, we sought out to identify the relevant Roquin2 mRNA targets in human DLBCL. To this purpose, we measured differential gene expression via RNA-seq analysis in U-2932 cells expressing Roquin2 or non-degradable Roquin2 upon BCR crosslinking.

2018-04-27 | GSE93675 | GEO

The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA.

Project description:A conserved stem-loop motif of the constitutive decay element (CDE) in the 3' UTR of mRNAs is recognized by the ROQ domain of Roquin, which mediates mRNA degradation. Here we report two crystal structures of the Homo sapiens ROQ domain in complex with CDE RNA. The ROQ domain has an elongated shape with three subdomains. The 19-nt Hmgxb3 CDE is bound as a stem-loop to domain III. The 23-nt TNF RNA is bound as a duplex to a separate site at the interface between domains I and II. Mutagenesis studies confirm that the ROQ domain has two separate RNA-binding sites, one for stem-loop RNA (A site) and the other for double-stranded RNA (B site). Mutation in either site perturbs the Roquin-mediated degradation of HMGXB3 and IL6 mRNAs in human cells, demonstrating the importance of both sites for mRNA decay.

| S-EPMC4125485 | biostudies-literature

Roquin suppresses PI3K-mTOR signaling to control T cell differentiation and Treg effector function

Project description:Roquin proteins are required to preclude spontaneous T cell activation and aberrant T follicular helper (Tfh) or T helper 17 (Th17) differentiation. Here, we show that deletion of Roquin encoding alleles in regulatory T cells (Tregs) also caused the activation of conventional T cells. These Tregs exhibited a follicular Treg phenotype, CD25 downregulation and could not protect from colitis. Mechanistically, Roquin was required for full expression and activity of Pten and Foxo1, two essential signaling molecules in Tregs and effector T cells. Roquin upregulated Pten by interfering with miR-17~92 binding to an overlapping cis-element in the Pten 3' UTR and downregulated the Foxo1-specific E3 ubiquitin ligase Itch. Loss of Roquin enhanced mTOR signaling and global protein synthesis, while inhibition of PI3K or mTOR in Roquin-deficient CD4+ T cells corrected increased Tfh and Th17 differentiation. Thereby, the control of PI3K-mTOR signaling by Roquin prevents autoimmunity through T cell-intrinsic and Treg-mediated regulation.

2018-01-08 | GSE86110 | GEO

RC3H1 posttranscriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kB pathway [PARCLIP]

Project description:The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNFalpha mRNA decay via a 3'UTR constitutive decay element (CDE). Here, we applied PAR-CLIP to human RC3H1 to identify about 3800 mRNA targets with more than 16000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins. RC3H1 binds preferentially short-lived and DNA damage induced mRNAs, indicating a role of this RNA-binding protein in the posttranscriptional regulation of the DNA damage response. Intriguingly, RC3H1 affects expression of NF-kB pathway regulators such as IkBalpha and A20. RC3H1 uses roquin and Zn-finger domains to contact a binding site in the A20 3'UTR, demonstrating a not yet recognized mode of RC3H1 binding. Knockdown of RC3H1 resulted in increased A20 protein expression, thereby interfering with IkB kinase and NF-kB activities, demonstrating that RC3H1 can modulate the activity of the IKK/NF-kB pathway.

2015-07-20 | GSE47078 | GEO

RC3H1 posttranscriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kB pathway [RNA-Seq]

2015-07-20 | GSE68611 | GEO

Comprehensive profiling of Roquin binding preferences for RNA stem-loops

Project description:Roquin proteins target specific RNA stem-loop motifs with their unique ROQ domain for mRNA degradation. The cellular levels of mRNAs are controlled by these post-transcriptional cis-regulatory stem-loop elements in the 3'-untranslated region (3'-UTR). Here, we first provide an RBNS (RNA Bind-n-Seq) experiment using pre-structured RNA libraries as input. This sRBNS (structured RBNS) was used to map Roquin's RNA binding preferences at nucleotide resolution, revealing preferences for loop sizes and consensus motifs for CDEs and ADEs.

2024-10-03 | GSE270841 | GEO

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