SAFB2 Enables the Processing of Suboptimal Stem-Loop Structures in Clustered Primary miRNA Transcripts

Hutter, Katharina; Lohmüller, Michael; Jukic, A; Eichin, Felix; Avci, Seymen; Labi, Verena; Szabó, Tamás; Hoser, Simon M.; Hüttenhofer, Alexander; Villunger, Andreas; Herzog, Sebastian

doi:10.1016/j.molcel.2020.05.011

Cited by 47 publications

(73 citation statements)

References 86 publications

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“…Finally, the human ERH homolog has recently been shown to support the microprocessor complex during microRNA (miRNA) processing (Fang and Bartel 2020; Hutter et al 2020; Kwon et al 2020). Microprocessor is a trimeric complex consisting of one copy of DROSHA and two copies of DGCR8 and dimerization of DGCR8 is necessary for miRNA processing (Faller et al 2007).…”

Section: Discussionmentioning

confidence: 99%

“…The dimeric ERH protein binds to a short linear motif located in the N-terminal region of DGCR8 and is thought to additionally contribute to DGCR8 dimerization (Kwon et al 2020). At the functional level, oligomerization facilitates processing of suboptimal miRNA hairpins located in clusters (Fang and Bartel 2020; Hutter et al 2020). In PETISCO, we find a similar architecture: PID-3 dimerizes through its RRM domain and is supported by the binding of ERH-2 to a motif upstream of the RRM (Figure 6D).…”

Section: Discussionmentioning

confidence: 99%

“…Within PETISCO, ERH-2 not only reinforces dimerization, but also binds the effector proteins TOST-1 and PID-1 at a surface opposite of PID-3. Similarly, SAFB has been shown to bind human ERH (Drakouli et al 2017) and help process suboptimal miRNAs (Hutter et al 2020; Fang and Bartel 2020). It thus appears that ERH homologs may act as signal integrators to control RNA processing.…”

Section: Discussionmentioning

confidence: 99%

“…Finally, ERH-2 is one of the two C. elegans paralogs of ‘enhancer of rudimentary’ (Erh), a factor that is conserved throughout eukaryotes (Weng and Luo 2013). Erh was shown to participate in the RNA exosome-mediated degradation of meiotic RNAs in Schizosaccharomyces pombe (S. pombe) (Sugiyama et al 2016) and to facilitate miRNA processing in human cells (Fang and Bartel 2020; Hutter et al 2020; Kwon et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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Structural basis of PETISCO complex assembly during piRNA biogenesis inC. elegans

Perez-Borrajero¹,

Podvalnaya

Holleis

et al. 2021

Preprint

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Piwi-interacting RNAs (piRNAs) constitute a class of small RNAs that bind PIWI proteins and are essential to repress transposable elements in the animal germline, thereby promoting genome stability and maintaining fertility. C. elegans piRNAs (21U RNAs) are transcribed individually from minigenes as precursors that require 5′ and 3′ processing. This process depends on the PETISCO complex, consisting of four proteins: IFE-3, TOFU-6, PID-3, and ERH-2. We employ biochemical and structural biology approaches to characterize the PETISCO architecture and its interaction with RNA, together with its effector proteins TOST-1 and PID-1. These two proteins define different PETISCO functions: PID-1 governs 21U processing whereas TOST-1 links PETISCO to an unknown process essential for early embryogenesis. Here, we show that PETISCO forms an octameric assembly with each subunit present in two copies. Determination of structures of the TOFU-6/PID-3 and PID-3/ERH-2 subcomplexes, supported by in vivo studies of subunit interaction mutants, allows us to propose a model for the formation of the TOFU-6/PID-3/ERH-2 core complex, and its functionality in germ cells and early embryos. Using NMR spectroscopy, we demonstrate that TOST-1 and PID-1 bind to a common surface on ERH-2, located opposite its PID-3 binding site, explaining how PETISCO can mediate different cellular roles.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Structural basis of PETISCO complex assembly during piRNA biogenesis inC. elegans

Perez-Borrajero¹,

Podvalnaya

Holleis

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…A second model would involve protein cofactors able to recruit the Microprocessor on the neighboring miRNA hairpin. Very recently, it was shown that ERH and SAFB2 can interact with the Microprocessor and their ability to dimerize may even mediate multimerization of the Microprocessor and allow its simultaneous binding to several hairpins (35, 38, 40, 44). However, this model remains to be clearly established.…”

Section: Discussionmentioning

confidence: 99%

Cisregulation within a cluster of viral microRNAs

Vilimova

Contrant

Randrianjafy

et al. 2020

Preprint

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MicroRNAs (miRNAs) are small regulatory RNAs involved in virtually all biological processes. Although a large number of them are co-expressed from clusters, little is known regarding the impact of this organization on the regulation of their accumulation. In this study, we set to decipher the regulatory mechanism controlling the expression of the ten clustered pre-miRNAs from Kaposi’s sarcoma associated herpesvirus (KSHV). We measured in vitro the efficiency of cleavage of each individual pre-miRNA by the Microprocessor. Strikingly, pre-miR-K1 and -K3 were the most efficiently cleaved pre-miRNAs but their mature forms accumulated at low levels, indicating that they might perform an additional function. A mutational analysis showed that they are indeed important for the optimal expression of the whole set of miRNAs. We showed that this solely relies on the presence of a canonical pre-miRNA at this localization since we could functionally replace pre-miR-K1 by a heterologous pre-miRNA. Further in vitro processing analysis suggests that the two stem-loops act in cis and that the cluster is cleaved in a sequential manner. Finally, we showed that we can exploit this feature of the cluster to inhibit the expression of the whole set of miRNAs by targeting the pre-miR-K1 with LNA-based antisense oligonucleotides.

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The SKP2‐p27 axis defines susceptibility to cell death upon CHK1 inhibition

et al. 2022

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Checkpoint kinase 1 (CHK1; encoded by CHEK1) is an essential gene that monitors DNA replication fidelity and prevents mitotic entry in the presence of under‐replicated DNA or exogenous DNA damage. Cancer cells deficient in p53 tumor suppressor function reportedly develop a strong dependency on CHK1 for proper cell cycle progression and maintenance of genome integrity, sparking interest in developing kinase inhibitors. Pharmacological inhibition of CHK1 triggers B‐Cell CLL/Lymphoma 2 (BCL2)‐regulated cell death in malignant cells largely independently of p53, and has been suggested to kill p53‐deficient cancer cells even more effectively. Next to p53 status, our knowledge about factors predicting cancer cell responsiveness to CHK1 inhibitors is limited. Here, we conducted a genome‐wide CRISPR/Cas9‐based loss‐of‐function screen to identify genes defining sensitivity to chemical CHK1 inhibitors. Next to the proapoptotic BCL2 family member, BCL2 Binding Component 3 (BBC3; also known as PUMA), the F‐box protein S‐phase Kinase‐Associated Protein 2 (SKP2) was validated to tune the cellular response to CHK1 inhibition. SKP2 is best known for degradation of the Cyclin‐dependent Kinase Inhibitor 1B (CDKN1B; also known as p27), thereby promoting G1‐S transition and cell cycle progression in response to mitogens. Loss of SKP2 resulted in the predicted increase in p27 protein levels, coinciding with reduced DNA damage upon CHK1‐inhibitor treatment and reduced cell death in S‐phase. Conversely, overexpression of SKP2, which consequently results in reduced p27 protein levels, enhanced cell death susceptibility to CHK1 inhibition. We propose that assessing SKP2 and p27 expression levels in human malignancies will help to predict the responsiveness to CHK1‐inhibitor treatment.

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SAFB2 Enables the Processing of Suboptimal Stem-Loop Structures in Clustered Primary miRNA Transcripts

Cited by 47 publications

References 86 publications

Structural basis of PETISCO complex assembly during piRNA biogenesis inC. elegans

Structural basis of PETISCO complex assembly during piRNA biogenesis inC. elegans

Cisregulation within a cluster of viral microRNAs

The SKP2‐p27 axis defines susceptibility to cell death upon CHK1 inhibition

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