Gemin5 plays a role in unassembled‐U1 sn<scp>RNA</scp> disposal in <scp>SMN</scp>‐deficient cells

Jiang, Dongxu; Zou, Xuan; Zhang, Cheng; Chen, Jincao; Li, Zhiqiang; Wang, Yunfu; Yu, Yi; Wang, Liangrong; Chen, Shi

doi:10.1002/1873-3468.13031

Cited by 9 publications

(4 citation statements)

References 41 publications

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“…Thus, RBP association with a particular snRNA can help to map its function to a particular step in splicing. Quantitating snRNA enrichment using the family-aware mapping described above, we recapitulated many known associations between RBPs and the spliceosome, including interactions of SF3B4 with U2 snRNA (47-and 32fold enriched in HepG2 and K562, respectively) [44] and GEMIN5 with U1 (11.2-fold enriched in K562) [45] (Fig. 7a).…”

Section: Insights Into Spliceosomal Association and Core Splicing Regmentioning

confidence: 99%

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

et al. 2020

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Background: A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis across datasets. The development of enhanced CLIP (eCLIP) enabled the mapping of targets for 150 RBPs in K562 and HepG2, creating a unique resource of RBP interactomes profiled with a standardized methodology in the same cell types. Results: Our analysis of 223 eCLIP datasets reveals a range of binding modalities, including highly resolved positioning around splicing signals and mRNA untranslated regions that associate with distinct RBP functions. Quantification of enrichment for repetitive and abundant multicopy elements reveals 70% of RBPs have enrichment for non-mRNA element classes, enables identification of novel ribosomal RNA processing factors and sites, and suggests that association with retrotransposable elements reflects multiple RBP mechanisms of action. Analysis of spliceosomal RBPs indicates that eCLIP resolves AQR association after intronic lariat formation, enabling identification of branch points with single-nucleotide resolution, and provides genome-wide validation for a branch point-based scanning model for 3′ splice site recognition. Finally, we show that eCLIP peak co-occurrences across RBPs enable the discovery of novel co-interacting RBPs. Conclusions: This work reveals novel insights into RNA biology by integrated analysis of eCLIP profiling of 150 RBPs with distinct functions. Further, our quantification of both mRNA and other element association will enable further research to identify novel roles of RBPs in regulating RNA processing.

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Section: Insights Into Spliceosomal Association and Core Splicing Regmentioning

confidence: 99%

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

et al. 2020

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show abstract

“…Thus, RBP association with a particular snRNA can help to map its function to a particular step in splicing. Quantitating snRNA enrichment using the family-aware mapping described above, we recapitulated many known associations between RBPs and the spliceosome, including interactions of SF3B4 with U2 snRNA (47-and 32-fold enriched in HepG2 and K562 respectively) [43] and GEMIN5 with U1 (11.2-fold enriched in K562) [44] (Fig. 7a).…”

Section: Insights Into Spliceosomal Association and Core Splicing Regmentioning

confidence: 99%

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

Nostrand

Pratt

Yee

et al. 2019

Preprint

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AbstractA critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enabled mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale integrated analysis across datasets. The development of enhanced CLIP (eCLIP) enabled the large-scale mapping of targets for 150 RBPs in K562 and HepG2, creating a unique resource of RBP interactomes profiled with a standardized methodology in the same cell types. Here we describe our analysis of 223 enhanced (eCLIP) datasets characterizing 150 RBPs in K562 and HepG2 cell lines, revealing a range of binding modalities, including highly resolved positioning around splicing signals and mRNA untranslated regions that associate with distinct RBP functions. Quantification of enrichment for repetitive and abundant multi-copy elements reveals 70% of RBPs have enrichment for non-mRNA element classes, enables identification of novel ribosomal RNA processing factors and sites and suggests that association with retrotransposable elements reflects multiple RBP mechanisms of action. Analysis of spliceosomal RBPs indicates that eCLIP resolves AQR association after intronic lariat formation (enabling identification of branch points with single-nucleotide resolution) and provides genome-wide validation for a branch point-based scanning model for 3’ splice site recognition. Further, we show that eCLIP peak co-occurrences across RBPs enables the discovery of novel co-interacting RBPs. Finally, we present a protocol for visualization of RBP:RNA complexes in the eCLIP workflow using biotin and standard chemiluminescent visualization reagents, enabling simplified confirmation of ribonucleoprotein enrichment without radioactivity. This work illustrates the value of integrated analysis across eCLIP profiling of RBPs with widely distinct functions to reveal novel RNA biology. Further, our quantification of both mRNA and other element association will enable further research to identify novel roles of RBPs in regulating RNA processing.

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“…Second, Gemin5 nuclear bodies do not colocalize with coilin, indicative of its absence in Cajal bodies [ 42 ]. Third, the increased association of U1 and U1A with Gemin5 in P bodies in SMN-deficient cells suggested a role in unassembled U1 snRNA disposal [ 54 ]. Furthermore, the protein colocalizes with eIF4G in arsenite-induced stress granules [ 55 ].…”

Section: Discussionmentioning

confidence: 99%

Oligomerization regulates the interaction of Gemin5 with members of the SMN complex and the translation machinery

Francisco-Velilla,

Abellan,

Embarc-Buh

et al. 2024

Cell Death Discov.

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RNA-binding proteins are multifunctional molecules impacting on multiple steps of gene regulation. Gemin5 was initially identified as a member of the survival of motor neurons (SMN) complex. The protein is organized in structural and functional domains, including a WD40 repeats domain at the N-terminal region, a tetratricopeptide repeat (TPR) dimerization module at the central region, and a non-canonical RNA-binding site at the C-terminal end. The TPR module allows the recruitment of the endogenous Gemin5 protein in living cells and the assembly of a dimer in vitro. However, the biological relevance of Gemin5 oligomerization is not known. Here we interrogated the Gemin5 interactome focusing on oligomerization-dependent or independent regions. We show that the interactors associated with oligomerization-proficient domains were primarily annotated to ribosome, splicing, translation regulation, SMN complex, and RNA stability. The presence of distinct Gemin5 protein regions in polysomes highlighted differences in translation regulation based on their oligomerization capacity. Furthermore, the association with native ribosomes and negative regulation of translation was strictly dependent on both the WD40 repeats domain and the TPR dimerization moiety, while binding with the majority of the interacting proteins, including SMN, Gemin2, and Gemin4, was determined by the dimerization module. The loss of oligomerization did not perturb the predominant cytoplasmic localization of Gemin5, reinforcing the cytoplasmic functions of this essential protein. Our work highlights a distinctive role of the Gemin5 domains for its functions in the interaction with members of the SMN complex, ribosome association, and RBP interactome.

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Gemin5 plays a role in unassembled‐U1 snRNA disposal in SMN‐deficient cells

Cited by 9 publications

References 41 publications

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

Oligomerization regulates the interaction of Gemin5 with members of the SMN complex and the translation machinery

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