The RNA helicase Ddx52 functions as a growth switch in juvenile zebrafish

Tseng, Tzu-Lun; Wang, Ying-Ting; Tsao, Chang-Yu; Ke, Yi-Teng; Lee, Yi-Ching; Hsu, Hwei-Jan; Poss, Kenneth D.; Chen, Chen‐Hui

doi:10.1242/dev.199578

Cited by 7 publications

(2 citation statements)

References 55 publications

(89 reference statements)

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“…• DDX52, a DEAD-box protein that is predicted to be involved in the maturation of the small ribosomal subunit 39,40 and RPS3, a structural protein contained within the small ribosomal RNA subunit, to distinct sites on the 18S rRNA (Figure 2A).…”

Section: Spidr Accurately Maps Dozens Of Rbps Within a Single Experim...mentioning

confidence: 99%

SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress

Wolin,

Guo,

Blanco

et al. 2023

Preprint

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RNA binding proteins (RBPs) play crucial roles in regulating every stage of the mRNA life cycle and mediating non-coding RNA functions. Despite their importance, the specific roles of most RBPs remain unexplored because we do not know what specific RNAs most RBPs bind. Current methods, such as crosslinking and immunoprecipitation followed by sequencing (CLIP-seq), have expanded our knowledge of RBP-RNA interactions but are generally limited by their ability to map only one RBP at a time. To address this limitation, we developed SPIDR (Split and Pool Identification of RBP targets), a massively multiplexed method to simultaneously profile global RNA binding sites of dozens to hundreds of RBPs in a single experiment. SPIDR employs split-pool barcoding coupled with antibody-bead barcoding to increase the throughput of current CLIP methods by two orders of magnitude. SPIDR reliably identifies precise, single-nucleotide RNA binding sites for diverse classes of RBPs simultaneously. Using SPIDR, we explored changes in RBP binding upon mTOR inhibition and identified that 4EBP1 acts as a dynamic RBP that selectively binds to 5'-untranslated regions of specific translationally repressed mRNAs only upon mTOR inhibition. This observation provides a potential mechanism to explain the specificity of translational regulation controlled by mTOR signaling. SPIDR has the potential to revolutionize our understanding of RNA biology and both transcriptional and post-transcriptional gene regulation by enabling rapid, de novo discovery of RNA-protein interactions at an unprecedented scale.

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Section: Spidr Accurately Maps Dozens Of Rbps Within a Single Experim...mentioning

confidence: 99%

SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress

Wolin,

Guo,

Blanco

et al. 2023

Preprint

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show abstract

“…For instance, studies on prostate cancer cells suggest that DDX52 inhibition can effectively retard cancer cell growth by modulating the c-Myc signaling pathway 8 . Findings from a zebrafish model emphasize DDX52’s role as a growth regulator during early developmental stages 9 . Similarly, targeting DDX52 has demonstrated suppression of melanoma cell proliferation through its influence on c-Myc 10 .…”

Section: Introductionmentioning

confidence: 99%

DDX52 gene expression in LUAD tissues indicates potential as a prognostic biomarker and therapeutic target

Xu,

Yang

2023

Sci Rep

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Lung adenocarcinoma (LUAD) remains a leading cause of cancer-related morbidity and mortality globally. While DDX52, an ATP-dependent RNA helicase, plays a role in several biological processes, its specific involvement in LUAD is yet to be elucidated. We utilized ROC curves to determine DDX52’s predictive potential for LUAD. Kaplan–Meier survival curves, along with univariate and multivariate Cox analyses, assessed the prognostic implications of DDX52 in LUAD. We constructed nomogram models to further delineate DDX52’s influence on prognosis, employed GSEA for functional analysis, and used qRT-PCR to examine DDX52 expression in LUAD tissues. DDX52 expression was notably higher in LUAD tissues, suggesting its potential as a negative prognostic marker. We observed a direct relationship between DDX52 expression and advanced T and N stages, as well as higher grading and staging in LUAD patients. Cox analyses further underscored DDX52’s role as an independent prognostic determinant for LUAD. GSEA insights indicated DDX52’s influence on LUAD progression via multiple signaling pathways. Our nomogram, founded on DDX52 expression, effectively projected LUAD patient survival, as validated by calibration curves. Elevated DDX52 expression in LUAD tissues signals its potential as a poor prognostic marker. Our findings emphasize DDX52’s role not only as an independent prognostic factor for LUAD but also as a significant influencer in its progression through diverse signaling pathways. The constructed nomogram also underscores the feasibility of predicting LUAD patient survival based on DDX52 expression.

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Proteomic analysis revealed gender-related differences in the skin mucus proteome of discus fish (Symphysodon haraldi) during the parental and non-parental care periods

Zhao,

Wen,

Gao

et al. 2024

Comparative Biochemistry and Physiology Part D: Genomics and Pr

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The RNA helicase Ddx52 functions as a growth switch in juvenile zebrafish

Cited by 7 publications

References 55 publications

SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress

SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress

DDX52 gene expression in LUAD tissues indicates potential as a prognostic biomarker and therapeutic target

Proteomic analysis revealed gender-related differences in the skin mucus proteome of discus fish (Symphysodon haraldi) during the parental and non-parental care periods

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