PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Hafner, Markus; Landthaler, Markus; Burger, Lukas; Khorshid, Mohsen; Hausser, Jean; Berninger, Philipp; Rothballer, Andrea; Ascano, Manuel; Jungkamp, Anna-Carina; Munschauer, Mathias; Wardle, Greg S.; Dewell, Scott; Zavolan, Mihaela; Tuschl, Thomas

doi:10.3791/2034-v

Cited by 20 publications

(13 citation statements)

References 2 publications

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“…Note that, psychiatric disorders are highly correlated in genetic foundation and clinical manifestation (77)(78)(79)(80)(81)(82). For example, PPM1L, encoding protein phosphatase, was detected to be responsible for the regulation of stress-activated protein kinase signaling cascade and apoptosis (83,84). It is worth noting that this gene also identified by a previous study (33).…”

Section: Discussionmentioning

confidence: 90%

How can childhood maltreatment affect post-traumatic stress disorder in adult: Results from a composite null hypothesis perspective of mediation analysis

Shao²,

Zhang³

et al. 2023

Front. Psychiatry

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BackgroundA greatly growing body of literature has revealed the mediating role of DNA methylation in the influence path from childhood maltreatment to psychiatric disorders such as post-traumatic stress disorder (PTSD) in adult. However, the statistical method is challenging and powerful mediation analyses regarding this issue are lacking.MethodsTo study how the maltreatment in childhood alters long-lasting DNA methylation changes which further affect PTSD in adult, we here carried out a gene-based mediation analysis from a perspective of composite null hypothesis in the Grady Trauma Project (352 participants and 16,565 genes) with childhood maltreatment as exposure, multiple DNA methylation sites as mediators, and PTSD or its relevant scores as outcome. We effectively addressed the challenging issue of gene-based mediation analysis by taking its composite null hypothesis testing nature into consideration and fitting a weighted test statistic.ResultsWe discovered that childhood maltreatment could substantially affected PTSD or PTSD-related scores, and that childhood maltreatment was associated with DNA methylation which further had significant roles in PTSD and these scores. Furthermore, using the proposed mediation method, we identified multiple genes within which DNA methylation sites exhibited mediating roles in the influence path from childhood maltreatment to PTSD-relevant scores in adult, with 13 for Beck Depression Inventory and 6 for modified PTSD Symptom Scale, respectively.ConclusionOur results have the potential to confer meaningful insights into the biological mechanism for the impact of early adverse experience on adult diseases; and our proposed mediation methods can be applied to other similar analysis settings.

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Section: Discussionmentioning

confidence: 90%

How can childhood maltreatment affect post-traumatic stress disorder in adult: Results from a composite null hypothesis perspective of mediation analysis

Shao²,

Zhang³

et al. 2023

Front. Psychiatry

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“…In contrast, the presence of all other RBPs, including TIS11B, HuR, PUM2, HNRNPC, and TIA1/L1, which bind to U-rich or AU-rich sequences (called here AU-RBPs) enhanced localization to either TGER or CRER (Fig. 3A, 3E-H)(Wang et al, 2010; Hafner et al, 2010; Lebedeva et al, 2011; Mukherjee et al, 2011; Meyer et al, 2018; Yugami et al, 2020). Although both LARP4B and METAP2 binding were correlated with cytosolic mRNA localization, few mRNAs ( N = 90) were exclusively bound by METAP2, whereas 740 were exclusively bound by LARP4B (Fig.…”

Section: Resultsmentioning

confidence: 99%

Subcytoplasmic location of translation controls protein output

Horste

Zhao

Fansler

et al. 2022

Preprint

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The cytoplasm is highly compartmentalized, but the extent of subcytoplasmic mRNA localization in non-polarized cells is largely unknown. We used fluorescent particle sorting to determine mRNA enrichment in three unenclosed cytoplasmic compartments: the canonical rough endoplasmic reticulum (CRER), the TIS granule-associated rough endoplasmic reticulum (TGER), and the cytosol. Focusing our analysis on non-membrane protein-encoding mRNAs, we observed that 53% have a unique subcytoplasmic localization pattern which is determined by a combinatorial code of 3′UTR-bound RNA-binding proteins. Compartment-enriched mRNAs differed in production and degradation rates and the expression levels and functional classes of their encoded proteins. The TGER domain enriches mRNAs that encode transcription factors, the CRER highly expressed proteins, and the cytosol unstable mRNAs. The rough ER environment is stimulatory as redirecting cytosolic mRNAs to the ER increases their protein expression by two-fold, independently of the bound RNA-binding proteins. We show that local translation environments functionally compartmentalize the cytoplasm.

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“…Candidate target miRNAs were predicted using the miRTarBase database and analyzed using the multiMiR package in R (version 1.18.0) (47). Photoactivatable ribonucleoside crosslinking and immunoprecipitation (PAR-CLIP) (48) is used to identify the binding sites of RNA-binding proteins and miRNA-containing ribonucleoprotein complexes. The miRNA validation level was set to "PAR-CLIP" to further screen miRNAs that interact with hub genes.…”

Section: Construction Of Mirna Interaction Networkmentioning

confidence: 99%

Bulk and single-cell transcriptome analyses of islet tissue unravel gene signatures associated with pyroptosis and immune infiltration in type 2 diabetes

Song

Jiang

et al. 2023

Front. Endocrinol.

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IntroductionType 2 diabetes (T2D) is a common chronic heterogeneous metabolic disorder. However, the roles of pyroptosis and infiltrating immune cells in islet dysfunction of patients with T2D have yet to be explored. In this study, we aimed to explore potential crucial genes and pathways associated with pyroptosis and immune infiltration in T2D.MethodsTo achieve this, we performed a conjoint analysis of three bulk RNA-seq datasets of islets to identify T2D-related differentially expressed genes (DEGs). After grouping the islet samples according to their ESTIMATE immune scores, we identified immune- and T2D-related DEGs. A clinical prediction model based on pyroptosis-related genes for T2D was constructed. Weighted gene co-expression network analysis was performed to identify genes positively correlated with pyroptosis-related pathways. A protein–protein interaction network was established to identify pyroptosis-related hub genes. We constructed miRNA and transcriptional networks based on the pyroptosis-related hub genes and performed functional analyses. Single-cell RNA-seq (scRNA-seq) was conducted using the GSE153885 dataset. Dimensionality was reduced using principal component analysis and t-distributed statistical neighbor embedding, and cells were clustered using Seurat. Different cell types were subjected to differential gene expression analysis and gene set enrichment analysis (GSEA). Cell–cell communication and pseudotime trajectory analyses were conducted using the samples from patients with T2D.ResultsWe identified 17 pyroptosis-related hub genes. We determined the abundance of 13 immune cell types in the merged matrix and found that these cell types were correlated with the 17 pyroptosis-related hub genes. Analysis of the scRNA-seq dataset of 1892 islet samples from patients with T2D and controls revealed 11 clusters. INS and IAPP were determined to be pyroptosis-related and candidate hub genes among the 11 clusters. GSEA of the 11 clusters demonstrated that the myc, G2M checkpoint, and E2F pathways were significantly upregulated in clusters with several differentially enriched pathways.DiscussionThis study elucidates the gene signatures associated with pyroptosis and immune infiltration in T2D and provides a critical resource for understanding of islet dysfunction and T2D pathogenesis.

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Cited by 20 publications

References 2 publications

How can childhood maltreatment affect post-traumatic stress disorder in adult: Results from a composite null hypothesis perspective of mediation analysis

How can childhood maltreatment affect post-traumatic stress disorder in adult: Results from a composite null hypothesis perspective of mediation analysis

Subcytoplasmic location of translation controls protein output

Bulk and single-cell transcriptome analyses of islet tissue unravel gene signatures associated with pyroptosis and immune infiltration in type 2 diabetes

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