RBP-Maps enables robust generation of splicing regulatory maps

Yee, Brian A.; Pratt, Gabriel A.; Graveley, Brenton R.; Nostrand, Eric L. Van; Yeo, G

doi:10.1261/rna.069237.118

Cited by 70 publications

(70 citation statements)

References 26 publications

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“…Splicing maps profiling normalized enrichment for SF3B4 and SF3A3 at RBP knockdown-responsive alternative 3′ splice site events were generated as previously described [20,76]. In brief, the set of differential 3′ splice site events for RBP-knockdown/RNA-seq was identified from rMATS analysis between RBP knockdown and paired non-target control.…”

Section: Enrichment Of Branch Point Factors At Alternative 3′ Splicementioning

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: Enrichment Of Branch Point Factors At Alternative 3′ Splicementioning

confidence: 99%

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

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…Splicing maps profiling normalized enrichment for SF3B4 and SF3A3 at RBP knockdownresponsive alternative 3' splice site events were generated as previously described [20,74]. In brief, the set of differential 3' splice site events for RBP-knockdown/RNA-seq was identified from rMATS analysis between RBP knockdown and paired non-target control.…”

Section: Enrichment Of Branch Point Factors At Alternative 3′ Splicementioning

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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“…Prdx1 mainly binds to the 3 UTR, CDS, and 5 UTR of the RNAs, indicating that its function may be related to the stability of RNA and AS (Mayr, 2016;Yee et al, 2019). To obtain a comprehensive view of Prdx1-dependent DEGs, control or Prdx1-overexpressing vector was transfected into HeLa cells ( Figure 6A and Supplementary Figure S5A) and RNA-seq was performed.…”

Section: Prdx1 Affects Inflammation-and Apoptosis-related Mrna Stabilitymentioning

confidence: 99%

Prdx1 Reduces Intracerebral Hemorrhage-Induced Brain Injury via Targeting Inflammation- and Apoptosis-Related mRNA Stability

et al. 2020

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RNA-binding proteins (RBPs) have been shown to be involved in posttranscriptional regulation, which plays an important role in the pathophysiology of intracerebral hemorrhage (ICH). Peroxiredoxin 1 (Prdx1), an RBP, plays an important role in regulating inflammation and apoptosis. On the basis that inflammation and apoptosis may contribute to ICH-induced brain injury, in this study, we used ICH models coupled with in vitro experiments, to investigate the role and mechanism of Prdx1 in regulating inflammation and apoptosis by acting as an RBP after ICH. We first found that Prdx1 was significantly up-regulated in response to ICH-induced brain injury and was mainly expressed in astrocytes and microglia in ICH rat brains. After overexpressing Prdx1 by injecting adeno-associated virus (AAV) into the striatum of rats at 3 weeks, we constructed ICH models and found that Prdx1 overexpression markedly reduced inflammation and apoptosis after ICH. Furthermore, RNA immunoprecipitation combined with high-throughput sequencing (RIP-seq) in vitro revealed that Prdx1 affects the stability of inflammation-and apoptosis-related mRNA, resulting in the inhibition of inflammation and apoptosis. Finally, overexpression of Prdx1 significantly alleviated the symptoms and mortality of rats subjected to ICH. Our results show that Prdx1 reduces ICH-induced brain injury by targeting inflammation-and apoptosis-related mRNA stability. Prdx1 may be an improved therapeutic target for alleviating the brain injury caused by ICH.

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RBP-Maps enables robust generation of splicing regulatory maps

Cited by 70 publications

References 26 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

Prdx1 Reduces Intracerebral Hemorrhage-Induced Brain Injury via Targeting Inflammation- and Apoptosis-Related mRNA Stability

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