POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

Hu, Boqin; Yang, Yu; Huang, Yiming; Zhu, Yumin; Lu, Zhi John

doi:10.1093/nar/gkw888

Cited by 117 publications

(92 citation statements)

References 91 publications

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“…Further efforts to profile multiple human RBPs in the same family or regulatory function by CLIP illustrated coordinated and complex auto-and cross-regulatory interactions among RBPs and their targets [8][9][10]. Rising interest in organizing public deeply sequenced CLIP datasets to enable the community to extract novel RNA biology is apparent from newly available computational databases and integrative methods [11,12]. However, methodological differences between CLIP approaches, combined with simple experimental variability between labs and variation in acceptable quality control metrics, add significant challenges to interpretation of differences observed.…”

Section: Introductionmentioning

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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Section: Introductionmentioning

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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“…Supplementary Table 1A: The three FUS mouse datasets used in this study. (Hu et al 2017) . When the same CLIP sample had been processed with more than one peak caller, the Piranha caller was selected for presentation.…”

Section: Figure 8: Cartoon Summarymentioning

confidence: 99%

FUSALS-causative mutations impactFUSautoregulation and the processing of RNA-binding proteins through intron retention

Humphrey

Birsa

Milioto

et al. 2019

Preprint

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Mutations in the RNA binding protein FUS cause amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease in which the loss of motor neurons induces progressive weakness and death from respiratory failure, typically only 3-5 years after onset.FUS has been established to have a role in numerous aspects of RNA processing, including splicing. However, the impact of ALS-causative mutations on splicing has not been fully characterised, as most disease models have been based on FUS overexpression, which in itself alters its RNA processing functions. To overcome this, we and others have recently created knock-in models, and have generated high depth RNA-sequencing data on FUS mutants in parallel to FUS knockout. We combined three independent datasets with a joint modelling approach, allowing us to compare the mutation-induced changes to genuine loss of function. We find that FUS ALS-mutations induce a widespread loss of function on expression and splicing, with a preferential effect on RNA binding proteins. Mutant FUS induces intron retention changes through RNA binding, and we identify an intron retention event in FUS itself that is associated with its autoregulation. Altered FUS regulation has been linked to disease, and intriguingly, we find FUS autoregulation to be altered not only by FUS mutations, but also in other genetic forms of ALS, including those caused by TDP-43,

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“…Using the same methodology, we tested for an overrepresentation of RBP targets in differentially expressed genes during the activation of fibroblasts. To construct reliable RBP-target networks, we utilized experimental evidence for RBP-RNA binding derived from eCLIP (n=117), PAR-CLIP 21 (n=58), HITS-CLIP (n=23) and iCLIP (n=22) data provided by ENCODE 22 and POSTAR 23 . RBP targets were predominantly enriched in DTEGs but not in DTGs, which suggests that RBPs shape the fibrotic response mainly through translational regulation and rarely influence transcript levels ( Figure 4b ).…”

Section: Rbp Target Over-representation Test In the Regulatory Groumentioning

confidence: 99%

“…Peak files from eCLIP experiments on ENCODE were downloaded and filtered for 8 fold-enrichment and 10 -5 p-value over the input. Peak files were also downloaded from POSTAR 23 and used with default filters. Similar to miRNAs, for each RBP we compared the number of actual targets in a regulation group to the number of targets found in a random gene set of the same size to obtain an empirical p-value and z-score (n=100,000 permutations).…”

Section: Mirna Sequencingmentioning

confidence: 99%

Translational control of cardiac fibrosis

Chothani

Schäfer

Adami

et al. 2018

Preprint

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BackgroundFibrosis is a common pathology in many cardiac disorders and is driven by the activation of resident fibroblasts.The global post-transcriptional mechanisms underlying fibroblast-to-myofibroblast conversion in the heart have not been explored. MethodsGenome-wide changes of RNA transcription and translation during human cardiac fibroblast activation were monitored with RNA sequencing and ribosome profiling. We then used miRNA-and RNA-binding protein-based analyses to identify translational regulators of fibrogenic genes. To reveal post-transcriptional mechanisms in the human fibrotic heart, we then integrated our findings with cardiac ribosome occupancy levels of 30 dilated cardiomyopathy patients. ResultsWe generated nucleotide-resolution translatome data during the TGFβ1-driven cellular transition of human cardiac fibroblasts to myofibroblasts. This identified dynamic changes of RNA transcription and translation at several time points during the fibrotic response, revealing transient and early-responder genes. Remarkably, about one-third of all changes in gene expression in activated fibroblasts are subject to translational regulation and dynamic variation in ribosome occupancy affects protein abundance independent of RNA levels. Targets of RNA-binding proteins were strongly enriched in post-transcriptionally regulated genes, suggesting genes such as MBNL2 can act as translational activators or repressors. Ribosome occupancy in the hearts of patients with dilated cardiomyopathy suggested an extensive post-transcriptional regulatory network underlying cardiac fibrosis. Key network hubs include RNA-binding proteins such as PUM2 and QKI that work in concert to regulate the translation of target transcripts in human diseased hearts. ConclusionsWe reveal widespread translational effects of TGFβ1 and define novel post-transcriptional events that control the fibroblast-to-myofibroblast transition. Regulatory networks that affect ribosome occupancy in fibroblasts are paralleled in human heart disease. Our findings show the central importance of translational control in fibrosis and highlight novel pathogenic mechanisms in heart failure.

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POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

Cited by 117 publications

References 91 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

FUSALS-causative mutations impactFUSautoregulation and the processing of RNA-binding proteins through intron retention

Translational control of cardiac fibrosis

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