Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation

Hafezqorani, Saber; Lafzi, Atefeh; Bruin, Ruben G. de; Zonneveld, Anton Jan van; Veer, Eric P. van der; Son, Yeşim Aydın; Kazan, Hilal

doi:10.1093/nar/gkw048

Cited by 32 publications

(36 citation statements)

References 46 publications

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“…As a result, these regions have been excluded from previous works analyzing the combined effect of RBPs and miRNAs in post-transcriptional regulation [26]. In our analysis, we observed that the number of RBPs that target a hotspot weakly correlates with mRNA expression (S14 Fig) regardless of the use of mFDR and RNA-seq normalization of CLIP data.…”

Section: Discussionmentioning

confidence: 81%

Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

2017

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Post-transcriptional regulation is regarded as one of the major processes involved in the regulation of gene expression. It is mainly performed by RNA binding proteins and microRNAs, which target RNAs and typically affect their stability. Recent efforts from the scientific community have aimed at understanding post-transcriptional regulation at a global scale by using high-throughput sequencing techniques such as cross-linking and immunoprecipitation (CLIP), which facilitates identification of binding sites of these regulatory factors. However, the diversity in the experimental procedures and bioinformatics analyses has hindered the integration of multiple datasets and thus limited the development of an integrated view of post-transcriptional regulation. In this work, we have performed a comprehensive analysis of 107 CLIP datasets from 49 different RBPs in HEK293 cells to shed light on the complex interactions that govern post-transcriptional regulation. By developing a more stringent CLIP analysis pipeline we have discovered the existence of conserved regulatory AU-rich regions in the 3’UTRs where miRNAs and RBPs that regulate several processes such as polyadenylation or mRNA stability bind. Analogous to promoters, many factors have binding sites overlapping or in close proximity in these hotspots and hence the regulation of the mRNA may depend on their relative concentrations. This hypothesis is supported by RBP knockdown experiments that alter the relative concentration of RBPs in the cell. Upon AGO2 knockdown (KD), transcripts containing “free” target sites show increased expression levels compared to those containing target sites in hotspots, which suggests that target sites within hotspots are less available for miRNAs to bind. Interestingly, these hotspots appear enriched in genes with regulatory functions such as DNA binding and RNA binding. Taken together, our results suggest that hotspots are functional regulatory elements that define an extra layer of regulation of post-transcriptional regulatory networks.

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Section: Discussionmentioning

confidence: 81%

Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

2017

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“…For example, integrative analysis of RBP binding and miRNA binding data will allow identification of cooperative and competitive combinatorial patterning of these regulatory factors (90,91). POSTAR represents an early step toward achieving these goals.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2016

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We present POSTAR (http://POSTAR.ncrnalab.org), a resource of POST-trAnscriptional Regulation coordinated by RNA-binding proteins (RBPs). Precise characterization of post-transcriptional regulatory maps has accelerated dramatically in the past few years. Based on new studies and resources, POSTAR supplies the largest collection of experimentally probed (∼23 million) and computationally predicted (approximately 117 million) RBP binding sites in the human and mouse transcriptomes. POSTAR annotates every transcript and its RBP binding sites using extensive information regarding various molecular regulatory events (e.g., splicing, editing, and modification), RNA secondary structures, disease-associated variants, and gene expression and function. Moreover, POSTAR provides a friendly, multi-mode, integrated search interface, which helps users to connect multiple RBP binding sites with post-transcriptional regulatory events, phenotypes, and diseases. Based on our platform, we were able to obtain novel insights into post-transcriptional regulation, such as the putative association between CPSF6 binding, RNA structural domains, and Li-Fraumeni syndrome SNPs. In summary, POSTAR represents an early effort to systematically annotate post-transcriptional regulatory maps and explore the putative roles of RBPs in human diseases.

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“…1B; Lin and Bundschuh 2015). An analogous mechanism has been proposed for cooperativity between proteins and miRNAs (Kedde et al 2010;Xue et al 2013;Hafezqorani et al 2016). RNA structural cooperativity (RSC) is particularly intriguing as a biological regulatory mechanism as it allows cooperativity and site occupancy to be adjusted individually for each RNA target via sequence.…”

Section: Introductionmentioning

confidence: 99%

Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2

Becker

Jarmoskaite

Vaidyanathan

et al. 2019

RNA

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Posttranslational gene regulation requires a complex network of RNA-protein interactions. Cooperativity, which tunes response sensitivities, originates from protein-protein interactions in many systems. For RNA-binding proteins, cooperativity can also be mediated through RNA structure. RNA structural cooperativity (RSC) arises when binding of one protein induces a redistribution of RNA conformational states that enhance access (positive cooperativity) or block access (negative cooperativity) to additional binding sites. As RSC does not require direct protein-protein interactions, it allows cooperativity to be tuned for individual RNAs, via alterations in sequence that alter structural stability. Given the potential importance of this mechanism of control and our desire to quantitatively dissect features that underlie physiological regulation, we developed a statistical mechanical framework for RSC and tested this model by performing equilibrium binding measurements of the human PUF family protein PUM2. Using 68 RNAs that contain two to five PUM2-binding sites and RNA structures of varying stabilities, we observed a range of structure-dependent cooperative behaviors. To test our ability to account for this cooperativity with known physical constants, we used PUM2 affinity and nearest-neighbor RNA secondary structure predictions. Our model gave qualitative agreement for our disparate set of 68 RNAs across two temperatures, but quantitative deviations arise from overestimation of RNA structural stability. Our results demonstrate cooperativity mediated by RNA structure and underscore the power of quantitative stepwise experimental evaluation of mechanisms and computational tools.

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Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation

Cited by 32 publications

References 46 publications

Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

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

Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2

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