Learning the language of post-transcriptional gene regulation

Gerstberger, Stefanie; Hafner, Markus; Tuschl, Thomas

doi:10.1186/gb-2013-14-8-130

Cited by 9 publications

(7 citation statements)

References 11 publications

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“…Large scale, high-throughput sequencing techniques, as well as mass spectrometry, have been used to identify mRNA targets and the functional effects of protein-RNA interactions [133, 134]. The widely used method for identifying RBP binding sites and partners consist of C ross L inking the RNP complexes followed by I mmuno P recipitation and then deep SEQ uencing of the bound RNA fragments also known as CLIP-Seq [135].…”

Section: Identifying the Rna Targets Of Rbpsmentioning

confidence: 99%

RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer

Chatterji

Rustgi

2018

Trends in Molecular Medicine

125

118

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The intestinal epithelium is highly proliferative and consists of crypt invaginations that house stem cells and villus projections with differentiated cells. There exists a dynamic equilibrium between proliferation, migration, differentiation, and senescence that is regulated by several factors. Among these are RNA binding proteins (RBPs) that bind their targets in a both context dependent and independent manner. RBP-RNA complexes act as rheostats by regulating expression of RNAs both co- and post-transcriptionally. This is important, especially in response to intestinal injury, to fuel regeneration. The manner in which these RBPs function in the intestine and their interactions with other pivotal pathways in colorectal cancer may provide a framework for new insights and potential therapeutic applications.

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Section: Identifying the Rna Targets Of Rbpsmentioning

confidence: 99%

RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer

Chatterji

Rustgi

2018

Trends in Molecular Medicine

125

118

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“…The candidate ER RNA-binding membrane proteins noted above lack known RNA-binding domains and thus, as proposed for other RBPs lacking canonical RNA-binding motifs, alternative mechanisms of protein-RNA recognition likely contribute to potential functions in mRNA localization, anchoring, and/or translational regulation on the ER (Castello et al 2012(Castello et al , 2015Beckmann et al 2015). Little is known regarding the mechanism(s) of RNA recognition by any of this newly discovered class of noncanonical RNAbinding proteins, though a recent proteomic analysis of RNA-protein interaction sites, captured via UV crosslinking, represents a substantial advance toward answering this fundamental question (Baltz et al 2012;Castello et al 2012Castello et al , 2016aGerstberger et al 2013;Kwon et al 2013). Viewed from the perspective of emerging evidence that many previously identified RNA-binding proteins are multifunctional, a role for nonconventional modes of RNA localization and anchoring to the ER membrane can now be reasonably considered (Mangus et al 2003;Sawicka et al 2008;Markus and Morris 2009;Turner and Hodson 2012).…”

Section: Introductionmentioning

confidence: 99%

Oncoprotein AEG-1 is an endoplasmic reticulum RNA-binding protein whose interactome is enriched in organelle resident protein-encoding mRNAs

Hsu

Reid

Hoffman

et al. 2018

RNA

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Astrocyte elevated gene-1 (AEG-1), an oncogene whose overexpression promotes tumor cell proliferation, angiogenesis, invasion, and enhanced chemoresistance, is thought to function primarily as a scaffolding protein, regulating PI3K/Akt and Wnt/β-catenin signaling pathways. Here we report that AEG-1 is an endoplasmic reticulum (ER) resident integral membrane RNA-binding protein (RBP). Examination of the AEG-1 RNA interactome by HITS-CLIP and PAR-CLIP methodologies revealed a high enrichment for endomembrane organelle-encoding transcripts, most prominently those encoding ER resident proteins, and within this cohort, for integral membrane protein-encoding RNAs. Cluster mapping of the AEG-1/RNA interaction sites demonstrated a normalized rank order interaction of coding sequence >5' untranslated region, with 3' untranslated region interactions only weakly represented. Intriguingly, AEG-1/membrane protein mRNA interaction sites clustered downstream from encoded transmembrane domains, suggestive of a role in membrane protein biogenesis. Secretory and cytosolic protein-encoding mRNAs were also represented in the AEG-1 RNA interactome, with the latter category notably enriched in genes functioning in mRNA localization, translational regulation, and RNA quality control. Bioinformatic analyses of RNA-binding motifs and predicted secondary structure characteristics indicate that AEG-1 lacks established RNA-binding sites though shares the property of high intrinsic disorder commonly seen in RBPs. These data implicate AEG-1 in the localization and regulation of secretory and membrane protein-encoding mRNAs and provide a framework for understanding AEG-1 function in health and disease.

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“…As descriptions of cellular RNA–protein interaction networks move towards systems-level, quantitative models 4,11,12 , and as other lines of research aim at engineering novel RNA-binding proteins 13–16 , a comprehensive, quantitative view on specificity and non-specificity is required. In this review, we discuss emerging approaches aimed at this goal.…”

mentioning

confidence: 99%

Specificity and nonspecificity in RNA–protein interactions

Jankowsky

Harris

2015

Nat Rev Mol Cell Biol

234

251

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Gene expression is regulated by complex networks of interactions between RNAs and proteins. Proteins that interact with RNA have been traditionally viewed as either specific or non-specific; specific proteins interact preferentially with defined RNA sequence or structure motifs, whereas non-specific proteins interact with RNA sites devoid of such characteristics. Recent studies indicate that the binary “specific vs. non-specific” classification is insufficient to describe the full spectrum of RNA–protein interactions. Here, we review new methods that enable quantitative measurements of protein binding to large numbers of RNA variants, and the concepts aimed as describing resulting binding spectra: affinity distributions, comprehensive binding models and free energy landscapes. We discuss how these new methodologies and associated concepts enable work towards inclusive, quantitative models for specific and non-specific RNA–protein interactions.

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Learning the language of post-transcriptional gene regulation

Abstract: A large-scale RNA in vitro selection study systematically identified RNA recognition elements for 205 RNA-binding proteins belonging to families conserved in most eukaryotes.

Cited by 9 publications

References 11 publications

RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer

RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer

Oncoprotein AEG-1 is an endoplasmic reticulum RNA-binding protein whose interactome is enriched in organelle resident protein-encoding mRNAs

Specificity and nonspecificity in RNA–protein interactions

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