In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target Sites

Jungkamp, Anna-Carina; Stoeckius, Marlon; Mecenas, Desirea; Grün, Dominic; Mastrobuoni, Guido; Kempa, Stefan; Rajewsky, Nikolaus

doi:10.1016/j.molcel.2011.11.009

Cited by 147 publications

(199 citation statements)

References 34 publications

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“…This includes miRISC components (48,52,53) , the Pumilio and FBF [Fem-3 binding factor] (PUF) domain family member Pumilio-2 (PUM2), the insulin-like growth factor 2 mRBPs 1, 2, and 3 (IGF2BP1-3), Quaking (QKI) (48) , heterogeneous nuclear ribonucleoprotein (hnRNP) particles (47) , T-cell intracellular antigen 1 (TIA1) and the related TIA1-like 1 (TIAL1) protein (54) , the splicing regulators TAR DNA binding protein 43 (TDP-43) (55) , Nova-1 and Nova-2 (43,56) , fragile X mental retardation protein (FMRP) (57) , the FET family proteins fused in sarcoma (FUS), Ewing sarcoma breakpoint region 1 (EWSR1) and TATA box binding protein (TBP)-associated factor 15 (TAF15) (58) , and human antigen R (HuR) (59,60) . Furthermore, PAR-CLIP has been applied in worms (61) and yeast (62) . Of note, databases for the deposition and visualization of CLIP experiments, such as CLIPZ (63) and PARalyzer (64) , have been set-up and are available to the community for data deposition or exploration (65) .…”

Section: Ribonomics -Global Methods For the Identifi Cation Of Rna-prmentioning

confidence: 99%

RNA regulons and the RNA-protein interaction network

Imig¹,

Kanitz²,

Gerber

2012

BioMolecular Concepts

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The development of genome-wide analysis tools has prompted global investigation of the gene expression program, revealing highly coordinated control mechanisms that ensure proper spatiotemporal activity of a cell ' s macromolecular components. With respect to the regulation of RNA transcripts, the concept of RNA regulons, which -by analogy with DNA regulons in bacteria -refers to the coordinated control of functionally related RNA molecules, has emerged as a unifying theory that describes the logic of regulatory RNA-protein interactions in eukaryotes. Hundreds of RNA-binding proteins and small non-coding RNAs, such as microRNAs, bind to distinct elements in target RNAs, thereby exerting specifi c and concerted control over posttranscriptional events. In this review, we discuss recent reports committed to systematically explore the RNA-protein interaction network and outline some of the principles and recurring features of RNA regulons: the coordination of functionally related mRNAs through RNAbinding proteins or non-coding RNAs, the modular structure of its components, and the dynamic rewiring of RNA-protein interactions upon exposure to internal or external stimuli. We also summarize evidence for robust combinatorial control of mRNAs, which could determine the ultimate fate of each mRNA molecule in a cell. Finally, the compilation and integration of global protein-RNA interaction data has yielded fi rst insights into network structures and provided the hypothesis that RNA regulons may, in part, constitute noise ' buffers ' to handle stochasticity in cellular transcription.

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Section: Ribonomics -Global Methods For the Identifi Cation Of Rna-prmentioning

confidence: 99%

RNA regulons and the RNA-protein interaction network

Imig¹,

Kanitz²,

Gerber

2012

BioMolecular Concepts

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“…While a single RRE was sufficient for GLD-1-dependent regulation, multiple RREs within the 39 UTR increased the effect. Using PAR-CLIP (photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation) in human embryonic kidney cells (HEK293) and C. elegans, our group and others expanded the QKI and GLD-1 target list and found similar RREs (Hafner et al 2010;Jungkamp et al 2011). In HEK293 cells, we found that >90% of the 2500 crosslinked binding sites present in 1500 transcripts contained at least one 5-nt YUAAY RRE.…”

mentioning

confidence: 93%

Structure–function studies of STAR family Quaking proteins bound to their in vivo RNA target sites

et al. 2013

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Mammalian Quaking (QKI) and its Caenorhabditis elegans homolog, GLD-1 (defective in germ line development), are evolutionarily conserved RNA-binding proteins, which post-transcriptionally regulate target genes essential for developmental processes and myelination. We present X-ray structures of the STAR (signal transduction and activation of RNA) domain, composed of Qua1, K homology (KH), and Qua2 motifs of QKI and GLD-1 bound to high-affinity in vivo RNA targets containing YUAAY RNA recognition elements (RREs). The KH and Qua2 motifs of the STAR domain synergize to specifically interact with bases and sugar-phosphate backbones of the bound RRE. Qua1-mediated homodimerization generates a scaffold that enables concurrent recognition of two RREs, thereby plausibly targeting tandem RREs present in many QKI-targeted transcripts. Structure-guided mutations reduced QKI RNA-binding affinity in vitro and in vivo, and expression of QKI mutants in human embryonic kidney cells (HEK293) significantly decreased the abundance of QKI target mRNAs. Overall, our studies define principles underlying RNA target selection by STAR homodimers and provide insights into the post-transcriptional regulatory function of mammalian QKI proteins.

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“…(E) EFL-1 targets (Gerstein et al 2010). (F) GLD-1 targets (Jungkamp et al 2011). n.s., not significant; **FDR , 1E-6; ***FDR , 1E-9.…”

Section: Sperm-only Adults Differ In Reprogramming Competencementioning

confidence: 99%

Competence for Chemical Reprogramming of Sexual Fate Correlates with an Intersexual Molecular Signature inCaenorhabditis elegans

2014

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In multicellular organisms, genetic programs guide cells to adopt cell fates as tissues are formed during development, maintained in adults, and repaired after injury. Here we explore how a small molecule in the environment can switch a genetic program from one fate to another. Wild-type Caenorhabditis elegans XX adult hermaphrodites make oocytes continuously, but certain mutant XX adults make sperm instead in an otherwise hermaphrodite soma. Thus, puf-8; lip-1 XX adults make only sperm, but they can be switched from sperm to oocyte production by treatment with a small-molecule MEK inhibitor. To ask whether this chemical reprogramming is common, we tested six XX sperm-only mutants, but found only one other capable of cell fate switching, fbf-1; lip-1. Therefore, reprogramming competence relies on genotype, with only certain mutants capable of responding to the MEK inhibitor with a cell fate change. To gain insight into the molecular basis of competence for chemical reprogramming, we compared polyadenylated transcriptomes of competent and noncompetent XX sperm-only mutants in the absence of the MEK inhibitor and hence in the absence of cell fate reprogramming. Despite their cellular production of sperm, competent mutants were enriched for oogenic messenger RNAs relative to mutants lacking competence for chemical reprogramming. In addition, competent mutants expressed the oocyte-specific protein RME-2, whereas those lacking competence did not. Therefore, mutants competent for reprogramming possess an intersexual molecular profile at both RNA and protein levels. We suggest that this intersexual molecular signature is diagnostic of an intermediate network state that poises the germline tissue for changing its cellular fate in response to environmental cues. C ELLS in multicellular organisms acquire specific fates, either during development as tissues are generated or during adulthood as tissues are renewed or repaired. A classical view holds that during development, a cell follows a specific genetic program to determine its differentiated fate, but more recent studies reveal that cells can be induced to switch from one genetic program to another. Such "reprogramming" of a cell fate program can occur in vivo in cancer (Friedl and Alexander 2011;Byun and Gardner 2013), wound healing (Wong et al. 2013), and regeneration (Xin et al. 2013;Ziv et al. 2013). Moreover, reprogramming can be stimulated by introduction of transcription factors (Takahashi and Yamanaka 2006) or small molecules (Morgan et al. 2010;Zhu et al. 2010;Li et al. 2014). Here we explore the effect of genotype on the capacity for a particular case of chemically induced cell fate reprogramming within an organism.The Caenorhabditis elegans germline provides a tractable model for analyses of cell fate reprogramming. The adult germline is an elongate tissue with 2000 cells, including germline stem cells (GSCs) (Figure 1A, yellow). GSCs continuously generate daughter cells that enter the meiotic cell cycle ( Figure 1A, green) and then differentiate as...

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In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target Sites

Cited by 147 publications

References 34 publications

RNA regulons and the RNA-protein interaction network

RNA regulons and the RNA-protein interaction network

Structure–function studies of STAR family Quaking proteins bound to their in vivo RNA target sites

Competence for Chemical Reprogramming of Sexual Fate Correlates with an Intersexual Molecular Signature inCaenorhabditis elegans

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