CLIP and complementary methods
Markus Hafner,Maria Katsantoni,Maria Katsantoni,Tino Köster,James Marks,Joyita Mukherjee,Joyita Mukherjee,Dorothee Staiger,Jernej Ule,Jernej Ule,Mihaela Zavolan,Mihaela Zavolan +11 more
- Vol. 1, Iss: 1, pp 1-23
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TLDR
The prospect of integrating data obtained by CLIP with complementary methods to gain a comprehensive view of RNP assembly and remodelling, unravel the spatial and temporal dynamics of RNPs in specific cell types and subcellular compartments and understand how defects in RNPs can lead to disease are discussed.Abstract:
RNA molecules start assembling into ribonucleoprotein (RNP) complexes during transcription. Dynamic RNP assembly, largely directed by cis-acting elements on the RNA, coordinates all processes in which the RNA is involved. To identify the sites bound by a specific RNA-binding protein on endogenous RNAs, cross-linking and immunoprecipitation (CLIP) and complementary, proximity-based methods have been developed. In this Primer, we discuss the main variants of these protein-centric methods and the strategies for their optimization and quality assessment, as well as RNA-centric methods that identify the protein partners of a specific RNA. We summarize the main challenges of computational CLIP data analysis, how to handle various sources of background and how to identify functionally relevant binding regions. We outline the various applications of CLIP and available databases for data sharing. We discuss the prospect of integrating data obtained by CLIP with complementary methods to gain a comprehensive view of RNP assembly and remodelling, unravel the spatial and temporal dynamics of RNPs in specific cell types and subcellular compartments and understand how defects in RNPs can lead to disease. Finally, we present open questions in the field and give directions for further development and applications. Ule and colleagues discuss cross-linking and immunoprecipitation (CLIP) methods for characterizing the RNA binding partners of RNA-binding proteins and explore the data analysis workflows, best practices and applications for these techniques. The Primer also considers methods for characterizing the protein binding partners of specific RNAs and discusses how data from these complementary methods can be integrated into CLIP workflows.read more
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References
More filters
Journal ArticleDOI
Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase.
B. van Steensel,Steven Henikoff +1 more
TL;DR: Using DamID, a number of expected and unexpected target loci for Drosophila heterochromatin protein 1 are identified, showing potential for genome-wide mapping of in vivo targets of chromatin proteins in various eukaryotes.
Journal ArticleDOI
CLIP: a method for identifying protein-RNA interaction sites in living cells.
TL;DR: An improved protocol that performs RNA linker ligation before the SDS-PAGE step is presented, and its application to the specific purification and amplification of RNA ligands of Nova in neurons is described.
Journal ArticleDOI
An improved smaller biotin ligase for BioID proximity labeling.
Dae In Kim,Samuel C. Jensen,Kyle A. Noble,Birendra Kc,Kenneth H. Roux,Khatereh Motamedchaboki,Kyle J. Roux +6 more
TL;DR: A smaller promiscuous biotin ligase for proximity biotinylation called BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, exhibits enhanced labeling of proximate proteins, and demonstrates the use of a flexible linker to modulate the biotin-labeling radius.
Journal ArticleDOI
An RNA map predicting Nova-dependent splicing regulation
Jernej Ule,Giovanni Stefani,Giovanni Stefani,Aldo Mele,Matteo Ruggiu,Xuning Wang,Bahar Taneri,Bahar Taneri,Bahar Taneri,Terry Gaasterland,Terry Gaasterland,Benjamin J. Blencowe,Robert B. Darnell +12 more
TL;DR: A genome-wide map relating the position of a cis-acting element to its regulation by an RNA binding protein reveals that Nova binding to YCAY clusters results in a local and asymmetric action to regulate spliceosome assembly and alternative splicing in neurons.
Journal ArticleDOI
A large-scale binding and functional map of human RNA-binding proteins
Eric L. Van Nostrand,Peter Freese,Gabriel A. Pratt,Xiaofeng Wang,Xintao Wei,Rui Xiao,Rui Xiao,Steven M. Blue,Jia-Yu Chen,Neal A.L. Cody,Daniel Dominguez,Sara Olson,Balaji Sundararaman,Lijun Zhan,Cassandra Bazile,Louis Philip Benoit Bouvrette,Julie Bergalet,Michael O. Duff,Keri E. Garcia,Chelsea Gelboin-Burkhart,Myles Hochman,Nicole J. Lambert,Hairi Li,Michael P. McGurk,Thai B. Nguyen,Tsultrim Palden,Ines Rabano,Shashank Sathe,Rebecca Stanton,Amanda Su,Ruth Wang,Brian A. Yee,Bing Zhou,Ashley L. Louie,Stefan Aigner,Xiang-Dong Fu,Eric Lécuyer,Eric Lécuyer,Christopher B. Burge,Brenton R. Graveley,Gene W. Yeo +40 more
TL;DR: The spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization are described.
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