GCLiPP: Global Crosslinking and Protein Purification Method for Constructing High-resolution Occupancy Maps for RNA Binding Proteins

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2023 Dec 8

PMID 38062486

Authors

Wandi S Zhu

Adam J Litterman

Harshaan S Sekhon

Robin Kageyama

Maya M Arce

Kimberly E Taylor

Wenxue Zhao

Lindsey A Criswell

Noah Zaitlen

David J Erle

K Mark Ansel

Affiliations

Soon will be listed here.

Abstract

GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCLiPP maps RBP-occupied sites at a higher resolution than phase separation-based techniques. GCLiPP sequence tags correspond with known RBP binding sites and are enriched for sites detected by RBP-specific crosslinking immunoprecipitation (CLIP) for abundant cytosolic RBPs. Comparison of human Jurkat T cells and mouse primary T cells uncovers shared peaks of GCLiPP signal across homologous regions of human and mouse 3' UTRs, including a conserved mRNA-destabilizing cis-regulatory element. GCLiPP signal overlapping with immune-related SNPs uncovers stabilizing cis-regulatory regions in CD5, STAT6, and IKZF1.

Citing Articles

GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins.

Zhu W, Litterman A, Sekhon H, Kageyama R, Arce M, Taylor K Genome Biol. 2023; 24(1):281.

PMID: 38062486 PMC: 10701951. DOI: 10.1186/s13059-023-03125-2.

References

Gebauer F, Schwarzl T, Valcarcel J, Hentze M . RNA-binding proteins in human genetic disease. Nat Rev Genet. 2020; 22(3):185-198. DOI: 10.1038/s41576-020-00302-y. View

Van Nostrand E, Freese P, Pratt G, Wang X, Wei X, Xiao R . A large-scale binding and functional map of human RNA-binding proteins. Nature. 2020; 583(7818):711-719. PMC: 7410833. DOI: 10.1038/s41586-020-2077-3. View

Martin K, Ephrussi A . mRNA localization: gene expression in the spatial dimension. Cell. 2009; 136(4):719-30. PMC: 2819924. DOI: 10.1016/j.cell.2009.01.044. View

Nicolet B, Zandhuis N, Lattanzio V, Wolkers M . Sequence determinants as key regulators in gene expression of T cells. Immunol Rev. 2021; 304(1):10-29. PMC: 9292449. DOI: 10.1111/imr.13021. View

Johansson L, Gafvelin G, Arner E . Selenocysteine in proteins-properties and biotechnological use. Biochim Biophys Acta. 2005; 1726(1):1-13. DOI: 10.1016/j.bbagen.2005.05.010. View

Baltz A, Munschauer M, Schwanhausser B, Vasile A, Murakawa Y, Schueler M . The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell. 2012; 46(5):674-90. DOI: 10.1016/j.molcel.2012.05.021. View

Zhao W, Siegel D, Biton A, Le Tonqueze O, Zaitlen N, Ahituv N . CRISPR-Cas9-mediated functional dissection of 3'-UTRs. Nucleic Acids Res. 2017; 45(18):10800-10810. PMC: 5737544. DOI: 10.1093/nar/gkx675. View

Proudfoot N . Ending the message: poly(A) signals then and now. Genes Dev. 2011; 25(17):1770-82. PMC: 3175714. DOI: 10.1101/gad.17268411. View

Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze M . The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest. Cell. 2018; 176(1-2):391-403.e19. DOI: 10.1016/j.cell.2018.11.004. View

10.

Perez-Perri J, Rogell B, Schwarzl T, Stein F, Zhou Y, Rettel M . Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture. Nat Commun. 2018; 9(1):4408. PMC: 6199288. DOI: 10.1038/s41467-018-06557-8. View

11.

Lorenz R, Bernhart S, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler P . ViennaRNA Package 2.0. Algorithms Mol Biol. 2011; 6:26. PMC: 3319429. DOI: 10.1186/1748-7188-6-26. View

12.

Steiner D, Thomas M, Hu J, Yang Z, Babiarz J, Allen C . MicroRNA-29 regulates T-box transcription factors and interferon-γ production in helper T cells. Immunity. 2011; 35(2):169-81. PMC: 3361370. DOI: 10.1016/j.immuni.2011.07.009. View

13.

Sievers F, Wilm A, Dineen D, Gibson T, Karplus K, Li W . Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011; 7:539. PMC: 3261699. DOI: 10.1038/msb.2011.75. View

14.

Schueler M, Munschauer M, Gregersen L, Finzel A, Loewer A, Chen W . Differential protein occupancy profiling of the mRNA transcriptome. Genome Biol. 2014; 15(1):R15. PMC: 4056462. DOI: 10.1186/gb-2014-15-1-r15. View

15.

Loeb G, Khan A, Canner D, Hiatt J, Shendure J, Darnell R . Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. Mol Cell. 2012; 48(5):760-70. PMC: 3562697. DOI: 10.1016/j.molcel.2012.10.002. View

16.

Queiroz R, Smith T, Villanueva E, Marti-Solano M, Monti M, Pizzinga M . Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS). Nat Biotechnol. 2019; 37(2):169-178. PMC: 6591131. DOI: 10.1038/s41587-018-0001-2. View

17.

Freeberg M, Han T, Moresco J, Kong A, Yang Y, Lu Z . Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biol. 2013; 14(2):R13. PMC: 4053964. DOI: 10.1186/gb-2013-14-2-r13. View

18.

Binder J, Pletscher-Frankild S, Tsafou K, Stolte C, ODonoghue S, Schneider R . COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database (Oxford). 2014; 2014:bau012. PMC: 3935310. DOI: 10.1093/database/bau012. View

19.

Corley M, Burns M, Yeo G . How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms. Mol Cell. 2020; 78(1):9-29. PMC: 7202378. DOI: 10.1016/j.molcel.2020.03.011. View

20.

Bassell G, Kelic S . Binding proteins for mRNA localization and local translation, and their dysfunction in genetic neurological disease. Curr Opin Neurobiol. 2004; 14(5):574-81. DOI: 10.1016/j.conb.2004.08.010. View