Decoding protein–RNA interactions using CLIP-based methodologies

Lunde, B. M., Moore, C. & Varani, G. RNA-binding proteins: modular design for efficient function. Nat. Rev. Mol. Cell Biol. 8, 479–490 (2007).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Castello, A. et al. Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap. Nat. Protoc. 12, 2447–2464 (2017).

Article  CAS  PubMed  Google Scholar 

Castello, A. et al. Comprehensive identification of RNA-binding domains in human cells. Mol. Cell 63, 696–671 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Licatalosi, D. D. et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456, 464–469 (2008). To our knowledge, this study is the first to couple high-throughput, short-read sequencing to ultraviolet crosslinking followed by immunoprecipitation (CLIP), providing a comprehensive protein–RNA interaction map of the neuronal splicing factor NOVA in the brain.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yeo, G. W. et al. An RNA code for the FOX2 splicing regulator revealed by mapping RNA–protein interactions in stem cells. Nat. Struct. Mol. Biol. 16, 130–137 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129–141 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

König, J. et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol. 17, 909–915 (2010).

Article  PubMed  PubMed Central  Google Scholar 

Van Nostrand, E. L. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat. Methods 13, 508–514 (2016). This study developed an improved CLIP methodology that was used to map the protein–RNA interactomes of 73 diverse RNA-binding proteins (RBPs) in two human cell lines.

Article  PubMed  PubMed Central  Google Scholar 

Zarnegar, B. J. et al. irCLIP platform for efficient characterization of protein-RNA interactions. Nat. Methods 13, 489–492 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lovci, M. T. et al. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat. Struct. Mol. Biol. 20, 1434–1442 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Uren, P. J. et al. Site identification in high-throughput RNA-protein interaction data. Bioinformatics 28, 3013–3020 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Corcoran, D. L. et al. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol. 12, R79 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boyle, E. A. et al. Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites. Cell Genom. 3, 100317 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luo, E. C. et al. Large-scale tethered function assays identify factors that regulate mRNA stability and translation. Nat. Struct. Mol. Biol. 27, 989–1000 (2020). This study is the first large-scale and systematic screen to directly assess the ability of RBPs to regulate mRNA stability and translation, identifying programmable translational enhancers.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Izaurralde, E. et al. A nuclear cap binding protein complex involved in pre-mRNA splicing. Cell 78, 657–668 (1994).

Article  CAS  PubMed  Google Scholar 

Calero, G. et al. Structural basis of m7GpppG binding to the nuclear cap-binding protein complex. Nat. Struct. Biol. 9, 912–917 (2002).

Article  CAS  PubMed  Google Scholar 

Giacometti, S. et al. Mutually exclusive CBC-containing complexes contribute to RNA fate. Cell Rep. 18, 2635–2650 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mazza, C., Segref, A., Mattaj, I. W. & Cusack, S. Large-scale induced fit recognition of an m(7)GpppG cap analogue by the human nuclear cap-binding complex. EMBO J. 21, 5548–5557 (2002).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dantsuji, S., Ohno, M. & Taniguchi, I. The hnRNP C tetramer binds to CBC on mRNA and impedes PHAX recruitment for the classification of RNA polymerase II transcripts. Nucleic Acids Res. 51, 1393–1408 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cordiner, R. A. et al. Temporal-iCLIP captures co-transcriptional RNA–protein interactions. Nat. Commun. 14, 696 (2023). This is one of the first papers to use CLIP data in conjunction with an inhibitory compound to map the spatiotemporal loading of specific RBPs onto mRNAs. A time-resolved iCLIP assay synchronized with inhibition of RNA polymerase II is used to detail the orchestrated recruitment of RBPs, including CBC, ALYREF and RBM7, onto nascent mRNA.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lagier-Tourenne, C. et al. Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. Nat. Neurosci. 15, 1488–1497 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ameur, A. et al. Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat. Struct. Mol. Biol. 18, 1435–1440 (2011).

Article  CAS  PubMed  Google Scholar 

Yu, Y. & Reed, R. FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP. Proc. Natl Acad. Sci. USA 112, 8608–8613 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xiao, R. et al. Pervasive chromatin–RNA binding protein interactions enable RNA-based regulation of transcription. Cell 178, 107–121.e18 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zeng, Y. et al. Lin28A binds active promoters and recruits tet1 to regulate gene expression. Mol. Cell 61, 153–160 (2016).

Article  CAS  PubMed  Google Scholar 

Barbieri, I. et al. Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control. Nature 552, 126–131 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fan, H. et al. The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes. Genome Res. 28, 192–202 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bi, X. et al. RNA targets ribogenesis factor WDR43 to chromatin for transcription and pluripotency control. Mol. Cell 75, 102–116.e9 (2019).

Article  CAS  PubMed  Google Scholar 

Ren, Y. et al. A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation. Genome Biol. 22, 290 (2021).

留言 (0)

沒有登入
gif