Licatalosi, D. D. & Darnell, R. B. RNA processing and its regulation: global insights into biological networks. Nat. Rev. Genet. 11, 75–87 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, M. & Manley, J. L. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol. 10, 741–754 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Scotti, M. M. & Swanson, M. S. RNA mis-splicing in disease. Nat. Rev. Genet. 17, 19–32 (2016).

Article  CAS  PubMed  Google Scholar 

Jankowsky, E. & Harris, M. E. Specificity and nonspecificity in RNA–protein interactions. Nat. Rev. Mol. Cell Biol. 16, 533–544 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ramskold, D., Wang, E. T., Burge, C. B. & Sandberg, R. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput. Biol. 5, e1000598 (2009).

Article  PubMed  PubMed Central  Google Scholar 

Kurosaki, T., Popp, M. W. & Maquat, L. E. Quality and quantity control of gene expression by nonsense-mediated mRNA decay. Nat. Rev. Mol. Cell Biol. 20, 406–420 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cooper, T. A., Wan, L. & Dreyfuss, G. RNA and disease. Cell 136, 777–793 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shendure, J. et al. DNA sequencing at 40: past, present and future. Nature 550, 345–353 (2017).

Article  CAS  PubMed  Google Scholar 

Ramanathan, M., Porter, D. F. & Khavari, P. A. Methods to study RNA–protein interactions. Nat. Methods 16, 225–234 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gebauer, F., Schwarzl, T., Valcarcel, J. & Hentze, M. W. RNA-binding proteins in human genetic disease. Nat. Rev. Genet. 22, 185–198 (2021).

Article  CAS  PubMed  Google Scholar 

Hentze, M. W., Castello, A., Schwarzl, T. & Preiss, T. A brave new world of RNA-binding proteins. Nat. Rev. Mol. Cell Biol. 19, 327–341 (2018).

Article  CAS  PubMed  Google Scholar 

Van Nostrand, E. L. et al. A large-scale binding and functional map of human RNA-binding proteins. Nature 583, 711–719 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Forch, P., Puig, O., Martinez, C., Seraphin, B. & Valcarcel, J. The splicing regulator TIA-1 interacts with U1-C to promote U1 snRNP recruitment to 5′ splice sites. EMBO J. 21, 6882–6892 (2002).

Article  PubMed  PubMed Central  Google Scholar 

Forch, P. et al. The apoptosis-promoting factor TIA-1 is a regulator of alternative pre-mRNA splicing. Mol. Cell 6, 1089–1098 (2000).

Article  CAS  PubMed  Google Scholar 

Sgromo, A. et al. A CAF40-binding motif facilitates recruitment of the CCR4–NOT complex to mRNAs targeted by Drosophila Roquin. Nat. Commun. 8, 14307 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sandler, H., Kreth, J., Timmers, H. T. & Stoecklin, G. Not1 mediates recruitment of the deadenylase Caf1 to mRNAs targeted for degradation by tristetraprolin. Nucleic Acids Res. 39, 4373–4386 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fabian, M. R. et al. Structural basis for the recruitment of the human CCR4–NOT deadenylase complex by tristetraprolin. Nat. Struct. Mol. Biol. 20, 735–739 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Leppek, K. et al. Roquin promotes constitutive mRNA decay via a conserved class of stem–loop recognition motifs. Cell 153, 869–881 (2013).

Article  CAS  PubMed  Google Scholar 

Cho, P. F. et al. A new paradigm for translational control: inhibition via 5′–3′ mRNA tethering by Bicoid and the eIF4E cognate 4EHP. Cell 121, 411–423 (2005).

Article  CAS  PubMed  Google Scholar 

Song, T. et al. Specific interaction of KIF11 with ZBP1 regulates the transport of beta-actin mRNA and cell motility. J. Cell Sci. 128, 1001–1010 (2015).

CAS  PubMed  PubMed Central  Google Scholar 

Wu, J. Y. & Maniatis, T. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75, 1061–1070 (1993). This study was the first to functionally characterize RBP–effector interactions and their impact on RNA processing by showing that PPIs between SR proteins and the spliceosome have a regulatory role in alternative splicing.

Article  CAS  PubMed  Google Scholar 

Park, E., Gleghorn, M. L. & Maquat, L. E. Staufen2 functions in Staufen1-mediated mRNA decay by binding to itself and its paralog and promoting UPF1 helicase but not ATPase activity. Proc. Natl Acad. Sci. USA 110, 405–412 (2013).

Article  CAS  PubMed  Google Scholar 

Alberti, S. & Hyman, A. A. Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing. Nat. Rev. Mol. Cell Biol. 22, 196–213 (2021).

Article  CAS  PubMed  Google Scholar 

Sabari, B. R., Dall’Agnese, A. & Young, R. A. Biomolecular condensates in the nucleus. Trends Biochem. Sci. 45, 961–977 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lyon, A. S., Peeples, W. B. & Rosen, M. K. A framework for understanding the functions of biomolecular condensates across scales. Nat. Rev. Mol. Cell Biol. 22, 215–235 (2021).

Article  CAS  PubMed  Google Scholar 

Roden, C. & Gladfelter, A. S. RNA contributions to the form and function of biomolecular condensates. Nat. Rev. Mol. Cell Biol. 22, 183–195 (2021).

Article  CAS  PubMed  Google Scholar 

Mengistu, H., Huizinga, J., Mouret, J. B. & Clune, J. The evolutionary origins of hierarchy. PLoS Comput. Biol. 12, e1004829 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Wilinski, D. et al. Recurrent rewiring and emergence of RNA regulatory networks. Proc. Natl Acad. Sci. USA 114, E2816–E2825 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moore, M. J. & Proudfoot, N. J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688–700 (2009).

Article  CAS  PubMed  Google Scholar 

Bose, M., Lampe, M., Mahamid, J. & Ephrussi, A. Liquid-to-solid phase transition of oskar ribonucleoprotein granules is essential for their function in Drosophila embryonic development. Cell 185, 1308–1324.e23 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Keskin, O., Gursoy, A., Ma, B. & Nussinov, R. Principles of protein–protein interactions: what are the preferred ways for proteins to interact? Chem. Rev. 108, 1225–1244 (2008).

Article  CAS  PubMed  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 

Adelman, K. & Lis, J. T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat. Rev. Genet. 13, 720–731 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Core, L. & Adelman, K. Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation. Genes Dev. 33, 960–982 (2019).

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 

Calo, E. et al. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature 518, 249–253 (2015).

Article  CAS