Schlee, M. & Hartmann, G. Discriminating self from non-self in nucleic acid sensing. Nat. Rev. Immunol. 16, 566–580 (2016).
Ivashkiv, L.B. & Donlin, L.T. Regulation of type I interferon responses. Nat. Rev. Immunol. 14, 36–49 (2014).
Gack, M.U. et al. TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity. Nature 446, 916–920 (2007).
Cao, X. Self-regulation and cross-regulation of pattern-recognition receptor signalling in health and disease. Nat. Rev. Immunol. 16, 35–50 (2016).
Zheng, Q. et al. Siglec1 suppresses antiviral innate immune response by inducing TBK1 degradation via the ubiquitin ligase TRIM27. Cell Res. 25, 1121–1136 (2015).
Portilho, D.M. et al. Endogenous TRIM5α function is regulated by SUMOylation and nuclear sequestration for efficient innate sensing in dendritic cells. Cell Rep. 14, 355–369 (2016).
Ansari, M.A. et al. Herpesvirus genome recognition induced acetylation of nuclear IFI16 is essential for its cytoplasmic translocation, inflammasome and IFN-b responses. PLoS Pathog. 11, e1005019 (2015).
Kim, T.W. et al. Transcriptional repression of IFN regulatory factor 7 by MYC is critical for type I IFN production in human plasmacytoid dendritic cells. J. Immunol. 197, 3348–3359 (2016).
Loo, Y.M. & Gale, M. Jr. Immune signaling by RIG-I-like receptors. Immunity 34, 680–692 (2011).
Zhang, Z. et al. The helicase DDX41 senses intracellular DNA mediated by the adaptor STING in dendritic cells. Nat. Immunol. 12, 959–965 (2011).
Parvatiyar, K. et al. The helicase DDX41 recognizes the bacterial secondary messengers cyclic di-GMP and cyclic di-AMP to activate a type I interferon immune response. Nat. Immunol. 13, 1155–1161 (2012).
Zhang, Z., Yuan, B., Lu, N., Facchinetti, V. & Liu, Y.J. DHX9 pairs with IPS-1 to sense double-stranded RNA in myeloid dendritic cells. J. Immunol. 187, 4501–4508 (2011).
Schröder, M., Baran, M. & Bowie, A.G. Viral targeting of DEAD box protein 3 reveals its role in TBK1/IKKepsilon-mediated IRF activation. EMBO J. 27, 2147–2157 (2008).
Linder, P. & Jankowsky, E. From unwinding to clamping - the DEAD box RNA helicase family. Nat. Rev. Mol. Cell Biol. 12, 505–516 (2011).
Calo, E. et al. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature 518, 249–253 (2015).
Hoernes, T.P., Hüttenhofer, A. & Erlacher, M.D. mRNA modifications: dynamic regulators of gene expression? RNA Biol. 13, 760–765 (2016).
Wang, X. & He, C. Dynamic RNA modifications in posttranscriptional regulation. Mol. Cell 56, 5–12 (2014).
Desrosiers, R., Friderici, K. & Rottman, F. Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells. Proc. Natl. Acad. Sci. USA 71, 3971–3975 (1974).
Liu, J. et al. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat. Chem. Biol. 10, 93–95 (2014).
Jia, G. et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885–887 (2011).
Wang, X. et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117–120 (2014).
Alarcón, C.R. et al. HNRNPA2B1 is a mediator of m(6)A-dependent nuclear RNA processing events. Cell 162, 1299–1308 (2015).
Liu, N. et al. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518, 560–564 (2015).
Geula, S. et al. Stem cells. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science 347, 1002–1006 (2015).
Zhao, X. et al. FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res. 24, 1403–1419 (2014).
Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013).
Fustin, J.M. et al. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell 155, 793–806 (2013).
Cordin, O. & Beggs, J.D. RNA helicases in splicing. RNA Biol. 10, 83–95 (2013).
Liang, W.W. & Cheng, S.C. A novel mechanism for Prp5 function in prespliceosome formation and proofreading the branch site sequence. Genes Dev. 29, 81–93 (2015).
Bourgeois, C.F., Mortreux, F. & Auboeuf, D. The multiple functions of RNA helicases as drivers and regulators of gene expression. Nat. Rev. Mol. Cell Biol. 17, 426–438 (2016).
Putnam, A.A. & Jankowsky, E. DEAD-box helicases as integrators of RNA, nucleotide and protein binding. Biochim. Biophys. Acta 1829, 884–893 (2013).
Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).
Xu, Y.Z. et al. Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA. EMBO J. 23, 376–385 (2004).
Hirabayashi, R., Hozumi, S., Higashijima, S. & Kikuchi, Y. Ddx46 is required for multi-lineage differentiation of hematopoietic stem cells in zebrafish. Stem Cells Dev. 22, 2532–2542 (2013).
Hozumi, S. et al. DEAD-box protein Ddx46 is required for the development of the digestive organs and brain in zebrafish. PLoS One 7, e33675 (2012).
Zarnack, K. et al. Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 152, 453–466 (2013).
Weber, M. et al. Incoming RNA virus nucleocapsids containing a 5′-triphosphorylated genome activate RIG-I and antiviral signaling. Cell Host Microbe 13, 336–346 (2013).
Sun, X. et al. Nuclear retention of full-length HTT RNA is mediated by splicing factors MBNL1 and U2AF65. Sci. Rep. 5, 12521 (2015).
Chen, L.L. & Carmichael, G.G. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol. Cell 35, 467–478 (2009).
Boutz, P.L., Bhutkar, A. & Sharp, P.A. Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Genes Dev. 29, 63–80 (2015).
Bahar Halpern, K. et al. Nuclear retention of mRNA in mammalian tissues. Cell Rep. 13, 2653–2662 (2015).
Kufel, J., Bousquet-Antonelli, C., Beggs, J.D. & Tollervey, D. Nuclear pre-mRNA decapping and 5′ degradation in yeast require the Lsm2-8p complex. Mol. Cell. Biol. 24, 9646–9657 (2004).
Li, X. et al. Methyltransferase Dnmt3a upregulates HDAC9 to deacetylate the kinase TBK1 for activation of antiviral innate immunity. Nat. Immunol. 17, 806–815 (2016).
Wang, P. et al. The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science 344, 310–313 (2014).
Liu, J. et al. Rhbdd3 controls autoimmunity by suppressing the production of IL-6 by dendritic cells via K27-linked ubiquitination of the regulator NEMO. Nat. Immunol. 15, 612–622 (2014).
Huppertz, I. et al. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65, 274–287 (2014).
Moore, M.J. et al. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat. Protoc. 9, 263–293 (2014).
Peritz, T. et al. Immunoprecipitation of mRNA-protein complexes. Nat. Protoc. 1, 577–580 (2006).
Katz, Y., Wang, E.T., Airoldi, E.M. & Burge, C.B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 7, 1009–1015 (2010).
Miller, J.C. et al. A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol. 29, 143–148 (2011).