The multifaceted effects of YTHDC1-mediated nuclear m6A recognition

Trends in Genetics - Tập 38 - Trang 325-332 - 2022
Jocelyn Widagdo1, Victor Anggono1, Justin J.-L. Wong2,3
1Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
2Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, New South Wales, 2050, Australia
3Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, 2050, Australia

Tài liệu tham khảo

Zaccara, 2019, Reading, writing and erasing mRNA methylation, Nat. Rev. Mol. Cell Biol., 20, 608, 10.1038/s41580-019-0168-5 Patil, 2017, Reading m6A in the transcriptome: m6A-binding proteins, Trends Cell Biol., 28, 113, 10.1016/j.tcb.2017.10.001 Zhang, 2010, The YTH domain is a novel RNA binding domain, J. Biol. Chem., 285, 14701, 10.1074/jbc.M110.104711 Theler, 2014, Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA, Nucleic Acids Res., 42, 13911, 10.1093/nar/gku1116 Xu, 2014, Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain, Nat. Chem. Biol., 10, 927, 10.1038/nchembio.1654 Xu, 2015, Structural basis for the discriminative recognition of N6-methyladenosine RNA by the human YT521-B homology domain family of proteins, J. Biol. Chem., 290, 24902, 10.1074/jbc.M115.680389 Luo, 2014, Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain, Proc. Natl. Acad. Sci. U. S. A., 111, 13834, 10.1073/pnas.1412742111 Imai, 1998, Cloning of a gene, YT521, for a novel RNA splicing-related protein induced by hypoxia/reoxygenation, Brain Res. Mol. Brain Res., 53, 33, 10.1016/S0169-328X(97)00262-3 Hartmann, 1999, The interaction and colocalization of Sam68 with the splicing-associated factor YT521-B in nuclear dots is regulated by the Src family kinase p59fyn, Mol. Biol. Cell, 10, 3909, 10.1091/mbc.10.11.3909 Nayler, 2000, The ER repeat protein YT521-B localizes to a novel subnuclear compartment, J. Cell Biol., 150, 949, 10.1083/jcb.150.5.949 Galganski, 2017, Nuclear speckles: molecular organization, biological function and role in disease, Nucleic Acids Res., 45, 10350, 10.1093/nar/gkx759 Cheng, 2021, N6-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation, Cancer Cell, 39, 958, 10.1016/j.ccell.2021.04.017 Lee, 2021, Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation, Mol. Cell, 81, 3368, 10.1016/j.molcel.2021.07.024 Fu, 2020, m6A-binding YTHDF proteins promote stress granule formation, Nat. Chem. Biol., 16, 955, 10.1038/s41589-020-0524-y Gao, 2019, Multivalent m6A motifs promote phase separation of YTHDF proteins, Cell Res., 29, 767, 10.1038/s41422-019-0210-3 Ries, 2019, m6A enhances the phase separation potential of mRNA, Nature, 571, 424, 10.1038/s41586-019-1374-1 Wang, 2020, Binding to m6A RNA promotes YTHDF2-mediated phase separation, Protein Cell, 11, 304, 10.1007/s13238-019-00660-2 Xiao, 2016, Nuclear m6A reader YTHDC1 regulates mRNA splicing, Mol. Cell, 61, 507, 10.1016/j.molcel.2016.01.012 Kasowitz, 2018, Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development, PLoS Genet., 14, 10.1371/journal.pgen.1007412 Roundtree, 2017, YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs, eLife, 6, 10.7554/eLife.31311 Louloupi, 2018, Transient N6-methyladenosine transcriptome sequencing reveals a regulatory role of m6A in splicing efficiency, Cell Rep., 23, 3429, 10.1016/j.celrep.2018.05.077 Lesbirel, 2018, The m6A-methylase complex recruits TREX and regulates mRNA export, Sci. Rep., 8, 13827, 10.1038/s41598-018-32310-8 Chen, 2019, N6-methyladenosine modification of circNSUN2 facilitates cytoplasmic export and stabilizes HMGA2 to promote colorectal liver metastasis, Nat. Commun., 10, 4695, 10.1038/s41467-019-12651-2 Chen, 2020, Nuclear export of chimeric mRNAs depends on an lncRNA-triggered autoregulatory loop in blood malignancies, Cell Death Dis., 11, 566, 10.1038/s41419-020-02795-1 Wang, 2021, N6-methyladenosine modification of MALAT1 promotes metastasis via reshaping nuclear speckles, Dev. Cell, 56, 702, 10.1016/j.devcel.2021.01.015 Huang, 2020, The biogenesis and precise control of RNA m(6)A methylation, Trends Genet., 36, 44, 10.1016/j.tig.2019.10.011 Li, 2020, N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2, Nat. Genet., 52, 870, 10.1038/s41588-020-0677-3 Adelman, 2012, Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans, Nat. Rev. Genet., 13, 720, 10.1038/nrg3293 Akhtar, 2021, m(6)A RNA methylation regulates promoter- proximal pausing of RNA polymerase II, Mol. Cell, 81, 3356, 10.1016/j.molcel.2021.06.023 Hnisz, 2017, A phase separation model for transcriptional control, Cell, 169, 13, 10.1016/j.cell.2017.02.007 Sabari, 2018, Coactivator condensation at super-enhancers links phase separation and gene control, Science, 361, 10.1126/science.aar3958 Chen, 2021, Nuclear m(6)A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos, Protein Cell, 12, 455, 10.1007/s13238-021-00837-8 Ji, 2021, A heat shock–responsive lncRNA Heat acts as a HSF1-directed transcriptional brake via m6A modification, Proc. Natl. Acad. Sci. U. S. A., 118, 10.1073/pnas.2102175118 Liu, 2020, N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription, Science, 367, 580, 10.1126/science.aay6018 Liu, 2021, The RNA m(6)A reader YTHDC1 silences retrotransposons and guards ES cell identity, Nature, 591, 322, 10.1038/s41586-021-03313-9 Patil, 2016, m6A RNA methylation promotes XIST-mediated transcriptional repression, Nature, 537, 369, 10.1038/nature19342 Xiong, 2021, RNA m6A modification orchestrates a LINE-1–host interaction that facilitates retrotransposition and contributes to long gene vulnerability, Cell Res., 31, 861, 10.1038/s41422-021-00515-8 Xu, 2021, METTL3 regulates heterochromatin in mouse embryonic stem cells, Nature, 591, 317, 10.1038/s41586-021-03210-1 Dueva, 2019, Neutralization of the positive charges on histone tails by RNA promotes an open chromatin structure, Cell Chem. Biol., 26, 1436, 10.1016/j.chembiol.2019.08.002 Chelmicki, 2021, m(6)A RNA methylation regulates the fate of endogenous retroviruses, Nature, 591, 312, 10.1038/s41586-020-03135-1 Sabari, 2020, Biomolecular condensates in the nucleus, Trends Biochem. Sci., 45, 961, 10.1016/j.tibs.2020.06.007 Liao, 2020, Splicing at the phase-separated nuclear speckle interface: a model, Nucleic Acids Res., 49, 636, 10.1093/nar/gkaa1209 Wang, 2019, Histone modifications regulate chromatin compartmentalization by contributing to a phase separation mechanism, Mol. Cell, 76, 646, 10.1016/j.molcel.2019.08.019 Meola, 2016, Identification of a nuclear exosome decay pathway for processed transcripts, Mol. Cell, 64, 520, 10.1016/j.molcel.2016.09.025 Anders, 2018, Dynamic m6A methylation facilitates mRNA triaging to stress granules, Life Sci. Alliance, 1, 10.26508/lsa.201800113 Langdon, 2018, mRNA structure determines specificity of a polyQ-driven phase separation, Science, 360, 922, 10.1126/science.aar7432 Liu, 2015, N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions, Nature, 518, 560, 10.1038/nature14234 Maharana, 2018, RNA buffers the phase separation behavior of prion-like RNA binding proteins, Science, 360, 918, 10.1126/science.aar7366 Wilson, 2020, Programmable m(6)A modification of cellular RNAs with a Cas13-directed methyltransferase, Nat. Biotechnol., 38, 1431, 10.1038/s41587-020-0572-6 Mo, 2020, TRADES: targeted RNA demethylation by SunTag System, Adv. Sci., 7, 10.1002/advs.202001402 Liu, 2019, Programmable RNA N(6)-methyladenosine editing by CRISPR-Cas9 conjugates, Nat. Chem. Biol., 15, 865, 10.1038/s41589-019-0327-1 Li, 2020, Targeted mRNA demethylation using an engineered dCas13b-ALKBH5 fusion protein, Nucleic Acids Res., 48, 5684, 10.1093/nar/gkaa269 Bedi, 2020, Selectively disrupting m6A-dependent protein–RNA interactions with fragments, ACS Chem. Biol., 15, 618, 10.1021/acschembio.9b00894