References
- Yang J, Antin P, Berx G, et al. Guidelines and definitions for research on epithelial–mesenchymal transition. Nat Rev Mol Cell Biol. 2020;21(6):341–352. doi: 10.1038/s41580-020-0237-9
- De Craene B, Berx G. Regulatory networks defining EMT during cancer initiation and progression. Nat Rev Cancer. 2013;13(2):97–110. doi: 10.1038/nrc3447
- Bracken CP, Gregory PA, Kolesnikoff N, et al. A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res. 2008;68(19):7846–7854. doi: 10.1158/0008-5472.CAN-08-1942
- Burk U, Schubert J, Wellner U, et al. A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells. EMBO Rep. 2008;9(6):582–589. doi: 10.1038/embor.2008.74
- Gregory PA, Bert AG, Paterson EL, et al. The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nat Cell Biol. 2008;10(5):593–601. doi: 10.1038/ncb1722
- Gregory PA, Bracken CP, Smith E, et al. An autocrine TGF-β/ZEB/miR-200 signaling network regulates establishment and maintenance of epithelial-mesenchymal transition. MBoC. 2011;22(10):1686–1698. doi: 10.1091/mbc.e11-02-0103
- Harvey SE, Xu Y, Lin X, et al. Coregulation of alternative splicing by hnRNPM and ESRP1 during EMT. RNA. 2018;24(10):1326–1338. doi: 10.1261/rna.066712.118
- Neumann DP, Goodall GJ, Gregory PA. Regulation of splicing and circularisation of RNA in epithelial mesenchymal plasticity. Semin Cell Dev Biol. 2018;75:50–60. doi: 10.1016/j.semcdb.2017.08.008
- Shapiro IM, Cheng AW, Flytzanis NC, et al. An EMT–driven alternative splicing program occurs in human breast Cancer and modulates cellular phenotype. PLoS Genet. 2011;7(8):e1002218. doi: 10.1371/journal.pgen.1002218
- Yang Y, Park JW, Bebee TW, et al. Determination of a comprehensive alternative splicing regulatory network and combinatorial regulation by key factors during the epithelial-to-mesenchymal transition. Mol Cell Biol. 2016;36(11):1704–1719. doi: 10.1128/MCB.00019-16
- Li J, Choi PS, Chaffer CL, et al. An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. Elife. 2018;7: doi: 10.7554/eLife.37184
- Pillman KA, Phillips CA, Roslan S, et al. miR-200/375 control epithelial plasticity-associated alternative splicing by repressing the RNA -binding protein Quaking. The EMBO Journal. 2018;37(13):miR–200/375. doi: 10.15252/embj.201899016
- Wu J, Zhou L, Tonissen K, et al. The quaking I-5 protein (QKI-5) has a novel nuclear localization signal and shuttles between the nucleus and the cytoplasm. J Biol Chem. 1999;274(41):29202–29210. doi: 10.1074/jbc.274.41.29202
- Larocque D, Galarneau A, Liu HN, et al. Protection of p27(Kip1) mRNA by quaking RNA binding proteins promotes oligodendrocyte differentiation. Nat Neurosci. 2005;8(1):27–33. doi: 10.1038/nn1359
- Larocque D, Pilotte J, Chen T, et al. Nuclear retention of mbp mRnas in the quaking viable mice. Neuron. 2002;36(5):815–829. doi: 10.1016/S0896-6273(02)01055-3
- Neumann DP, Goodall GJ, Gregory PA. The Quaking RNA-binding proteins as regulators of cell differentiation. Wiley Interdiscip Rev RNA. 2022;13(6):e1724. doi: 10.1002/wrna.1724
- Sakers K, Liu Y, Llaci L, et al. Loss of Quaking RNA binding protein disrupts the expression of genes associated with astrocyte maturation in mouse brain. Nat Commun. 2021;12(1):1537. doi: 10.1038/s41467-021-21703-5
- Yamagishi R, Tsusaka T, Mitsunaga H, et al. The star protein QKI-7 recruits PAPD4 to regulate post-transcriptional polyadenylation of target mRnas. Nucleic Acids Res. 2016;44(6):2475–2490. doi: 10.1093/nar/gkw118
- Zhao L, Ku L, Chen Y, et al. QKI binds map1b mrna and enhances map1b expression during oligodendrocyte development. Mol Biol Cell. 2006;17(10):4179–4186. doi: 10.1091/mbc.e06-04-0355
- Mitschka S, Mayr C. Context-specific regulation and function of mRNA alternative polyadenylation. Nat Rev Mol Cell Biol. 2022;23(12):779–796. doi: 10.1038/s41580-022-00507-5
- Tian B, Manley JL. Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol. 2017;18(1):18–30. doi: 10.1038/nrm.2016.116
- Mayr C, Bartel DP. Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in Cancer cells. Cell. 2009;138(4):673–684. doi: 10.1016/j.cell.2009.06.016
- Xia Z, Donehower LA, Cooper TA, et al. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types. Nat Commun. 2014;5(1):5274. doi: 10.1038/ncomms6274
- Lianoglou S, Garg V, Yang JL, et al. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes Dev. 2013;27(21):2380–2396. doi: 10.1101/gad.229328.113
- Wang R, Zheng D, Yehia G, et al. A compendium of conserved cleavage and polyadenylation events in mammalian genes. Genome Res. 2018;28(10):1427–1441. doi: 10.1101/gr.237826.118
- Harrison PF, Powell DR, Clancy JL, et al. PAT-seq: a method to study the integration of 3′-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA. 2015;21(8):1502–1510. doi: 10.1261/rna.048355.114
- Swaminathan A, Harrison PF, Preiss T, et al. PAT-Seq: a method for simultaneous quantitation of gene expression, poly(A)-site selection and poly(A)-length distribution in yeast transcriptomes. Methods Mol Biol. 2019;2049:141–164.
- Darbelli L, Choquet K, Richard S, et al. Transcriptome profiling of mouse brains with qkI-deficient oligodendrocytes reveals major alternative splicing defects including self-splicing. Sci Rep. 2017;7(1):7554. doi: 10.1038/s41598-017-06211-1
- Fagg WS, Liu N, Fair JH, et al. Autogenous cross-regulation of Quaking mRNA processing and translation balances quaking functions in splicing and translation. Genes Dev. 2017;31(18):1894–1909. doi: 10.1101/gad.302059.117
- Hafner M, Katsantoni M, Köster T, et al. CLIP and complementary methods. Nat Rev Dis Primers. 2021;1(1):1–23. doi: 10.1038/s43586-021-00018-1
- Hafner M, Landthaler M, Burger L, et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 2010;141(1):129–141. doi: 10.1016/j.cell.2010.03.009
- Van Nostrand EL, Pratt GA, Shishkin AA, et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods. 2016;13(6):508–514. doi: 10.1038/nmeth.3810
- Galarneau A, Richard S. Target RNA motif and target mRnas of the Quaking STAR protein. Nat Struct Mol Biol. 2005;12(8):691–698. doi: 10.1038/nsmb963
- Herrmann CJ, Schmidt R, Kanitz A, et al. PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3’ end sequencing. Nucleic Acids Res. 2020;48:D174–D179. doi: 10.1093/nar/gkz918
- Barretina J, Caponigro G, Stransky N, et al. The Cancer cell line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012;483(7391):603–607. doi: 10.1038/nature11003
- Dittmar KA, Jiang P, Park JW, et al. Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Mol Cell Biol. 2012;32(8):1468–1482. doi: 10.1128/MCB.06536-11
- Chhabra ES, Higgs HN. INF2 is a WASP homology 2 motif-containing formin that severs actin filaments and accelerates both polymerization and depolymerization. J Biol Chem. 2006;281(36):26754–26767. doi: 10.1074/jbc.M604666200
- Schell C, Rogg M, Suhm M, et al. The FERM protein EPB41L5 regulates actomyosin contractility and focal adhesion formation to maintain the kidney filtration barrier. Proc Natl Acad Sci U S A. 2017;114(23):E4621–E4630. doi: 10.1073/pnas.1617004114
- Doukhanine E, Gavino C, Haines JD, et al. The QKI-6 RNA binding protein regulates actin-interacting protein-1 mRNA stability during oligodendrocyte differentiation. Mol Biol Cell. 2010;21(17):3029–3040. doi: 10.1091/mbc.e10-04-0305
- Thangaraj MP, Furber KL, Gan JK, et al. RNA-binding Protein Quaking Stabilizes Sirt2 mRNA during Oligodendroglial Differentiation. J Biol Chem. 2017;292(13):5166–5182. doi: 10.1074/jbc.M117.775544
- Brumbaugh J, Di Stefano B, Wang X, et al. Nudt21 controls cell fate by connecting alternative polyadenylation to chromatin signaling. Cell. 2018;172(1–2):106–120 e121. doi: 10.1016/j.cell.2017.11.023
- Lau AG, Irier HA, Gu J, et al. Distinct 3′UTRs differentially regulate activity-dependent translation of brain-derived neurotrophic factor (BDNF). Proc Natl Acad Sci USA. 2010;107(36):15945–15950. doi: 10.1073/pnas.1002929107
- Aiello NM, Maddipati R, Norgard RJ, et al. EMT subtype influences epithelial plasticity and mode of cell migration. Developmental Cell. 2018;45(6):681–695 e684. doi: 10.1016/j.devcel.2018.05.027
- Berkovits BD, Mayr C. Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization. Nature. 2015;522(7556):363–367. doi: 10.1038/nature14321
- Muller-McNicoll M, Rossbach O, Hui J, et al. Auto-regulatory feedback by RNA-binding proteins. J Mol Cell Biol. 2019;11(10):930–939. doi: 10.1093/jmcb/mjz043
- Mani SA, Guo W, Liao MJ, et al. The epithelial-mesenchymal transition generates cells with properties of stem cells. Cell. 2008;133(4):704–715. doi: 10.1016/j.cell.2008.03.027
- Jensen KB, Darnell RB. CLIP: crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins. Methods Mol Biol. 2008;488:85–98.
- Sutandy FX, Hildebrandt A, Konig J. Profiling the binding sites of RNA-Binding proteins with nucleotide resolution using iCLIP. Methods Mol Biol. 2016;1358:175–195.
- Turner RE, Henneken LM, Liem-Weits M, et al. Requirement for cleavage factor II m in the control of alternative polyadenylation in breast cancer cells. RNA. 2020;26(8):969–981. doi: 10.1261/rna.075226.120
- Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137
- Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576–589. doi: 10.1016/j.molcel.2010.05.004
- Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178–192. doi: 10.1093/bib/bbs017
- Kent WJ, Sugnet CW, Furey TS, et al. The human genome browser at UCSC. Genome Res. 2002;12(6):996–1006. doi: 10.1101/gr.229102
- Liao Y, Wang J, Jaehnig EJ, et al. Webgestalt 2019: gene set analysis toolkit with revamped UIs and APIs. Nucleic Acids Res. 2019;47(W1):W199–W205. doi: 10.1093/nar/gkz401