Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis

References

• Nohales MA, Kay SA. Molecular mechanisms at the core of the plant circadian oscillator. Nat Struct Mol Biol. 2016;23(12):1061–1069.
   PubMed Web of Science ®Google Scholar
• Torres M, Becquet D, Franc JL, et al. Circadian processes in the RNA life cycle. Wiley Interdiscip Rev RNA. 2018;9(3):e1467.
   PubMed Web of Science ®Google Scholar
• Greenham K, McClung CR. Integrating circadian dynamics with physiological processes in plants. Nat Rev Genet. 2015;16(10):598–610.
   PubMed Web of Science ®Google Scholar
• Schaffer R, Landgraf J, Accerbi M, et al. Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell. 2001;13(1):113–123.
   PubMed Web of Science ®Google Scholar
• Blasing OE, Gibon Y, Gunther M, et al. Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell. 2005;17(12):3257–3281.
   PubMed Web of Science ®Google Scholar
• Filichkin SA, Breton G, Priest HD, et al. Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules. PLoS One. 2011;6(6):e16907.
   PubMed Web of Science ®Google Scholar
• Higashi T, Aoki K, Nagano AJ, et al. Circadian oscillation of the lettuce transcriptome under constant light and light-dark conditions. Front Plant Sci. 2016;7:1114.
   PubMed Web of Science ®Google Scholar
• Kim JA, Shim D, Kumari S, et al. Transcriptome analysis of diurnal gene expression in Chinese cabbage. Genes (Basel). 2019;10(2):10.
   Web of Science ®Google Scholar
• Oakenfull RJ, Davis SJ. Shining a light on the Arabidopsis circadian clock. Plant Cell Environ. 2017;40(11):2571–2585.
   PubMed Web of Science ®Google Scholar
• Nagel DH, Kay SA. Complexity in the wiring and regulation of plant circadian networks. Curr Biol. 2012;22(16):R648–R57.
   PubMed Web of Science ®Google Scholar
• Locke JC, Kozma-Bognar L, Gould PD, et al. Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Mol Syst Biol. 2006;2(1):59.
   PubMed Web of Science ®Google Scholar
• Nakamichi N, Kiba T, Henriques R, et al. PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the arabidopsis circadian clock. Plant Cell. 2010;22(3):594–605.
   PubMed Web of Science ®Google Scholar
• Farre EM, Harmer SL, Harmon FG, et al. Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Curr Biol. 2005;15(1):47–54.
   PubMed Web of Science ®Google Scholar
• Herrero E, Kolmos E, Bujdoso N, et al. EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock. Plant Cell. 2012;24(2):428–443.
   PubMed Web of Science ®Google Scholar
• Brown SA, Kowalska E, Dallmann R. (Re)inventing the circadian feedback loop. Dev Cell. 2012;22(3):477–487.
   PubMed Web of Science ®Google Scholar
• Saini R, Jaskolski M, Davis SJ. Circadian oscillator proteins across the kingdoms of life: structural aspects. BMC Biol. 2019;17:13.
   PubMed Web of Science ®Google Scholar
• Tian B, Manley JL. Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol. 2017;18(1):18–30.
   PubMed Web of Science ®Google Scholar
• Loke JC, Stahlberg EA, Strenski DG, et al. Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol. 2005;138(3):1457–1468.
   PubMed Web of Science ®Google Scholar
• Shi Y. Alternative polyadenylation: new insights from global analyses. RNA. 2012;18(12):2105–2117.
   PubMed Web of Science ®Google Scholar
• Shi Y, Manley JL. The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Gene Dev. 2015;29(9):889–897.
   PubMed Web of Science ®Google Scholar
• Hunt AG, Xu R, Addepalli B, et al. Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling. BMC Genomics. 2008;9(1):220.
   PubMed Web of Science ®Google Scholar
• Thomas PE, Wu X, Liu M, et al. Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis. Plant Cell. 2012;24(11):4376–4388.
   PubMed Web of Science ®Google Scholar
• Lin J, Xu R, Wu X, et al. Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination. Plant J. 2017;91(5):829–839.
   PubMed Web of Science ®Google Scholar
• Zhao Z, Wu X, Kumar PKR, et al. Bioinformatics analysis of alternative polyadenylation in green alga chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms. G3 (Bethesda). 2014;4(5):871–883.
   PubMedGoogle Scholar
• Zhou X, Zhang Y, Michal JJ, et al. Alternative polyadenylation coordinates embryonic development, sexual dimorphism and longitudinal growth in Xenopus tropicalis. Cell Mol Life Sci. 2019;76(11):2185–2198.
   PubMed Web of Science ®Google Scholar
• Fu H, Yang D, Su W, et al. Genome-wide dynamics of alternative polyadenylation in rice. Genome Res. 2016;26(12):1753–1760.
   PubMed Web of Science ®Google Scholar
• Wu X, Gaffney B, Hunt AG, et al. Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014;15(1):615.
   PubMed Web of Science ®Google Scholar
• Zhu S, Wu X, Fu H, et al. Modeling of genome-wide polyadenylation signals in Xenopus tropicalis. Front Genet. 2019;10:647.
   Web of Science ®Google Scholar
• Chakrabarti M, Dinkins RD, Hunt AG. Genome-wide atlas of alternative polyadenylation in the forage legume red clover. Sci Rep. 2018;8(1):11379.
   PubMed Web of Science ®Google Scholar
• Xing D, Li QQ. Alternative polyadenylation and gene expression regulation in plants. Wiley Interdiscip Rev RNA. 2011;2(3):445–458.
   PubMed Web of Science ®Google Scholar
• Deng X, Cao X. Roles of pre-mRNA splicing and polyadenylation in plant development. Curr Opin Plant Biol. 2017;35:45–53.
   PubMed Web of Science ®Google Scholar
• Chen W, Jia Q, Song Y, et al. Alternative polyadenylation: methods, findings, and impacts. Genomics Proteomics Bioinformatics. 2017;15(5):287–300.
   PubMed Web of Science ®Google Scholar
• Xing D, Wang Y, Xu R, et al. The regulatory role of Pcf11-similar-4 (PCFS4) in Arabidopsis development by genome-wide physical interactions with target loci. BMC Genomics. 2013;14(1):598.
   PubMed Web of Science ®Google Scholar
• Liu Y, Hu W, Murakawa Y, et al. Cold-induced RNA-binding proteins regulate circadian gene expression by controlling alternative polyadenylation. Sci Rep. 2013;3(1):2054.
   PubMed Web of Science ®Google Scholar
• Gendreau KL, Unruh BA, Zhou C, et al. Identification and Characterization of transcripts regulated by circadian alternative polyadenylation in mouse liver. G3 (Bethesda). 2018;8(11):3539–3548.
   PubMedGoogle Scholar
• Ptitsyna N, Boughorbel S, El Anbari M, et al. The role of alternative Polyadenylation in regulation of rhythmic gene expression. BMC Genomics. 2017;18(1):576.
   PubMed Web of Science ®Google Scholar
• Song Q, Huang TY, Yu HH, et al. Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis. Genome Biol. 2019;20(1):170.
   PubMed Web of Science ®Google Scholar
• Lee C-Y, Chen L. Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines. Bioinformatics. 2013;29(14):1713–1717.
   PubMed Web of Science ®Google Scholar
• Lin J, Hung FY, Ye C, et al. HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis. Genome Res. 2020;30(10):1407–1417.
   PubMed Web of Science ®Google Scholar
• Wang J, Zhao Y, Zhou X, et al. Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation. BMC Genomics. 2018;19(1):633.
   PubMed Web of Science ®Google Scholar
• Kurup JT, Kidder BL. Identification of H4K20me3- and H3K4me3-associated RNAs using CARIP-Seq expands the transcriptional and epigenetic networks of embryonic stem cells. J Biol Chem. 2018;293(39):15120–15135.
   PubMed Web of Science ®Google Scholar
• Nojima T, Al E, Grosso A. Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA processing. Cell. 2015;161(3):526–540.
   PubMed Web of Science ®Google Scholar
• Kamieniarz-Gdula K, Gdula MR, Panser K, et al. Selective roles of Vertebrate PCF11 in premature and full-length transcript termination. Mol Cell. 2019;74(158–72.e9):158–172.e9.
   PubMed Web of Science ®Google Scholar
• Ma L, Pati PK, Liu M, et al. High throughput characterizations of poly(A) site choice in plants. Methods. 2014;67(1):74–83.
   PubMed Web of Science ®Google Scholar
• Wu G, Anafi RC, Hughes ME, et al. MetaCycle: an integrated R package to evaluate periodicity in large scale data. Bioinformatics. 2016;32(21):3351–3353.
   PubMed Web of Science ®Google Scholar
• Elkon R, Ugalde AP, Agami R. Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet. 2013;14(7):496–506.
   PubMed Web of Science ®Google Scholar
• Li W, You B, Hoque M, et al. Systematic profiling of poly (A)+ transcripts modulated by core 3ʹend processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genet. 2015;11(4):e1005166.
   PubMed Web of Science ®Google Scholar
• Neve J, Burger K, Li W, et al. Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation. Genome Res. 2016;26(1):24–35.
   PubMed Web of Science ®Google Scholar
• Zhu J, Liu M, Liu X, et al. RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis. Nat Plants. 2018;4(12):1112–1123.
   PubMed Web of Science ®Google Scholar
• Maury E, Ramsey KM, Bass J. Circadian rhythms and metabolic syndrome: from experimental genetics to human disease. Circ Res. 2010;106(3):447–462.
   PubMed Web of Science ®Google Scholar
• Seney ML, Cahill K, Enwright JF, et al. Diurnal rhythms in gene expression in the prefrontal cortex in schizophrenia. Nat Commun. 2019;10(1):3355.
   PubMed Web of Science ®Google Scholar
• Harmer SL, Hogenesch JB, Straume M, et al. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science. 2000;290(5499):2110–2113.
   PubMed Web of Science ®Google Scholar
• Vollmers C, Gill S, DiTacchio L, et al. Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression. Proc Natl Acad Sci U S A. 2009;106(50):21453–21458.
   PubMed Web of Science ®Google Scholar
• Lowrey PL, Takahashi JS. Mammalian circadian biology: elucidating genome-wide levels of temporal organization. Annu Rev Genomics Hum Genet. 2004;5(1):407–441.
   PubMed Web of Science ®Google Scholar
• Yang Y, Li Y, Sancar A, et al. The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation. J Biol Chem. 2020;295(22):7608–7619.
   PubMed Web of Science ®Google Scholar
• Duffield GE. DNA microarray analyses of circadian timing: the genomic basis of biological time. J Neuroendocrinol. 2003;15(10):991–1002.
   PubMed Web of Science ®Google Scholar
• Nadon R, Shoemaker J. Statistical issues with microarrays: processing and analysis. Trends Genet. 2002;18(5):265–271.
   PubMed Web of Science ®Google Scholar
• Muller NA, Wijnen CL, Srinivasan A, et al. Domestication selected for deceleration of the circadian clock in cultivated tomato. Nat Genet. 2016;48(1):89–93.
   PubMed Web of Science ®Google Scholar
• Zhang R, Lahens NF, Ballance HI, et al. A circadian gene expression atlas in mammals: implications for biology and medicine. Proc Natl Acad Sci U S A. 2014;111(45):16219–16224.
   PubMed Web of Science ®Google Scholar
• Hughes ME, Grant GR, Paquin C, et al. Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Genome Res. 2012;22(7):1266–1281.
   PubMed Web of Science ®Google Scholar
• Pickrell JK, Marioni JC, Pai AA, et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010;464(7289):768–772.
   PubMed Web of Science ®Google Scholar
• Ni T, Majerciak V, Zheng ZM, et al. PA-seq for global identification of RNA polyadenylation sites of kaposi’s sarcoma-associated herpesvirus transcripts. Curr Protoc Microbiol. 2016;41(1):14E.7.1–E.7.8.
   PubMedGoogle Scholar
• Covington MF, Harmer SL. The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biol. 2007;5:e222.
   PubMed Web of Science ®Google Scholar
• De Lorenzo L, Sorenson R, Baileyserres J, et al. Noncanonical alternative polyadenylation contributes to gene regulation in response to hypoxia. Plant Cell. 2017;29(6):1262–1277.
   PubMed Web of Science ®Google Scholar
• Huang H, Chen J, Liu H, et al. The nucleosome regulates the usage of polyadenylation sites in the human genome. BMC Genomics. 2013;14(1):912.
   PubMed Web of Science ®Google Scholar
• Zhang J, Addepalli B, Yun KY, et al. A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana. PloS One. 2008;3(6):e2410.
   PubMed Web of Science ®Google Scholar
• Herr AJ, Molnar A, Jones A, et al. Defective RNA processing enhances RNA silencing and influences flowering of Arabidopsis. Proc Natl Acad Sci U S A. 2006;103(41):14994–15001.
   PubMed Web of Science ®Google Scholar
• Wu X, Liu M, Downie B, et al. Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci U S A. 2011;108(30):12533–12538.
   PubMed Web of Science ®Google Scholar
• Bray NL, Pimentel H, Melsted P, et al. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34(5):525–527.
   PubMed Web of Science ®Google Scholar