Characteristics of N 6-Methyladenosine Modification During Sexual Reproduction of Chlamydomonas Reinhardtii

Sakakibara, 2013, KNOX2 genes regulate the haploid-to-diploid morphological transition in land plants, Science, 339, 1067, 10.1126/science.1230082 Kariyawasam, 2019, TALE homeobox heterodimer GSM1/GSP1 is a molecular switch that prevents unwarranted genetic recombination in Chlamydomonas, Plant J, 100, 938, 10.1111/tpj.14486 Zhao, 2001, Ectopic expression of a Chlamydomonas mt+-specific homeodomain protein in mt− gametes initiates zygote development without gamete fusion, Gene Dev, 15, 2767, 10.1101/gad.919501 Merchant, 2007, The Chlamydomonas genome reveals the evolution of key animal and plant functions, Science, 318, 245, 10.1126/science.1143609 Piao, 2009, A microtubule depolymerizing kinesin functions during both flagellar disassembly and flagellar assembly in Chlamydomonas, Proc Natl Acad Sci U S A, 106, 4713, 10.1073/pnas.0808671106 Yang, 2015, Algae after dark: mechanisms to cope with anoxic/hypoxic conditions, Plant J, 82, 481, 10.1111/tpj.12823 Cross, 2015, The Chlamydomonas cell cycle, Plant J, 82, 370, 10.1111/tpj.12795 Nishimura, 2012, Gsp1 triggers the sexual developmental program including inheritance of chloroplast DNA and mitochondrial DNA in Chlamydomonas reinhardtii, Plant Cell, 24, 2401, 10.1105/tpc.112.097865 Sasso, 2018, From molecular manipulation of domesticated Chlamydomonas reinhardtii to survival in nature, Elife, 7, e39233, 10.7554/eLife.39233 Harris, 2001, Chlamydomonas as a model organism, Annu Rev Plant Phys, 52, 363, 10.1146/annurev.arplant.52.1.363 Tulin, 2015, Cyclin-dependent kinase regulation of diurnal transcription in Chlamydomonas, Plant Cell, 27, 2727 Cizkova, 2008, CDKA and CDKB kinases from Chlamydomonas reinhardtii are able to complement cdc28 temperature-sensitive mutants of Saccharomyces cerevisiae, Protoplasma, 232, 183, 10.1007/s00709-008-0285-z Ikui, 2021, Control of pre-replicative complex during the division cycle in Chlamydomonas reinhardtii, PLoS Genet, 17, e1009471, 10.1371/journal.pgen.1009471 Goodenough, 2007, Sex determination in Chlamydomonas, Semin Cell Dev Biol, 18, 350, 10.1016/j.semcdb.2007.02.006 Ferris, 1997, Mating type in Chlamydomonas is specified by mid, the minus-dominance gene, Genetics, 146, 859, 10.1093/genetics/146.3.859 Kubo, 2008, Characterization of novel genes induced by sexual adhesion and gamete fusion and of their transcriptional regulation in Chlamydomonas reinhardtii, Plant Cell Physiol, 49, 981, 10.1093/pcp/pcn076 Lee, 2008, Early sexual origins of homeoprotein heterodimerization and evolution of the plant KNOX/BELL family, Cell, 133, 829, 10.1016/j.cell.2008.04.028 Ferris, 2005, Plus and minus sexual agglutinins from Chlamydomonas reinhardtii, Plant Cell, 17, 597, 10.1105/tpc.104.028035 Fedry, 2017, The ancient gamete fusogen HAP2 is a eukaryotic class II fusion protein, Cell, 168, 904, 10.1016/j.cell.2017.01.024 Liu, 2010, Membrane fusion triggers rapid degradation of two gamete-specific, fusion-essential proteins in a membrane block to polygamy in Chlamydomonas, Development, 137, 1473, 10.1242/dev.044743 Misamore, 2003, The Chlamydomonas Fus1 protein is present on the mating type plus fusion organelle and required for a critical membrane adhesion event during fusion with minus gametes, Mol Biol Cell, 14, 2530, 10.1091/mbc.e02-12-0790 Pasquale, 1987, Cyclic AMP functions as a primary sexual signal in gametes of Chlamydomonas reinhardtii, J Cell Biol, 105, 2279, 10.1083/jcb.105.5.2279 Liu, 2015, The cytoplasmic domain of the gamete membrane fusion protein HAP2 targets the protein to the fusion site in Chlamydomonas and regulates the fusion reaction, Development, 142, 962 Lopez, 2015, Dynamic changes in the transcriptome and methylome of Chlamydomonas reinhardtii throughout its life cycle, Plant Physiol, 169, 2730 Roundtree, 2017, Dynamic RNA modifications in gene expression regulation, Cell, 169, 1187, 10.1016/j.cell.2017.05.045 Xiao, 2016, Nuclear m6A reader YTHDC1 regulates mRNA splicing, Mol Cell, 61, 507, 10.1016/j.molcel.2016.01.012 Roundtree, 2017, YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs, Elife, 6, e31311, 10.7554/eLife.31311 Du, 2016, YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex, Nat Commun, 7, 12626, 10.1038/ncomms12626 Wang, 2014, N 6-methyladenosine-dependent regulation of messenger RNA stability, Nature, 505, 117, 10.1038/nature12730 Shi, 2017, YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA, Cell Res, 27, 315, 10.1038/cr.2017.15 Li, 2017, Cytoplasmic m6A reader YTHDF3 promotes mRNA translation, Cell Res, 27, 444, 10.1038/cr.2017.10 Yang, 2018, Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism, Cell Res, 28, 616, 10.1038/s41422-018-0040-8 Shi, 2019, Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers, Mol Cell, 74, 640, 10.1016/j.molcel.2019.04.025 Bokar, 1997, Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase, RNA, 3, 1233 Ping, 2014, Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase, Cell Res, 24, 177, 10.1038/cr.2014.3 Liu, 2014, A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation, Nat Chem Biol, 10, 93, 10.1038/nchembio.1432 Yue, 2018, VIRMA mediates preferential m6A mRNA methylation in 3′ UTR and near stop codon and associates with alternative polyadenylation, Cell Discov, 4, 10, 10.1038/s41421-018-0019-0 Knuckles, 2018, Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d, Gene Dev, 32, 415, 10.1101/gad.309146.117 Fujita, 2002, Hakai, a c-Cbl-like protein, ubiquitinates and induces endocytosis of the E-cadherin complex, Nat Cell Biol, 4, 222, 10.1038/ncb758 Frayling, 2007, A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity, Science, 316, 889, 10.1126/science.1141634 Jia, 2011, N 6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO, Nat Chem Biol, 7, 885, 10.1038/nchembio.687 Zheng, 2013, ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility, Mol Cell, 49, 18, 10.1016/j.molcel.2012.10.015 Alarcon, 2015, HNRNPA2B1 is a mediator of m6A-dependent nuclear RNA processing events, Cell, 162, 1299, 10.1016/j.cell.2015.08.011 Hsu, 2017, Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis, Cell Res, 27, 1115, 10.1038/cr.2017.99 Liu, 2015, N 6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions, Nature, 518, 560, 10.1038/nature14234 Wang, 2015, N 6-methyladenosine modulates messenger RNA translation efficiency, Cell, 161, 1388, 10.1016/j.cell.2015.05.014 Geula, 2015, m6A mRNA methylation facilitates resolution of naive pluripotency toward differentiation, Science, 347, 1002, 10.1126/science.1261417 Kasowitz, 2018, Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development, PLoS Genet, 14, e1007412, 10.1371/journal.pgen.1007412 Fukusumi, 2008, Wtap is required for differentiation of endoderm and mesoderm in the mouse embryo, Dev Dynam, 237, 618, 10.1002/dvdy.21444 Arribas-Hernandez, 2020, Occurrence and functions of m6A and other covalent modifications in plant mRNA, Plant Physiol, 182, 79, 10.1104/pp.19.01156 Hou, 2021, CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis, Mol Plant, 14, 688, 10.1016/j.molp.2021.01.013 Song, 2021, Arabidopsis N 6-methyladenosine reader CPSF30-L recognizes FUE signals to control polyadenylation site choice in liquid-like nuclear bodies, Mol Plant, 14, 571, 10.1016/j.molp.2021.01.014 Zhong, 2008, MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor, Plant Cell, 20, 1278, 10.1105/tpc.108.058883 Liang, 2020, Epigenetic modifications of mRNA and DNA in plants, Mol Plant, 13, 14, 10.1016/j.molp.2019.12.007 Zhang, 2019, The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice, PLoS Genet, 15, e1008120, 10.1371/journal.pgen.1008120 Zhou, 2019, RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening, Genome Biol, 20, 156, 10.1186/s13059-019-1771-7 Pan, 1997, Characterization of blue light signal transduction chains that control development and maintenance of sexual competence in Chlamydomonas reinhardtii, Plant Physiol, 115, 1241, 10.1104/pp.115.3.1241 Pan, 2002, Kinesin-II is required for flagellar sensory transduction during fertilization in Chlamydomonas, Mol Biol Cell, 13, 1417, 10.1091/mbc.01-11-0531 Vespa, 2004, The immunophilin-interacting protein AtFIP37 from Arabidopsis is essential for plant development and is involved in trichome endoreduplication, Plant Physiol, 134, 1283, 10.1104/pp.103.028050 Yu, 2021, RNA demethylation increases the yield and biomass of rice and potato plants in field trials, Nat Biotechnol, 39, 1581, 10.1038/s41587-021-00982-9 Du, 2020, Global profiling of N6-methyladenosine methylation in maize callus induction, Plant Genome, 13, e20018, 10.1002/tpg2.20018 Luo, 2014, Unique features of the m6A methylome in Arabidopsis thaliana, Nat Commun, 5, 5630, 10.1038/ncomms6630 Dominissini, 2012, Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq, Nature, 485, 201, 10.1038/nature11112 Shen, 2016, N 6-methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis, Dev Cell, 38, 186, 10.1016/j.devcel.2016.06.008 Duan, 2017, ALKBH10B is an RNA N6-methyladenosine demethylase affecting Arabidopsis floral transition, Plant Cell, 29, 2995, 10.1105/tpc.16.00912 Cole, 1998, Chlamydomonas kinesin-II-dependent intraflagellar transport (IFT): IFT particles contain proteins required for ciliary assembly in Caenorhabditis elegans sensory neurons, J Cell Biol, 141, 993, 10.1083/jcb.141.4.993 DiBella, 2001, Dynein motors of the Chlamydomonas flagellum, Int Rev Cytol, 210, 227, 10.1016/S0074-7696(01)10007-0 Khan, 2005, Proteome analysis of separated male and female gametocytes reveals novel sex-specific Plasmodium biology, Cell, 121, 675, 10.1016/j.cell.2005.03.027 Zeeshan, 2019, Kinesin-8B controls basal body function and flagellum formation and is key to malaria transmission, Life Sci Alliance, 2, e201900488, 10.26508/lsa.201900488 Hom, 2011, A unified taxonomy for ciliary dyneins, Cytoskeleton (Hoboken), 68, 555, 10.1002/cm.20533 Zhao, 2017, Post-transcriptional gene regulation by mRNA modifications, Nat Rev Mol Cell Biol, 18, 31, 10.1038/nrm.2016.132 Chen, 2015, m6A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency, Cell Stem Cell, 16, 289, 10.1016/j.stem.2015.01.016 Zhao, 2017, m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition, Nature, 542, 475, 10.1038/nature21355 Karpowicz, 2011, The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage, J Biol Chem, 286, 21427, 10.1074/jbc.M111.233734 Park, 2015, The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis, Plant J, 81, 611, 10.1111/tpj.12747 Siersma, 1971, Conservation and degradation of cytoplasmic and chloroplast ribosomes in Chlamydomonas reinhardtii, J Mol Biol, 58, 167, 10.1016/0022-2836(71)90239-7 Huang, 2003, Phototropin is the blue-light receptor that controls multiple steps in the sexual life cycle of the green alga Chlamydomonas reinhardtii, Proc Natl Acad Sci U S A, 100, 6269, 10.1073/pnas.0931459100 Wang, 2021, A photoregulatory mechanism of the circadian clock in Arabidopsis, Nat Plants, 7, 1397, 10.1038/s41477-021-01002-z Zhang, 2021, N 6-methyladenosine regulates RNA abundance of SARS-CoV-2, Cell Discov, 7, 7, 10.1038/s41421-020-00241-2 Martin, 2017, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet J, 17, 10, 10.14806/ej.17.1.200 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nat Methods, 12, 357, 10.1038/nmeth.3317 Liao, 2014, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, 30, 923, 10.1093/bioinformatics/btt656 Meng, 2014, A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package, Methods, 69, 274, 10.1016/j.ymeth.2014.06.008 Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033 Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616 Tian, 2017, agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update, Nucleic Acids Res, 45, W122, 10.1093/nar/gkx382 Ke, 2015, A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation, Genes Dev, 29, 2037, 10.1101/gad.269415.115 Heinz, 2010, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol Cell, 38, 576, 10.1016/j.molcel.2010.05.004 Zhao, 2013, Different B-type methionine sulfoxide reductases in Chlamydomonas may protect the alga against high-light, sulfur-depletion, or oxidative stress, J Integr Plant Biol, 55, 1054, 10.1111/jipb.12104 Chen, 2021, The Genome Sequence Archive Family: toward explosive data growth and diverse data types, Genomics Proteomics Bioinformatics, 19, 578, 10.1016/j.gpb.2021.08.001