N6-Methyladenosine modification of mRNA contributes to the transition from 2D to 3D growth in the moss Physcomitrium patens
dc.contributor.author | Garcias-Morales, David | |
dc.contributor.author | Palomar, V. Miguel | |
dc.contributor.author | Charlot, Florence | |
dc.contributor.author | Nogué, Fabien | |
dc.contributor.author | Covarrubias, Alejandra A. | |
dc.contributor.author | Reyes, José L. | |
dc.date.accessioned | 2023-04-04T17:39:11Z | |
dc.date.available | 2024-05-04 13:39:08 | en |
dc.date.available | 2023-04-04T17:39:11Z | |
dc.date.issued | 2023-04 | |
dc.identifier.citation | Garcias-Morales, David ; Palomar, V. Miguel; Charlot, Florence; Nogué, Fabien ; Covarrubias, Alejandra A.; Reyes, José L. (2023). "N6- Methyladenosine modification of mRNA contributes to the transition from 2D to 3D growth in the moss Physcomitrium patens." The Plant Journal (1): 7-22. | |
dc.identifier.issn | 0960-7412 | |
dc.identifier.issn | 1365-313X | |
dc.identifier.uri | https://hdl.handle.net/2027.42/176027 | |
dc.publisher | Humana Press | |
dc.publisher | Wiley Periodicals, Inc. | |
dc.subject.other | epitranscriptome | |
dc.subject.other | MTA | |
dc.subject.other | MTB | |
dc.subject.other | FIP37 | |
dc.subject.other | PpAPB | |
dc.subject.other | gametophore bud formation | |
dc.title | N6-Methyladenosine modification of mRNA contributes to the transition from 2D to 3D growth in the moss Physcomitrium patens | |
dc.type | Article | |
dc.rights.robots | IndexNoFollow | |
dc.subject.hlbsecondlevel | Natural Resources and Environment | |
dc.subject.hlbtoplevel | Science | |
dc.description.peerreviewed | Peer Reviewed | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/176027/1/tpj16149.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/176027/2/tpj16149-sup-0006-FigureS6.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/176027/3/tpj16149-sup-0007-FigureS7.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/176027/4/tpj16149-sup-0005-FigureS5.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/176027/5/tpj16149_am.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/176027/6/tpj16149-sup-0002-FigureS2.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/176027/7/tpj16149-sup-0001-FigureS1.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/176027/8/tpj16149-sup-0003-FigureS3.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/176027/9/tpj16149-sup-0004-FigureS4.pdf | |
dc.identifier.doi | 10.1111/tpj.16149 | |
dc.identifier.source | The Plant Journal | |
dc.identifier.citedreference | Niklas, K.J. ( 2000 ) The evolution of plant body plans—a biomechanical perspective. Annals of Botany, 85, 411 – 438. | |
dc.identifier.citedreference | Harrison, C.J., Roeder, A.H.K., Meyerowitz, E.M. & Langdale, J.A. ( 2009 ) Local cues and asymmetric cell divisions underpin body plan transitions in the Moss Physcomitrella patens. Current Biology, 19, 461 – 471. | |
dc.identifier.citedreference | Hu, J., Cai, J., Park, S.J., Lee, K., Li, Y., Chen, Y. et al. ( 2021 ) N 6 -Methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis. The Plant Journal, 106, 1759 – 1775. | |
dc.identifier.citedreference | Ivanova, I., Much, C., Di Giacomo, M. et al. ( 2017 ) The RNA m 6 a reader YTHDF2 is essential for the post-transcriptional regulation of the maternal transcriptome and oocyte competence. Molecular Cell, 67, 1059 – 1067.e4. | |
dc.identifier.citedreference | Johansen, W., Ako, A.E., Demko, V., Perroud, P.-F., Rensing, S.A., Mekhlif, A.K. et al. ( 2016 ) The DEK1 calpain linker functions in three-dimensional body patterning in Physcomitrella patens. Plant Physiology, 172, 1089 – 1104. | |
dc.identifier.citedreference | Johri, M.M. & Desai, S. ( 1973 ) Auxin regulation of Caulonema formation in Moss Protonema. Nature New Biology, 245, 223 – 224. | |
dc.identifier.citedreference | Langmead, B. & Salzberg, S.L. ( 2012 ) Fast gapped-read alignment with bowtie 2. Nature Methods, 9, 357 – 359. | |
dc.identifier.citedreference | Lopez-Obando, M., Hoffmann, B., Géry, C., Guyon-Debast, A., Téoulé, E., Rameau, C. et al. ( 2016 ) Simple and efficient targeting of multiple genes through CRISPR-Cas9 in Physcomitrella patens. G3 GenesGenomesGenetics, 6, 3647 – 3653. | |
dc.identifier.citedreference | Luo, G.-Z., MacQueen, A., Zheng, G., Duan, H., Dore, L.C., Lu, Z. et al. ( 2014 ) Unique features of the m6A methylome in Arabidopsis thaliana. Nature Communications, 5, 5630. | |
dc.identifier.citedreference | Meinke, D.W. & Sussex, I.M. ( 1979 ) Embryo-lethal mutants of Arabidopsis thaliana: a model system for genetic analysis of plant embryo development. Developmental Biology, 72, 50 – 61. | |
dc.identifier.citedreference | Menand, B., Calder, G. & Dolan, L. ( 2007 ) Both chloronemal and caulonemal cells expand by tip growth in the moss Physcomitrella patens. Journal of Experimental Botany, 58, 1843 – 1849. | |
dc.identifier.citedreference | Moody, L.A. ( 2019 ) The 2D to 3D growth transition in the moss Physcomitrella patens. Current Opinion in Plant Biology, 47, 88 – 95. | |
dc.identifier.citedreference | Moody, L.A., Kelly, S., Rabbinowitsch, E. & Langdale, J.A. ( 2018 ) Genetic regulation of the 2D to 3D growth transition in the Moss Physcomitrella patens. Current Biology, 28, 473 – 478.e5. | |
dc.identifier.citedreference | Perroud, P., Demko, V., Johansen, W., Wilson, R.C., Olsen, O. & Quatrano, R.S. ( 2014 ) Defective Kernel 1 ( DEK 1) is required for three-dimensional growth in P hyscomitrella patens. The New Phytologist, 203, 794 – 804. | |
dc.identifier.citedreference | Perroud, P.-F., Meyberg, R., Demko, V., Quatrano, R.S., Olsen, O.-A. & Rensing, S.A. ( 2020 ) DEK1 displays a strong subcellular polarity during Physcomitrella patens 3D growth. The New Phytologist, 226, 1029 – 1041. | |
dc.identifier.citedreference | Růžička, K., Zhang, M., Campilho, A., Bodi, Z., Kashif, M., Saleh, M. et al. ( 2017 ) Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. The New Phytologist, 215, 157 – 172. | |
dc.identifier.citedreference | Shen, L., Liang, Z., Gu, X., Chen, Y., Teo, Z.W.N., Hou, X. et al. ( 2016 ) N 6 -Methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis. Developmental Cell, 38, 186 – 200. | |
dc.identifier.citedreference | Shi, H., Wei, J. & He, C. ( 2019 ) Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers. Molecular Cell, 74, 640 – 650. | |
dc.identifier.citedreference | Sun, J.G., Yao, X.L., Yang, Z.X. & Zhu, Z.P. ( 1998 ) An Arabidopsis embryonic lethal mutant with reduced expression of alanyl-tRNA synthetase gene. Cell Research, 8, 119 – 134. | |
dc.identifier.citedreference | Wang, Y.-J., Yang, B., Lai, Q., Shi, J.F., Peng, J.Y., Zhang, Y. et al. ( 2021 ) Reprogramming of m6A epitranscriptome is crucial for shaping of transcriptome and proteome in response to hypoxia. RNA Biology, 18, 131 – 143. | |
dc.identifier.citedreference | Wickett, N.J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N. et al. ( 2014 ) Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences of the United States of America, 111, E4859 – E4868. | |
dc.identifier.citedreference | Xu, Z., Shi, X., Bao, M., Song, X., Zhang, Y., Wang, H. et al. ( 2021 ) Transcriptome-wide analysis of RNA m6A methylation and gene expression changes among two Arabidopsis ecotypes and their reciprocal hybrids. Frontiers in Plant Science, 12, 685189. Available from: https://doi.org/10.3389/fpls.2021.685189 | |
dc.identifier.citedreference | Yue, H., Nie, X., Yan, Z. & Weining, S. ( 2019 ) N6-methyladenosine regulatory machinery in plants: composition, function and evolution. Plant Biotechnology Journal, 17, 1194 – 1208. | |
dc.identifier.citedreference | Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E. et al. ( 2008 ) Model-based analysis of ChIP-Seq (MACS). Genome Biology, 9, R137. | |
dc.identifier.citedreference | Zhong, S., Li, H., Bodi, Z., Button, J., Vespa, L., Herzog, M. et al. ( 2008 ) MTA is an Arabidopsis messenger RNA adenosine Methylase and interacts with a homolog of a sex-specific splicing factor. Plant Cell, 20, 1278 – 1288. | |
dc.identifier.citedreference | Zhou, L., Gao, G., Tang, R., Wang, W., Wang, Y., Tian, S. et al. ( 2022 ) M 6 A-mediated regulation of crop development and stress responses. Plant Biotechnology Journal, 20, 1447 – 1455. | |
dc.identifier.citedreference | Anderson, S.J., Kramer, M.C., Gosai, S.J., Yu, X., Vandivier, L.E., Nelson, A.D.L. et al. ( 2018 ) N6-Methyladenosine inhibits local Ribonucleolytic cleavage to stabilize mRNAs in Arabidopsis. Cell Reports, 25, 1146 – 1157. | |
dc.identifier.citedreference | Aoyama, T., Hiwatashi, Y., Shigyo, M., Kofuji, R., Kubo, M., Ito, M. et al. ( 2012 ) AP2-type transcription factors determine stem cell identity in the moss Physcomitrella patens. Development, 139, 3120 – 3129. | |
dc.identifier.citedreference | Arribas-Hernández, L., Bressendorff, S., Hansen, M.H., Poulsen, C., Erdmann, S. & Brodersen, P. ( 2018 ) An m 6 A-YTH module controls developmental timing and morphogenesis in Arabidopsis. Plant Cell, 30, 952 – 967. | |
dc.identifier.citedreference | Bailey, T.L., Johnson, J., Grant, C.E. & Noble, W.S. ( 2015 ) The MEME suite. Nucleic Acids Research, 43, W39 – W49. | |
dc.identifier.citedreference | Bibeau, J.P. & Vidali, L. ( 2014 ) Morphological Analysis of Cell Growth Mutants in Physcomitrella. In: Žárský, V. & Cvrčková, F. (Eds.) Plant Cell Morphogenesis. Methods in Molecular Biology. Totowa, NJ: Humana Press, pp. 201 – 213. Available from: https://doi.org/10.1007/978-1-62703-643-6_17 | |
dc.identifier.citedreference | Bodi, Z., Zhong, S., Mehra, S., Song, J., Graham, N., Li, H. et al. ( 2012 ) Adenosine methylation in Arabidopsis mRNA is associated with the 3′ end and reduced levels cause developmental defects. Frontiers in Plant Science, 3, 48. | |
dc.identifier.citedreference | Bowman, J.L., Floyd, S.K. & Sakakibara, K. ( 2007 ) Green genes—comparative genomics of the green branch of life. Cell, 129, 229 – 234. | |
dc.identifier.citedreference | Robinson, M.D., McCarthy, D.J. & Smyth, G.K. ( 2010 ) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139 – 140. | |
dc.identifier.citedreference | Charlot, F., Goudounet, G., Nogué, F. & Perroud, P.-F. ( 2022 ) Physcomitrium patens Protoplasting and Protoplast Transfection. In: Wang, K. & Zhang, F. (Eds.) Protoplast Technology. Methods in Molecular Biology. New York, NY: Springer US, pp. 3 – 19. Available from: https://doi.org/10.1007/978-1-0716-2164-6_1 | |
dc.identifier.citedreference | Cove, D., Bezanilla, M., Harries, P. & Quatrano, R. ( 2006 ) Mosses as model systems for the study of metabolism and development. Annual Review of Plant Biology, 57, 497 – 520. | |
dc.identifier.citedreference | Cove, D.J. & Knight, C.D. ( 1993 ) The Moss Physcomitrella patens, a model system with potential for the study of plant reproduction. Plant Cell, 5, 1483 – 1488. | |
dc.identifier.citedreference | Demko, V., Perroud, P.-F., Johansen, W., Delwiche, C.F., Cooper, E.D., Remme, P. et al. ( 2014 ) Genetic analysis of DEFECTIVE KERNEL1 loop function in three-dimensional body patterning in Physcomitrella patens. Plant Physiology, 166, 903 – 919. | |
dc.identifier.citedreference | Dominissini, D., Moshitch-Moshkovitz, S., Salmon-Divon, M., Amariglio, N. & Rechavi, G. ( 2013 ) Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing. Nature Protocols, 8, 176 – 189. | |
dc.identifier.citedreference | Frank, M.H. & Scanlon, M.J. ( 2015 ) Cell-specific transcriptomic analyses of three-dimensional shoot development in the moss Physcomitrella patens. Plant Journal, 83, 743 – 751. | |
dc.identifier.citedreference | Frye, M., Harada, B.T., Behm, M. & He, C. ( 2018 ) RNA modifications modulate gene expression during development. Science, 361, 1346 – 1349. | |
dc.identifier.citedreference | Garcias Morales, D. & Reyes, J.L. ( 2021 ) A birds’-eye view of the activity and specificity of the mRNA m 6 A methyltransferase complex. WIREs RNA, 12, E1618. Available from: https://doi.org/10.1002/wrna.1618 | |
dc.identifier.citedreference | Ge, S.X., Jung, D. & Yao, R. ( 2020 ) ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics, 36, 2628 – 2629. | |
dc.identifier.citedreference | Govindan, G., Sharma, B., Li, Y., Armstrong, C.D., Merum, P., Rohila, J.S. et al. ( 2022 ) mRNA N 6 -methyladenosine is critical for cold tolerance in Arabidopsis. Plant Journal, 111 ( 4 ), 1052 – 1068. Available from: https://10.1111/tpj.15872 | |
dc.identifier.citedreference | Graham, L.E., Cook, M.E. & Busse, J.S. ( 2000 ) The origin of plants: body plan changes contributing to a major evolutionary radiation. Proceedings of the National Academy of Sciences of the United States of America, 97, 4535 – 4540. | |
dc.working.doi | NO | en |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
Files in this item
Remediation of Harmful Language
The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.
Accessibility
If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.