リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

大学・研究所にある論文を検索できる 「A guiding role of the Arabidopsis circadian clock in cell differentiation revealed by time-series single-cell RNA sequencing」の論文概要。リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

コピーが完了しました

URLをコピーしました

論文の公開元へ論文の公開元へ
書き出し

A guiding role of the Arabidopsis circadian clock in cell differentiation revealed by time-series single-cell RNA sequencing

Torii, Kotaro Inoue, Keisuke Bekki, Keita Haraguchi, Kazuya Kubo, Minoru Kondo, Yuki Suzuki, Takamasa Kubota, Akane Uemoto, Kyohei Shimizu, Hanako Saito, Masato Fukuda, Hiroo Araki, Takashi Endo, Motomu 京都大学 DOI:10.1016/j.celrep.2022.111059

2022.07.12

概要

Circadian rhythms and progression of cell differentiation are closely coupled in multicellular organisms. However, whether establishment of circadian rhythms regulates cell differentiation or vice versa has not been elucidated due to technical limitations. Here, we exploit high cell fate plasticity of plant cells to perform single-cell RNA sequencing during the entire process of cell differentiation. By analyzing reconstructed actual time series of the differentiation processes at single-cell resolution using a method we developed (PeakMatch), we find that the expression profile of clock genes is changed prior to cell differentiation, including induction of the clock gene LUX ARRYTHMO (LUX). ChIP sequencing analysis reveals that LUX induction in early differentiating cells directly targets genes involved in cell-cycle progression to regulate cell differentiation. Taken together, these results not only reveal a guiding role of the plant circadian clock in cell differentiation but also provide an approach for time-series analysis at single-cell resolution.

この論文で使われている画像

参考文献

Aihara, K., Naramoto, S., Hara, M., and Mizoguchi, T. (2014). Increase in vascular pattern complexity caused by mutations in LHY and CCA1 in Arabi- dopsis thaliana under continuous light. Plant Biotechnol. 31, 43–47. https:// doi.org/10.5511/plantbiotechnology.13.1015a.

Anders, S., and Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biol. 11, R106. https://doi.org/10.1186/gb-2010-11-10- r106.

Bhadra, U., Thakkar, N., Das, P., and Pal Bhadra, M. (2017). Evolution of circa- dian rhythms: from bacteria to human. Sleep Med. 35, 49–61. https://doi.org/ 10.1016/j.sleep.2017.04.008.

Brown, S.A. (2014). Circadian clock-mediated control of stem cell division and differentiation: beyond night and day. Development 141, 3105–3111. https:// doi.org/10.1242/dev.104851.

Campbell, L., and Turner, S. (2017). Regulation of vascular cell division. J. Exp. Bot. 68, 27–43. https://doi.org/10.1093/jxb/erw448.

Collins, C., Maruthi, N.M., and Jahn, C.E. (2015). CYCD3 D-type cyclins regu- late cambial cell proliferation and secondary growth in Arabidopsis. J. Exp. Bot. 66, 4595–4606. https://doi.org/10.1093/jxb/erv218.

de Jager, S.M., Scofield, S., Huntley, R.P., Robinson, A.S., den Boer, B.G.W., and Murray, J.A.H. (2009). Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3;1, E2Fa and E2Fc. Plant Mol. Biol. 71, 345–365. https://doi.org/10.1007/s11103-009-9527-5.

De Veylder, L., Beeckman, T., and Inze´ , D. (2007). The ins and outs of the plant cell cycle. Nat. Rev. Mol. Cell Biol. 8, 655–665. https://doi.org/10.1038/ nrm2227.

Desvoyes, B., de Mendoza, A., Ruiz-Trillo, I., and Gutierrez, C. (2014). Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division. J. Exp. Bot. 65, 2657–2666. https://doi.org/10. 1093/jxb/ert411.

Dewitte, W., Scofield, S., Alcasabas, A.A., Maughan, S.C., Menges, M., Braun, N., Collins, C., Nieuwland, J., Prinsen, E., Sundaresan, V., and Murray, J.A.H. (2007). Arabidopsis CYCD3 D-type cyclins link cell proliferation and endo- cycles and are rate-limiting for cytokinin responses. Proc. Natl. Acad. Sci. USA 104, 14537–14542. https://doi.org/10.1073/pnas.0704166104.

Dierickx, P., Van Laake, L.W., and Geijsen, N. (2018). Circadian clocks: from stem cells to tissue homeostasis and regeneration. EMBO Rep. 19, 18–28. https://doi.org/10.15252/embr.201745130.

Endo, M., Shimizu, H., Nohales, M.A., Araki, T., and Kay, S.A. (2014). Tissue- specific clocks in Arabidopsis show asymmetric coupling. Nature 515, 419–422. https://doi.org/10.1038/nature13919.

Ezer, D., Jung, J.H., Lan, H., Biswas, S., Gregoire, L., Box, M.S., Charoensa- wan, V., Cortijo, S., Lai, X., Sto¨ ckle, D., et al. (2017). The evening complex co- ordinates environmental and endogenous signals in Arabidopsis. Nat. Plants 3, 17087. https://doi.org/10.1038/nplants.2017.87.

Fukuda, H., Ukai, K., and Oyama, T. (2012). Self-arrangement of cellular circa- dian rhythms through phase-resetting in plant roots. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 86, 041917. https://doi.org/10.1103/PhysRevE.86.041917.

Fung-Uceda, J., Lee, K., Seo, P.J., Polyn, S., De Veylder, L., and Mas, P. (2018). The circadian clock sets the time of DNA replication licensing to regu- late growth in Arabidopsis. Dev. Cell 45, 101–113.e4. https://doi.org/10.1016/j. devcel.2018.02.022.

Golden, S.S., Ishiura, M., Johnson, C.H., and Kondo, T. (1997). Cyanobacterial circadian rhythms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 48, 327–354. https://doi.org/10.1146/annurev.arplant.48.1.327.

Harashima, H., and Schnittger, A. (2010). The integration of cell division, growth and differentiation. Curr. Opin. Plant Biol. 13, 66–74. https://doi.org/ 10.1016/j.pbi.2009.11.001.

Helfer, A., Nusinow, D.A., Chow, B.Y., Gehrke, A.R., Bulyk, M.L., and Kay, S.A. (2011). LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock. Curr. Biol. 21, 126–133. https:// doi.org/10.1016/j.cub.2010.12.021.

Hut, R.A., and Beersma, D.G.M. (2011). Evolution of time-keeping mecha- nisms: early emergence and adaptation to photoperiod. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366, 2141–2154. https://doi.org/10.1098/rstb.2010. 0409.

Inoue, K., Araki, T., and Endo, M. (2018). Oscillator networks with tissue-spe- cific circadian clocks in plants. Semin. Cell Dev. Biol. 83, 78–85. https://doi. org/10.1016/j.semcdb.2017.09.002.

Islam, S., Zeisel, A., Joost, S., La Manno, G., Zajac, P., Kasper, M., Lo¨ nner- berg, P., and Linnarsson, S. (2014). Quantitative single-cell RNA-seq with unique molecular identifiers. Nat. Methods 11, 163–166. https://doi.org/10. 1038/nmeth.2772.

Kang, C.Y., Lian, H.L., Wang, F.F., Huang, J.R., and Yang, H.Q. (2009). Cryp- tochromes, phytochromes, and COP1 regulate light-controlled stomatal development in Arabidopsis. Plant Cell 21, 2624–2641. https://doi.org/10. 1105/tpc.109.069765.

Kim, D., Langmead, B., and Salzberg, S.L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360. https://doi.org/10. 1038/nmeth.3317.

Kondo, Y., Ito, T., Nakagami, H., Hirakawa, Y., Saito, M., Tamaki, T., Shirasu, K., and Fukuda, H. (2014). Plant GSK3 proteins regulate xylem cell differenti- ation downstream of TDIF-TDR signalling. Nat. Commun. 5, 3504. https:// doi.org/10.1038/ncomms4504.

Kondo, Y., Nurani, A.M., Saito, C., Ichihashi, Y., Saito, M., Yamazaki, K., Mit- suda, N., Ohme-Takagi, M., and Fukuda, H. (2016). Vascular cell induction cul- ture system using Arabidopsis leaves (VISUAL) reveals the sequential differen- tiation of sieve element-like cells. Plant Cell 28, 1250–1262. https://doi.org/10. 1105/tpc.16.00027.

Kowalska, E., Moriggi, E., Bauer, C., Dibner, C., and Brown, S.A. (2010). The circadian clock starts ticking at a developmentally early stage. J. Biol. Rhythms 25, 442–449. https://doi.org/10.1177/0748730410385281.

Kubo, M., Nishiyama, T., Tamada, Y., Sano, R., Ishikawa, M., Murata, T., Imai, A., Lang, D., Demura, T., Reski, R., and Hasebe, M. (2019). Single-cell tran- scriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation. Nucleic Acids Res. 47, 4539–4553. https://doi. org/10.1093/nar/gkz181.

Kuwabara, A., and Gruissem, W. (2014). Arabidopsis RETINOBLASTOMA- RELATED and Polycomb group proteins: cooperation during plant cell differ- entiation and development. J. Exp. Bot. 65, 2667–2676. https://doi.org/10. 1093/jxb/eru069.

Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25. https://doi.org/10.1186/gb-2009-10-3-r25.

Li, L., Yu, X., Thompson, A., Guo, M., Yoshida, S., Asami, T., Chory, J., and Yin, Y. (2009). Arabidopsis MYB30 is a direct target of BES1 and cooperates with BES1 to regulate brassinosteroid-induced gene expression. Plant J. 58, 275–286. https://doi.org/10.1111/j.1365-313X.2008.03778.x.

Li, G., Siddiqui, H., Teng, Y., Lin, R., Wan, X.y., Li, J., Lau, O.S., Ouyang, X., Dai, M., Wan, J., et al. (2011). Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat. Cell Biol. 13, 616–622. https://doi.org/ 10.1038/ncb2219.

Li, Q.F., Lu, J., Yu, J.W., Zhang, C.Q., He, J.X., and Liu, Q.Q. (2018). The bras-sinosteroid-regulated transcription factors BZR1/BES1 function as a coordi- nator in multisignal-regulated plant growth. Biochim. Biophys. Acta Gene Regul. Mech. 1861, 561–571. https://doi.org/10.1016/j.bbagrm.2018.04.003.

Malucelli, F., Ottmann, T., and Pretolani, D. (1993). Efficient labelling algo- rithms for the maximum noncrossing matching problem. Discrete Appl. Math. 47, 175–179. https://doi.org/10.1007/978-3-642-77489-8_30.

Mermigka, G., Amprazi, M., Mentzelopoulou, A., Amartolou, A., and Sarris,P.F. (2020). Plant and animal innate immunity complexes: fighting different en- emies with similar weapons. Trends Plant Sci. 25, 80–91. https://doi.org/10. 1016/j.tplants.2019.09.008.

Michael, T.P., Mockler, T.C., Breton, G., McEntee, C., Byer, A., Trout, J.D., Ha- zen, S.P., Shen, R., Priest, H.D., Sullivan, C.M., et al. (2008). Network discovery pipeline elucidates conserved time-of-day–specific cis-regulatory modules. PLoS Genet. 4, e14. https://doi.org/10.1371/journal.pgen.0040014.

Nakagawa, T., Kurose, T., Hino, T., Tanaka, K., Kawamukai, M., Niwa, Y., Toyooka, K., Matsuoka, K., Jinbo, T., and Kimura, T. (2007). Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. J. Biosci. Bioeng. 104, 34–41. https://doi.org/10.1263/jbb.104.34.

Nelms, B., and Walbot, V. (2019). Defining the developmental program leading to meiosis in maize. Science 364, 52–56. https://doi.org/10.1126/science. aav6428.

Nishimura, T., Yokota, E., Wada, T., Shimmen, T., and Okada, K. (2003). An Arabidopsis ACT2 dominant-negative mutation, which disturbs F-actin poly- merization, reveals its distinctive function in root development. Plant Cell Physiol. 44, 1131–1140. https://doi.org/10.1093/pcp/pcg158.

Niwa, Y., Ito, S., Nakamichi, N., Mizoguchi, T., Niinuma, K., Yamashino, T., and Mizuno, T. (2007). Genetic linkages of the circadian clock-associated genes, TOC1, CCA1 and LHY, in the photoperiodic control of flowering time in Arabi- dopsis thaliana. Plant Cell Physiol. 48, 925–937. https://doi.org/10.1093/pcp/ pcm067.

Nusinow, D.A., Helfer, A., Hamilton, E.E., King, J.J., Imaizumi, T., Schultz, T.F., Farre´ , E.M., and Kay, S.A. (2011). The ELF4-ELF3-LUX complex links the circa- dian clock to diurnal control of hypocotyl growth. Nature 475, 398–402. https:// doi.org/10.1038/nature10182.

Paulose, J.K., Rucker, E.B., and Cassone, V.M. (2012). Toward the beginning of time: circadian rhythms in metabolism precede rhythms in clock gene expression in mouse embryonic stem cells. PLoS One 7, e49555. https:// doi.org/10.1371/journal.pone.0049555.

Quint, M., Drost, H.G., Gabel, A., Ullrich, K.K., Bo¨ nn, M., and Grosse, I. (2012). A transcriptomic hourglass in plant embryogenesis. Nature 490, 98–101. https://doi.org/10.1038/nature11394.

Ryu, K.H., Huang, L., Kang, H.M., and Schiefelbein, J. (2019). Single-cell RNA sequencing resolves molecular relationships among individual plant cells. Plant Physiol. 179, 1444–1456. https://doi.org/10.1104/pp.18.01482pp.18.01482.

Saito, M., Kondo, Y., and Fukuda, H. (2018). BES1 and BZR1 redundantly pro- mote phloem and xylem differentiation. Plant Cell Physiol. 59, 590–600. https://doi.org/10.1093/pcp/pcy012.

Satija, R., Farrell, J.A., Gennert, D., Schier, A.F., and Regev, A. (2015). Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495–502. https://doi.org/10.1038/nbt.3192.

Schaffer, R., Ramsay, N., Samach, A., Corden, S., Putterill, J., Carre, I.A., and Coupland, G. (1998). The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93, 1219–1229. https://doi.org/10.1016/S0092-8674(00)81465-8.

Setty, M., Tadmor, M.D., Reich-Zeliger, S., Angel, O., Salame, T.M., Kathail, P., Choi, K., Bendall, S., Friedman, N., and Pe’er, D. (2016). Wishbone iden- tifies bifurcating developmental trajectories from single-cell data. Nat. Bio- technol. 34, 637–645. https://doi.org/10.1038/nbt.3569.

Sharma, M., Pandey, A., and Pandey, G.K. (2014). b-catenin in plants and an- imals: common players but different pathways^I2-catenin in plants and animals: common players but different pathways. Front. Plant Sci. 5, 143. https://doi. org/10.3389/fpls.2014.00143.

Shimada, T.L., Shimada, T., and Hara-Nishimura, I. (2010). A rapid and non- destructive screenable marker, FAST, for identifying transformed seeds of Arabidopsis thaliana. Plant J. 61, 519–528. https://doi.org/10.1111/j.1365- 313X.2009.04060.x.

Shulse, C.N., Cole, B.J., Ciobanu, D., Lin, J., Yoshinaga, Y., Gouran, M., Turco, G.M., Zhu, Y., O’Malley, R.C., Brady, S.M., and Dickel, D.E. (2019). High- throughput single-cell transcriptome profiling of plant cell types. Cell Rep. 27, 2241–2247.e4. https://doi.org/10.1016/j.celrep.2019.04.054.

Sun, N., Yu, X., Li, F., Liu, D., Suo, S., Chen, W., Chen, S., Song, L., Green, C.D., McDermott, J., et al. (2017). Inference of differentiation time for single cell transcriptomes using cell population reference data. Nat. Commun. 8, 1856. https://doi.org/10.1038/s41467-017-01860-2.

Taylor-Teeples, M., Lin, L., de Lucas, M., Turco, G., Toal, T.W., Gaudinier, A., Young, N.F., Trabucco, G.M., Veling, M.T., Lamothe, R., et al. (2015). An Ara- bidopsis gene regulatory network for secondary cell wall synthesis. Nature 517, 571–575. https://doi.org/10.1038/nature14099.

Tsuchiya, Y., Umemura, Y., and Yagita, K. (2020). Circadian clock and cancer: from a viewpoint of cellular differentiation. Int. J. Urol. 27, 518–524. https://doi. org/10.1111/iju.14231.

Voß, U., Wilson, M.H., Kenobi, K., Gould, P.D., Robertson, F.C., Peer, W.A., Lucas, M., Swarup, K., Casimiro, I., Holman, T.J., et al. (2015). The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana. Nat. Commun. 6, 7641. https://doi.org/10.1038/ncomms8641.

Weger, M., Diotel, N., Dorsemans, A.C., Dickmeis, T., and Weger, B.D. (2017). Stem cells and the circadian clock. Dev. Biol. 431, 111–123. https://doi.org/10. 1016/j.ydbio.2017.09.012.

Yagita, K., Horie, K., Koinuma, S., Nakamura, W., Yamanaka, I., Urasaki, A., Shigeyoshi, Y., Kawakami, K., Shimada, S., Takeda, J., and Uchiyama, Y. (2010). Development of the circadian oscillator during differentiation of mouse embryonic stem cells in vitro. Proc. Natl. Acad. Sci. USA 107, 3846–3851. https://doi.org/10.1073/pnas.0913256107.

Yamaguchi, M., Mitsuda, N., Ohtani, M., Ohme-Takagi, M., Kato, K., and De- mura, T. (2011). VASCULAR-RELATED NAC-DOMAIN7 directly regulates the expression of a broad range of genes for xylem vessel formation. Plant J. 66, 579–590. https://doi.org/10.1111/j.1365-313X.2011.04514.x.

Yamaguchi, N., Winter, C.M., Wu, M.F., Kwon, C.S., William, D.A., and Wag- ner, D. (2014). PROTOCOLS: chromatin immunoprecipitation from Arabidop- sis tissues. Arabidopsis Book 12, e0170. https://doi.org/10.1199/tab.0170.

Yamazaki, K., Kondo, Y., Kojima, M., Takebayashi, Y., Sakakibara, H., and Fu- kuda, H. (2018). Suppression of DELLA signaling induces procambial cell for- mation in culture. Plant J. 94, 48–59. https://doi.org/10.1111/tpj.13840.

Yin, Y., Wang, Z.Y., Mora-Garcia, S., Li, J., Yoshida, S., Asami, T., and Chory, J. (2002). BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell 109, 181–191. https://doi.org/10.1016/s0092-8674(02)00721-3.

Youn, J.H., and Kim, T.W. (2015). Functional insights of plant GSK3-like ki- nases: multi-taskers in diverse cellular signal transduction pathways. Mol. Plant 8, 552–565. https://doi.org/10.1016/j.molp.2014.12.006.

Yu, X., Li, L., Zola, J., Aluru, M., Ye, H., Foudree, A., Guo, H., Anderson, S., Aluru, S., Liu, P., et al. (2011). A brassinosteroid transcriptional network re- vealed by genome-wide identification of BESI target genes in Arabidopsis thaliana. Plant J. 65, 634–646. https://doi.org/10.1111/j.1365-313X.2010. 04449.x.

Yu, X., Rollins, D., Ruhn, K.A., Stubblefield, J.J., Green, C.B., Kashiwada, M., Rothman, P.B., Takahashi, J.S., and Hooper, L.V. (2013). TH17 cell differenti- ation is regulated by the circadian clock. Science 342, 727–730. https://doi. org/10.1126/science.1243884.

Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., and Liu, X.S. (2008). Model- based analysis of ChIP-seq (MACS). Genome Biol. 9, R137. https://doi.org/ 10.1186/gb-2008-9-9-r137.

参考文献をもっと見る

全国の大学の
卒論・修論・学位論文

一発検索!

この論文の関連論文を見る