SDG711 Tham Gia vào Sự Phát Triển Hạt Lúa Thông Qua Việc Điều Chỉnh Biểu Hiện Gen Trao Đổi Tinh Bột Kết Hợp với Các Biến Đổi Histone Khác

Rice - Tập 14 - Trang 1-13 - 2021
Xiaoyun Liu1, Junling Luo2, Tiantian Li3, Huilan Yang1, Ping Wang1, Lufang Su1, Yu Zheng1, Chun Bao1, Chao Zhou4
1Institute for Interdisciplinary Research, Jianghan University, Wuhan, China
2Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
3Institute for Systems Biology, Jianghan University, Wuhan, China
4Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, China

Tóm tắt

SDG711 là một transmethylase của histone H3K27me2/3 ở cây lúa, đồng đẳng với CLF ở Arabidopsis, và đóng vai trò quan trọng trong việc điều chỉnh thời gian ra hoa và phát triển cụm hoa. Trong nghiên cứu này, chúng tôi đã điều tra vai trò của SDG711 trong sự phát triển của hạt lúa. Việc thúc đẩy biểu hiện quá mức và giảm biểu hiện SDG711 dẫn đến sự giảm và tăng mức độ biểu hiện của các gen liên quan đến tích trữ tinh bột, dẫn đến việc hạt nhỏ hơn hoặc thậm chí bị hỏng. Phân tích ChIP cho thấy rằng H3K27me3 được trung gian bởi SDG711 thay đổi đáng kể trong các gen liên quan đến sự phát triển nội nhũ, và SDG711 có thể gắn trực tiếp vào vùng cơ thể gen của một số gen tổng hợp tinh bột và gen amylase. Thêm vào đó, các biến đổi H3K4me3 và H3K9ac cũng phối hợp với H3K27me3 để điều chỉnh sự phát triển của nội nhũ. Kết quả của chúng tôi cho thấy rằng sự giao thoa giữa H3K27me3 do SDG711 trung gian, H3K4me3, và H3K9ac tham gia vào việc tích trữ tinh bột để kiểm soát sự phát triển bình thường của hạt.

Từ khóa

#SDG711 #lúa #phát triển hạt #trao đổi tinh bột #biến đổi histone

Tài liệu tham khảo

Asatsuma S, Sawada C, Kitajima A, Asakura T, Mitsui T (2006) α-Amylase affects starch accumulation in Rice grains. J Appl Glycosci 53(3):187–192 Baroux C, Gagliardini V, Page DR, Grossniklaus U (2006) Dynamic regulatory interactions of Polycomb group genes: MEDEA autoregulation is required for imprinted gene expression in Arabidopsis. Genes Dev 20(9):1081–1086. https://doi.org/10.1101/gad.378106 Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125(2):315–326. https://doi.org/10.1016/j.cell.2006.02.041 Berr A, McCallum EJ, Menard R, Meyer D, Fuchs J, Dong A, Shen WH (2010) Arabidopsis SET DOMAIN GROUP2 is required for H3K4 trimethylation and is crucial for both sporophyte and gametophyte development. Plant Cell 22(10):3232–3248. https://doi.org/10.1105/tpc.110.079962 Blanco E, Gonzalez-Ramirez M, Alcaine-Colet A, Aranda S, Di Croce L (2020) The bivalent genome: characterization, structure, and regulation. Trends in genetics: TIG 36(2):118–131. https://doi.org/10.1016/j.tig.2019.11.004 Charron JB, He H, Elling AA, Deng XW (2009) Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21(12):3732–3748. https://doi.org/10.1105/tpc.109.066845 Chen M, Xie S, Ouyang Y, Yao J (2017) Rice PcG gene OsEMF2b controls seed dormancy and seedling growth by regulating the expression of OsVP1. Plant Science 260:80–89. https://doi.org/10.1016/j.plantsci.2017.04.005 Czermin B, Melfi R, McCabe D, Seitz V, Pirrotta V (2002) Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111(2):185–196 Dunican DS, Mjoseng HK, Duthie L, Flyamer IM, Bickmore WA, Meehan RR (2020) Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells. BMC Biol 18(1):25. https://doi.org/10.1186/s12915-020-0752-3 Fischle W, Wang Y, Allis CD (2003) Binary switches and modification cassettes in histone biology and beyond. Nature 425(6957):475–479 Folsom JJ, Begcy K, Hao X, Wang D, Walia H (2014) Rice fertilization-independent Endosperm1 regulates seed size under heat stress by controlling early endosperm development. Plant Physiol 165(1):238–248. https://doi.org/10.1104/pp.113.232413 Fu FF, Xue HW (2010) Coexpression analysis identifies Rice starch Regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator. Plant Physiol 154(2):927–938. https://doi.org/10.1104/pp.110.159517 Ge G, Zheng X, Wu J, Ye Z, Shi C (2007) Analysis of the conditional correlations from different genetic systems between the protein content and the appearance quality traits of indica rice. Journal of Genetics and Genomics 34(2):129–137 He G, Elling AA, Deng XW (2011) The epigenome and plant development. Annu Rev Plant Biol 62:411–435. https://doi.org/10.1146/annurev-arplant-042110-103806 He Y, Amasino RM (2005) Role of chromatin modification in flowering-time control. Trends Plant Sci 10(1):30–35. https://doi.org/10.1016/j.tplants.2004.11.003 Hennig L, Derkacheva M (2009) Diversity of Polycomb group complexes in plants: same rules, different players? Trends in genetics: TIG 25(9):414–423. https://doi.org/10.1016/j.tig.2009.07.002 Hu Y, Liu D, Zhong X, Zhang C, Zhang Q, Zhou DX (2012) CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome. Proc Natl Acad Sci U S A 109(15):5773–5778. https://doi.org/10.1073/pnas.1203148109 Huang X, Lu Z, Wang X, Ouyang Y, Chen W, Xie K, Wang D, Luo M, Luo J, Yao J (2016) Imprinted gene OsFIE1 modulates rice seed development by influencing nutrient metabolism and modifying genome H3K27me3. Plant J 87(3):305–317. https://doi.org/10.1111/tpj.13202 Juliano B (1971) A simplified assay for milled rice amylose. Cereal Sci Today 16:334–360 Kinoshita T, Yadegari R, Harada JJ, Goldberg RB, Fischer RL (1999) Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. Plant Cell 11(10):1945–1952 Kuang Q, Wang Y, Li S (2019) Detailed observation on expression dynamics of Polycomb group genes during rice early endosperm development in subspecies hybridization reveals their characteristics of parent-of-origin genes. Rice 12(1):64. https://doi.org/10.1186/s12284-019-0306-x Li S, Zhou B, Peng X, Kuang Q, Huang X, Yao J, Du B, Sun MX (2014) OsFIE2 plays an essential role in the regulation of rice vegetative and reproductive development. New phytologist 201(1):66–79. https://doi.org/10.1111/nph.12472 Liu N, Fromm M, Avramova Z (2014a) H3K27me3 and H3K4me3 chromatin environment at super-induced dehydration stress memory genes of Arabidopsis thaliana. Mol Plant 7(3):502–513. https://doi.org/10.1093/mp/ssu001 Liu X, Wei X, Sheng Z, Jiao G, Tang S, Luo J, Hu P (2016) Polycomb protein OsFIE2 affects plant height and grain yield in Rice. PLoS One 11(10):e0164748. https://doi.org/10.1371/journal.pone.0164748 Liu X, Zhou C, Zhao Y, Zhou S, Wang W, Zhou DX (2014b) The rice enhancer of zeste [E(z)] genes SDG711 and SDG718 are respectively involved in long day and short day signaling to mediate the accurate photoperiod control of flowering time. Front Plant Sci 5:591. https://doi.org/10.3389/fpls.2014.00591 Liu X, Zhou S, Wang W, Ye Y, Zhao Y, Xu Q, Zhou C, Tan F, Cheng S, Zhou DX (2015) Regulation of histone methylation and reprogramming of gene expression in the rice inflorescence meristem. Plant Cell 27(5):1428–1444. https://doi.org/10.1105/tpc.15.00201 Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25(4):402–408. https://doi.org/10.1006/meth.2001.1262 Luo M, Bilodeau P, Dennis ES, Peacock WJ, Chaudhury A (2000) Expression and parent-of-origin effects for FIS2, MEA, and FIE in the endosperm and embryo of developing Arabidopsis seeds. Proc Natl Acad Sci U S A 97(19):10637–10642. https://doi.org/10.1073/pnas.170292997 Luo M, Platten D, Chaudhury A, Peacock WJ, Dennis ES (2009) Expression, imprinting, and evolution of rice homologs of the polycomb group genes. Mol Plant 2(4):711–723. https://doi.org/10.1093/mp/ssp036 Luo M, Taylor JM, Spriggs A, Zhang H, Wu X, Russell S, Singh M, Koltunow A (2011) A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet 7(6):e1002125. https://doi.org/10.1371/journal.pgen.1002125 Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, Meeley RB, Myers CL, Vaughn MW, Springer NM (2013) Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell 25(3):780–793. https://doi.org/10.1105/tpc.112.106427 Nallamilli BR, Zhang J, Mujahid H, Malone BM, Bridges SM, Peng Z (2013) Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis. PLoS Genet 9(3):e1003322. https://doi.org/10.1371/journal.pgen.1003322 Ohdan T, Francisco PB Jr, Sawada T, Hirose T, Terao T, Satoh H, Nakamura Y (2005) Expression profiling of genes involved in starch synthesis in sink and source organs of rice. J Exp Bot 56(422):3229–3244. https://doi.org/10.1093/jxb/eri292 Peng C, Wang Y, Liu F, Ren Y, Zhou K, Lv J, Zheng M, Zhao S, Zhang L, Wang C, Jiang L, Zhang X, Guo X, Bao Y, Wan J (2014) FLOURY ENDOSPERM6 encodes a CBM48 domain-containing protein involved in compound granule formation and starch synthesis in rice ENDOSPERM. Plant J 77(6):917–930. https://doi.org/10.1111/tpj.12444 Qian S, Lv X, Scheid RN, Lu L, Yang Z, Chen W, Liu R, Boersma MD, Denu JM, Zhong X, Du J (2018) Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL. Nat Commun 9(1):2425. https://doi.org/10.1038/s41467-018-04836-y Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470(7333):279–283. https://doi.org/10.1038/nature09692 Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Zilberman D (2013) Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proc Natl Acad Sci 110(19):7934–7939 Schmidt R, Schippers JH, Mieulet D, Watanabe M, Hoefgen R, Guiderdoni E, Mueller-Roeber B (2014) SALT-RESPONSIVE ERF1 is a negative regulator of grain filling and gibberellin-mediated seedling establishment in rice. Mol Plant 7(2):404–421. https://doi.org/10.1093/mp/sst131 Schreiber SL, Bernstein BE (2002) Signaling network model of chromatin. Cell 111(6):771–778 Schuettengruber B, Cavalli G (2009) Recruitment of polycomb group complexes and their role in the dynamic regulation of cell fate choice. Development 136(21):3531–3542. https://doi.org/10.1242/dev.033902 Sequeira-Mendes J, Araguez I, Peiro R, Mendez-Giraldez R, Zhang X, Jacobsen SE, Bastolla U, Gutierrez C (2014) The functional topography of the Arabidopsis genome is organized in a reduced number of linear motifs of chromatin states. Plant Cell 26(6):2351–2366. https://doi.org/10.1105/tpc.114.124578 She KC, Kusano H, Koizumi K, Yamakawa H, Hakata M, Imamura T, Fukuda M, Naito N, Tsurumaki Y, Yaeshima M, Tsuge T, Matsumoto K, Kudoh M, Itoh E, Kikuchi S, Kishimoto N, Yazaki J, Ando T, Yano M, Aoyama T, Sasaki T, Satoh H, Shimada H (2010) A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. Plant Cell 22(10):3280–3294. https://doi.org/10.1105/tpc.109.070821 Spillane C, MacDougall C, Stock C, Köhler C, Vielle-Calzada J, Nunes SM, Grossniklaus U, Goodrich J (2000) Interaction of the Arabidopsis Polycomb group proteins FIE and MEA mediates their common phenotypes. Curr Biol 10(23):1535–1538 Steffen PA, Ringrose L (2014) What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory. Nat Rev Mol Cell Biol 15(5):340–356. https://doi.org/10.1038/nrm3789 Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403(6765):41–45 Turner DH, Turner J (1960) The hydrolysis of glucose monophosphates by a phosphatase preparation from pea seeds. Biochem J 74(3):486 Wang JC, Xu H, Zhu Y, Liu QQ, Cai XL (2013) OsbZIP58, a basic leucine zipper transcription factor, regulates starch biosynthesis in rice endosperm. J Exp Bot 64(11):3453–3466. https://doi.org/10.1093/jxb/ert187 Xiang Y, Zhang Y, Xu Q, Zhou C, Liu B, Du Z, Zhang K, Zhang B, Wang X, Gayen S, Liu L, Wang Y, Li Y, Wang Q, Kalantry S, Li L, Xie W (2020) Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency. Nat Genet 52(1):95–105. https://doi.org/10.1038/s41588-019-0545-1 Xing MQ, Zhang YJ, Zhou SR, Hu WY, Wu XT, Ye YJ, Wu XX, Xiao YP, Li X, Xue HW (2015) Global analysis reveals the crucial roles of DNA methylation during Rice seed development. Plant Physiol 168(4):1417–1432. https://doi.org/10.1104/pp.15.00414 Yang Z, Qian S, Scheid RN, Lu L, Chen X, Liu R, Du X, Lv X, Boersma MD, Scalf M, Smith LM, Denu JM, Du J, Zhong X (2018) EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Nat Genet 50(9):1247–1253. https://doi.org/10.1038/s41588-018-0187-8 Yuan J, Chen S, Jiao W, Wang L, Wang L, Ye W, Lu J, Hong D, You S, Cheng Z, Yang DL, Chen ZJ (2017) Both maternally and paternally imprinted genes regulate seed development in rice. The New phytologist 216(2):373–387. https://doi.org/10.1111/nph.14510 Zeng Z, Zhang W, Marand AP, Zhu B, Buell CR, Jiang J (2019) Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato. Genome Biol 20(1):123. https://doi.org/10.1186/s13059-019-1731-2 Zentner GE, Tesar PJ, Scacheri PC (2011) Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res 21(8):1273–1283. https://doi.org/10.1101/gr.122382.111 Zhang H, Lu Y, Zhao Y, Zhou DX (2016) OsSRT1 is involved in rice seed development through regulation of starch metabolism gene expression. Plant Sci 248:28–36. https://doi.org/10.1016/j.plantsci.2016.04.004 Zhang K, Dent SY (2005) Histone modifying enzymes and cancer: going beyond histones. J Cell Biochem 96(6):1137–1148. https://doi.org/10.1002/jcb.20615 Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE (2009) Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol 10(6):R62. https://doi.org/10.1186/gb-2009-10-6-r62 Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5(5):e129. https://doi.org/10.1371/journal.pbio.0050129 Zhao XD, Han X, Chew JL, Liu J, Chiu KP, Choo A, Orlov YL, Sung WK, Shahab A, Kuznetsov VA, Bourque G, Oh S, Ruan Y, Ng HH, Wei CL (2007) Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1(3):286–298. https://doi.org/10.1016/j.stem.2007.08.004 Zhong J, Peng Z, Peng Q, Cai Q, Peng W, Chen M, Yao J (2018) Regulation of plant height in rice by the Polycomb group genes OsEMF2b, OsFIE2 and OsCLF. Plant Sci 267:157–167. https://doi.org/10.1016/j.plantsci.2017.11.007 Zhu Y, Cai XL, Wang ZY, Hong MM (2003) An interaction between a MYC protein and an EREBP protein is involved in transcriptional regulation of the rice Wx gene. J Biol Chem 278(48):47803–47811. https://doi.org/10.1074/jbc.M302806200