| 770 | 1 | 136 |
| 下载次数 | 被引频次 | 阅读次数 |
大豆(Glycine max)是重要的经济作物，可以为人类提供蛋白质和油脂等重要的营养物质。大豆根瘤发育是大豆一生中众多关键生物学过程之一，可以帮助大豆固定空气中的氮气，为大豆的生长发育提供所需要的氮。DNA甲基化作为重要的表观遗传修饰，可以通过调控基因表达、抑制转座子活性参与许多重要的生物学过程。然而，大豆根瘤形成的表观遗传调控机制尚不清楚。在本研究中，通过重亚硫酸盐全基因组测序技术，从单碱基分辨率的水平上对大豆的根瘤和根进行DNA甲基化的全面分析，结果发现根瘤的CG和CHG全基因组DNA甲基化水平要低于根的，而CHH甲基化水平高于根的。此外，还识别了大量的差异甲基化区域(differential methylation regions, DMRs),特别是在转座子(transposon)和基因间区(intergenic regions)。除此之外，这些差异甲基化区域还在基因编码区和上下游区域广泛分布。通过转录组测序技术，发现这些差异甲基化相关基因发生了显著的表达差异，尤其是CHH类型的甲基化变异可以促进许多重要基因的表达，比如NIN,NF-YA和SymRK等，这些基因都是参与根瘤发育的重要基因。综上所述，本研究结果可以帮助人们理解大豆根瘤发育的DNA甲基化调控机制，并为大豆其他研究提供重要的表观修饰资源。
Abstract：Soybean(Glycine max) is the important economic crop, which can provide nutrients such as oil and protein for human beings. Nodule development is one of the most critical biological processes of soybean, which can help soybean fix nitrogen in the air and obtain nitrogen needed for growth and development. However, the epigenetic regulation mechanism of soybean nodule formation is still unclear. In this study, DNA methylome analysis was performed between soybean nodule and root by genome-wide bisulfite sequencing at a single base resolution. Nodules showed lower CG and CHG genome-wide DNA methylation than that in roots, but higher CHH methylation. Moreover, thousands of differential methylation regions(DMRs) were found, especially in TE and intergenic regions. In addition, gene body and upstream/downstream regions also contained a large number of DMRs, suggesting that these DMRs may be involved in the expression regulation of soybean nodule. Combined with transcriptome data, many DMRs were associated with differential expression genes, and these DMR-associated differential expression genes contained some important nodule-related genes, such as NIN, NF-YA, and SymRK. Taken together, our findings can explain the DNA methylation regulation of transcription difference between nodule and root of soybean.
Akalin A.,Kormaksson M.,Li S.,Garrett-Bakelman F.E.,Figueroa M.E.,Melnick A.,and Mason C.E.,2012,MethylKit:a comprehensive R package for the analysis of genome-wide DNA methylation profiles,Genome Biol.,13(10):R87.
Cai S.G.,Shen Q.F.,Huang Y.Q.,Han Z.G.,Wu D.Z.,Chen Z.H.,Nevo E.,and Zhang G.P.,2021,Multi-omics analysis reveals the mechanism underlying the edaphic adaptation in wild barley at evolution slope (Tabigha),Adv.Sci.,8(20):e2101374.
Canfield D.E.,Glazer A.N.,and Falkowski P.G.,2010,The evolution and future of earth’s nitrogen cycle,Science,330(6001):192-196.
Chen S.F.,Zhou Y.Q.,Chen Y.R.,and Gu J.,2018,Fastp:an ultra-fast all-in-one FASTQ preprocessor,Bioinforma-tics,34(17):i884-i890.
Combier J.P.,Frugier F.,de Billy F.,Boualem A.,El-Yahyaoui F.,Moreau S.,Vernie T.,Ott T.,Gamas P.,Crespi M.,and Niebel A.,2006,MtHAP2-1 is a key transcriptional regulator of symbiotic nodule development regulated by microRNA169 in Medicago truncatula,Genes Dev.,20(22):3084-3088.
Daccord N.,Celton J.M.,Linsmith G.,Becker C.,Choisne N.,Schijlen E.,van de Geest H.,Bianco L.,Micheletti D.,Velasco R.,Di-Pierro E.A.,Gouzy J.,Rees D.J.G.,Guérif P.,Muranty H.,Durel C.E.,Laurens F.,Lespi-nasse Y.,Gaillard S.,Aubourg S.,Quesneville H.,Weigel D.,van de Weg E.,Troggio M.,and Bucher E.,2017,High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development,Nat.Genet.,49(7):1099-1106.
Desbrosses G.J.,and Stougaard J.,2011,Root nodula-tion:A paradigm for how plant-microbe symbiosis influences host developmental pathways,Cell Host Microbe,10(4):348-358.
Dixon R.,and Kahn D.,2004,Genetic regulation of biological nitrogen fixation,Nat.Rev.Microbiol.,2(8):621-631.
Feng S.,Cokus S.J.,Zhang X.,Chen P.Y.,Bostick M.,Goll M.G.,Hetzel J.,Jain J.,Strauss S.H.,Halpern M.E.,Ukomadu C.,Sadler K.C.,Pradhan S.,Pellegrini M.,and Jacobsen S.E.,2010,Conservation and divergence of methylation patterning in plants and animals,Proc.Natl.Acad.Sci.USA,107(19):8689-8694.
Ferguson B.J.,Indrasumunar A.,Hayashi S.,Lin M.H.,Lin Y.H.,Reid D.E.,and Gresshoff P.M.,2010,Molecular analysis of legume nodule development and autoregulation,J.Integr.Plant Biol.,52(1):61-76.
Forster P.,and Ramaswamy V.,eds.,2007,Changes in atmospheric constituents and in radiative forcing,Cambridge Univ.Press,UK,Cambridge,pp.143-145.
Galloway J.N.,Townsend A.R.,Erisman J.W.,Bekunda M.,Cai Z.,Freney J.R.,Martinelli L.A.,Seitzinger S.P.,and Sutton M.A.,2008,Transformation of the nitro-gen cycle:recent trends,questions,and potential solutions,Science,320(5878):889-892.
Gent J.I.,Ellis N.A.,Guo L.,Harkess A.E.,Yao Y.Y.,Zhang X.Y.,and Dawe R.K.,2013,CHH islands:de novo DNA methylation in near-gene chromatin regula-tion in maize,Genome Res.,23(4):628-637.
Huang H.,Liu R.E.,Niu Q.F.,Tang K.,Zhang B.,Zhang H.,Chen K.S.,Zhu J.K.,and Lang Z.B.,2019,Global increase in DNA methylation during orange fruit development and ripening,Proc.Natl.Acad.Sci.USA,116(4):1430-1436.
Ikeuchi M.,Iwase A.,and Sugimoto K.,2015,Control of plant cell differentiation by histone modification and DNA methylation,Curr.Opin.Plant Biol.,28:60-67.
Indrasumunar A.,Wilde J.,Hayashi S.,Li D.,and Gresshoff P.M.,2015,Functional analysis of duplica-ted symbiosis receptor kinase(SymRK) genes during nodulation and mycorrhizal infection in soybean (Glycine max),J.Plant Physiol.,176:157-168.
Inukai S.,Kock K.H.,and Bulyk M.L.,2017,Transc-ription factor-DNA binding:beyond binding site motifs,Current Opinion in Genetics & Development,43:110-119.
Lang Z.B.,Wang Y.H.,Tang K.,Tang D.G.,Datsenka T.,Cheng J.F.,Zhang Y.J.,Handa A.K.,and Zhu J.K.,2017,Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit,Proc.Natl.Acad.Sci.USA,114(22):E4511-E4519.
Laporte P.,Lepage A.,Fournier J.,Catrice O.,Moreau S.,Jardinaud M.F.,Mun J.H.,Larrainzar E.,Cook D.R.,Gamas P.,and Niebel A.,2014,The CCAAT box-binding transcription factor NF-YA1 controls rhizobial infection,J.Exp.Bot.65(2):481-494.
Law J.A.,and Jacobsen S.E.,2010,Establishing,main-taining and modifying DNA methylation patterns in plants and animals,Nat.Rev.Genet.,11(3):204-220.
Li Q.,Gent J.I.,Zynda G.,Song J.,Makarevitch I.,Hirsch C.D.,Hirsch C.N.,Dawe R.K.,Madzima T.F.,McGinnis K.M.,Lisch D.,Schmitz R.J.,Vaughn M.W.,and Springer N.M.,2015a,RNA-directed DNA methylation enforces boundaries between hetero-chromatin and euchro-matin in the maize genome,Proc.Natl.Acad.Sci.USA,112(47):14728-14733.
Li Q.,Song J.,West P.T.,Zynda G.,Eichten S.R.,Vaughn M.W.,and Springer N.M.,2015b,Examining the causes and consequences of context-specific differential DNA methylation in maize,Plant Physiol.,168(4):1262-1274.
Lin J.Y.,Le B.H.,Chen M.,Henry K.F.,Hur J.,Hsieh T.F.,Chen P.Y.,Pelletier J.M.,Pellegrini M.,Fischer R.L.,Harada J.J.,and Goldberg R.B.,2017,Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development,Proc.Natl.Acad.Sci.USA,114(45):E9730-E9739.
Liu C.W.,and Murray J.D.,2016,The role of flavonoids in nodulation host-range specificity:an update,Plants:Basel,5(3):33.
Liu C.W.,Breakspear A.,Guan D.,Cerri M.R.,Jackson K.,Jiang S.Y.,Robson F.,Radhakrishnan G.V.,Roy S.,Bone C.,Stacey N.,Rogers C.,Trick M.,Niebel A.,Oldroyd G.E.D.,De Carvalho-Niebel F.,and Murray J.D.,2019,NIN acts as a network hub controlling a growth module required for rhizobial infection,Plant Physiol.,179(4):1704-1722.
Love M.I.,Huber W.,and Anders,S.,2014,Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2,Genome Biol.,15(12):550.
Mergaert P.,Kereszt A.,and Kondorosi E.,2020,Gene expression in nitrogen-fixing symbiotic nodule cells in Medicago truncatula and other nodulating plants,The Plant Cell,32(1):42-68.
Nagymihály M.,Veluchamy A.,Gy?rgypál Z.,Ariel F.,Jégu T.,Benhamed M.,Szücs A.,Kereszt A.,Mergaert P.,and Kondorosi é.,2017,Ploidy-dependent changes in the epigenome of symbiotic cells correlate with specific patterns of gene expression,Proc.Natl.Acad.Sci.USA,114(17):4543-4548.
Oldroyd G.E.D.,2013,Speak,friend,and enter:signal-ling systems that promote beneficial symbiotic associations in plants,Nat.Rev.Microbiol.,11(4):252-263.
Pertea M.,Kim D.,Pertea G.M.,Leek J.T.,and Salzberg S.L.,2016,Transcript-level expression analysis of RNA-seq experiments with HISAT,StringTie and Ballgown,Nat.Protoc.,11(9):1650-1667.
Quach T.N.,Nguyen H.T.M.,Valliyodan B.,Joshi T.,Xu D.,and Nguyen H.T.,2015,Genome-wide expres-sion analysis of soybean NF-Y genes reveals potential function in development and drought response,Mol.Genet.Genomics,290(3):1095-1115.
Radutoiu S.,Madsen L.H.,Madsen E.B.,Felle H.H.,Umehara Y.,Gr?nlund M.,Sato S.,Nakamura Y.,Tabata S.,Sandal N.,and Stougaard J.,2003,Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases,Nature,425(6958):585-592.
Roy S.,Liu W.,Nandety R.S.,Crook A.,Mysore K.S.,Pislariu C.I.,Frugoli J.,Dickstein R.,and Udvardi M.K.,2020,Celebrating 20 years of genetic discove-ries in legume nodulation and symbiotic nitrogen fixation,Plant Cell,32(1):15-41.
Satgé C.,Moreau S.,Sallet E.,Lefort G.,Auriac M.C.,Remblière C.,Cottret L.,Gallardo K.,Noirot C.,Jardinaud M.F.,and Gamas P.,2016,Reprogram-ming of DNA methylation is critical for nodule development in Medicago truncatula,Nat.Plants,2:16166.
Shi Y.,Zhang X.T.,Chang X.J.,Yan M.K.,Zhao H.M.,Qin Y.,and Wang H.F.,2021,Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple,BMC Plant Biol.,21(1):19.
Song Q.X.,Lu X.,Li Q.T.,Chen H.,Hu X.Y.,Ma B.,Zhang W.K.,Chen S.Y.,and Zhang J.S.,2013,Genome-wide analysis of DNA methylation in soybean,Mol.Plant,6(6):1961-1974.
Soyano T.,and Hayashi M.,2014,Transcriptional networks leading to symbiotic nodule organogenesis,Curr.Opin.Plant Biol.,20:146-154.
Soyano T.,Kouchi H.,Hirota A.,and Hayashi M.,2013,Nodule inception directly targets NF-Y subunit genes to regulate essential processes of root nodule develop-ment in Lotus japonicus,PLoS Genet,9(3):e1003352.
Spaink H.P.,2000,Root nodulation and infection factors produced by rhizobial bacteria,Annu.Rev.Micro-biol.,54(1):257-288.
Stroud H.,Du J.M.,Zhong X.H.,Feng S.H.,Johnson L.,Patel D.J.,and Jacobsen S.E.,2014,Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis,Nat.Struct.Mol.Biol.,21(1):64-72.
Suelves M.,Carrió E.,Núňez-álvarez Y.,and Peinado M.A.,2016,DNA methylation dynamics in cellular commitment and differentiation,Brief.Funct.Genomics,15(6):443-453.
Tsyganova A.V.,Brewin N.J.,and Tsyganov V.E.,2021,Structure and development of the legume-rhizobial symbiotic interface in infection threads,Cells,10(5):1050.
Udvardi M.K.,and Day D.A.,1997,Metabolite transport across symbiotic membranes of legume nodules,Annu.Rev.Plant.Physiol.Plant.Mol.Biol.,48:493-523.
Valliyodan B.,Cannon S.B.,Bayer P.E.,Shu S.,Brown A.V.,Ren L.,Jenkins J.,Chung C.Y.L.,Chan T.,Daum C.G.,Plott C.,Hastie A.,Baruch K.,Barry K.W.,Huang W.,Patil G.,Varshney R.K.,Hu H.,Batley J.,Yuan Y.X.,Song Q.J.,Stupar R.M.,Goodstein D.M.,Stacey G.,Lam H.M.,Jackson S.A.,Schmtuz J.,Grimwood J.,Edwards D.,and Nguyen H.T.,2019,Construction and comparison of three reference-quality genome assemblies for soybean,The Plant Journal,100(5):1066-1082.
Wang H.,Beyene G.,Zhai J.,Feng S.,Fahlgren N.,Taylor N.J.,Bart R.,Carrington J.C.,Jacobsen S.E.,and Ausin I.,2015,CG gene body DNA methylation changes and evolution of duplicated genes in cassava,Proceedings of the National Academy of Sciences,112(44):13729-13734.
Wang L.,Shi Y.,Chang X.,Jing S.,Zhang Q.,You C.,Yuan H.,and Wang H.,2019,DNA methylome analysis provides evidence that the expansion of the tea genome is linked to TE bursts,Plant Biotechno-logy Journal,17(4):826-835.
Wu T.Z.,Hu E.Q.,Xu S.B.,Chen M.J.,Guo P.F.,Dai Z.H.,Feng T.Z.,Zhou L.,Tang W.L.,Zhan L.,Fu X.C.,Liu S.S.Bo X.C.,and Yu G.C.,2021,clusterProfiler 4.0:A universal enrichment tool for interpreting omics data,The Innovation:N Y,2(3):100141.
Xi Y.X.,and Li W.,2009,BSMAP:whole genome bisulfite sequence MAPping program,BMC Bioinform.,10(1):1-9.
Xu J.D.,Zhou S.S.,Gong X.Q.,Song Y.,van Nocker S.,Ma F.W.and Guan Q.M.,2018,Single-base methy-lome analysis reveals dynamic epigenomic differences associated with water deficit in apple,Plant Biotech-nol.J.,16(2):672-687.
Zhang H.M.,Lang Z.B.,and Zhu J.K.,2018,Dynamics and function of DNA methylation in plants,Nat.Rev.Mol.Cell Biol.,19(8):489-506.
Zhang X.Y.,Yazaki J.,Sundaresan A.,Cokus S.,Chan S.W.L.Chen H.M.,Henderson I.R.,Shinn P.,Pellegrini M.,Jacobsen S.E.,and Ecker J.R.,2006,Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis,Cell,126(6):1189-1201.
基本信息:
DOI：10.13417/j.gab.041.000115
中图分类号:S565.1
引用信息:
[1]张超,于航,薛亚杰,等.多组学研究揭示DNA甲基化在大豆根瘤发育基因表达动态变化的重要调控作用[J].基因组学与应用生物学,2022,41(01):115-127.DOI:10.13417/j.gab.041.000115.
基金信息:
国家自然科学基金(32160142); 广西科技重大专项(桂科2018-266-Z01); 广西研究生教育创新计划资助项目(YCBZ2021005)共同资助
2021-10-27
2021-10-27
2021-10-27