Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (7): 48-55.doi: 10.13560/j.cnki.biotech.bull.1985.2022-1555
Previous Articles Next Articles
Received:
2022-12-27
Online:
2023-07-26
Published:
2023-08-17
Contact:
LI Ying
E-mail:liying@icbr.ac.cn
LI Ying, YUE Xiang-hua. Application of DNA Methylation in Interpreting Natural Variation in Moso Bamboo[J]. Biotechnology Bulletin, 2023, 39(7): 48-55.
[1] | 郑世慧, 刘广路, 岳祥华, 等. 中国竹资源培育现状与增产潜力[J]. 世界竹藤通讯, 2022, 20(5): 75-80. |
Zheng SH, Liu GL, Yue XH, et al. Current situation of bamboo resource cultivation and growth potentials in its production in China[J]. World Bamboo Rattan, 2022, 20(5): 75-80. | |
[2] | 国家林业和草原局编制. 中国森林资源报告-2014-2018[M]. 北京: 中国林业出版社, 2019. |
National Forestry and Grassland Administrator. China forest resource report[M]. Beijing: China Forestry Publishing House, 2019. | |
[3] | 高志民, 杨丽, 赵韩生, 等. 竹类植物基因组学发展的机遇与挑战[J]. 世界竹藤通讯, 2013, 11(6): 1-6. |
Gao ZM, Yang L, Zhao HS, et al. Progress in bamboo genomics research and its challenges with opportunities[J]. World Bamboo Rattan, 2013, 11(6): 1-6. | |
[4] | 谢云胜. 毛竹生物学特性及造林技术[J]. 现代农业科技, 2018(10): 168-169. |
Xie YS. Biological characteristics and afferestation techniques of Phyllostachys pubescens[J]. Mod Agric Sci Technol, 2018(10): 168-169. | |
[5] | 杨光耀, 黎祖尧, 杜天真, 等. 毛竹新栽培变种——厚皮毛竹[J]. 江西农业大学学报, 1997, 19(4): 97-98. |
Yang GY, Li ZY, Du TZ, et al. A new cultivated variety of moso bamboo[J]. Acta Agric Univ Jiangxiensis, 1997, 19(4): 97-98. | |
[6] | 江泽慧. 中国竹类植物图鉴[M]. 北京: 科学出版社, 2020. |
Jiang ZH. Illustrations of bamboos in China[M]. Beijing: Science Press, 2020. | |
[7] | 郭雯, 漆良华, 雷刚, 等. 毛竹及其变种叶片化学计量与养分重吸收效率[J]. 南京林业大学学报: 自然科学版, 2021, 45(1): 79-85. |
Guo W, Qi LH, Lei G, et al. Leaf stoichiometry and nutrient reabsorption efficiency of Phyllostachys edulis and its varieties[J]. J Nanjing For Univ Nat Sci Ed, 2021, 45(1): 79-85. | |
[8] | 龙春玲, 刘腾飞, 于芬, 等. 厚壁毛竹与毛竹叶片的光学解剖结构比较分析[J]. 安徽农业大学学报, 2015, 42(1): 39-44. |
Long CL, Liu TF, Yu F, et al. Comparative anatomy of leaves between Phyllostachys edulis ‘Pachyloen’ and Phyllostachys edulis[J]. J Anhui Agric Univ, 2015, 42(1): 39-44. | |
[9] | 魏强, 高志鹏, 陈铭, 等. 厚壁毛竹与毛竹地下茎发育规律的比较[J]. 南京林业大学学报: 自然科学版, 2018, 42(2): 197-201. |
Wei Q, Gao ZP, Chen M, et al. Morphological and cellular characterization of rhizome development of Phyllostachys edulis‘Pachyloen’ and Phyllostachys edulis[J]. J Nanjing For Univ Nat Sci Ed, 2018, 42(2): 197-201. | |
[10] | 张莹, 田埂, 路慧萍, 等. 厚壁毛竹六个节气笋芽发育的转录组分析[J]. 江西农业大学学报, 2015, 37(3): 466-474. |
Zhang Y, Tian G, Lu HP, et al. Transcriptome characterization of Phyllostachys edulis‘pachyloen’Shoots in different solar terms[J]. Acta Agric Univ Jiangxiensis, 2015, 37(3): 466-474. | |
[11] | 黄红兰. 运用EST、SSR分子标记分析厚壁毛竹的遗传变异[D]. 南昌: 江西农业大学, 2007. |
Huang HL. Analysis of genetic variation of Phyllostachys pubescens by EST and SSR molecular markers[D]. Nanchang: Jiangxi Agricultural University, 2007. | |
[12] | 阮晓赛. 毛竹种源及栽培变种遗传变异的AFLP和ISSR分析[D]. 杭州: 浙江林学院, 2008. |
Ruan XS. Assessment of AFLP and ISSR-based genetic variations of provenances and cultivars of Phyllostachys edulis[D]. Hangzhou: Zhejiang A & F University, 2008. | |
[13] |
Wei Q, Jiao C, Guo L, et al. Exploring key cellular processes and candidate genes regulating the primary thickening growth of Moso underground shoots[J]. New Phytol, 2017, 214(1): 81-96.
doi: 10.1111/nph.14284 pmid: 27859288 |
[14] |
Li Y, Zhang DQ, Zhang SQ, et al. Transcriptome and miRNAome analysis reveals components regulating tissue differentiation of bamboo shoots[J]. Plant Physiol, 2022, 188(4): 2182-2198.
doi: 10.1093/plphys/kiac018 pmid: 35157078 |
[15] |
Ziller MJ, Gu HC, Müller F, et al. Charting a dynamic DNA methylation landscape of the human genome[J]. Nature, 2013, 500(7463): 477-481.
doi: 10.1038/nature12433 |
[16] |
Wu H, Zhang Y. Reversing DNA methylation: mechanisms, genomics, and biological functions[J]. Cell, 2014, 156(1/2): 45-68.
doi: 10.1016/j.cell.2013.12.019 URL |
[17] |
Saze H, Tsugane K, Kanno T, et al. DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation[J]. Plant Cell Physiol, 2012, 53(5): 766-784.
doi: 10.1093/pcp/pcs008 pmid: 22302712 |
[18] |
Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals[J]. Nat Genet, 2003, 33 Suppl: 245-254.
pmid: 12610534 |
[19] |
Gao LH, Diarso M, Zhang A, et al. Heritable alteration of DNA methylation induced by whole-chromosome aneuploidy in wheat[J]. New Phytol, 2016, 209(1): 364-375.
doi: 10.1111/nph.13595 pmid: 26295562 |
[20] | Halter T, Wang JY, Amesefe D, et al. The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions[J]. eLife, 2021, 10: e62994. |
[21] |
Yang LP, Lang CJ, Wu YJ, et al. ROS1-mediated decrease in DNA methylation and increase in expression of defense genes and stress response genes in Arabidopsis thaliana due to abiotic stresses[J]. BMC Plant Biol, 2022, 22(1): 104.
doi: 10.1186/s12870-022-03473-4 |
[22] |
Zhu JH, Kapoor A, Sridhar VV, et al. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis[J]. Curr Biol, 2007, 17(1): 54-59.
doi: 10.1016/j.cub.2006.10.059 URL |
[23] |
Guo SS, Zheng YY, Meng DM, et al. DNA and coding/non-coding RNA methylation analysis provide insights into tomato fruit ripening[J]. Plant J, 2022, 112(2): 399-413.
doi: 10.1111/tpj.v112.2 URL |
[24] |
Ngernprasirtsiri J, Kobayashi H, Akazawa T. DNA methylation occurred around lowly expressed genes of plastid DNA during tomato fruit development[J]. Plant Physiol, 1988, 88(1): 16-20.
doi: 10.1104/pp.88.1.16 pmid: 16666259 |
[25] |
Niu SH, Li J, Bo WH, et al. The Chinese pine genome and methylome unveil key features of conifer evolution[J]. Cell, 2022, 185(1): 204-217.e14.
doi: 10.1016/j.cell.2021.12.006 URL |
[26] |
He L, Huang H, Bradai M, et al. DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development[J]. Nat Commun, 2022, 13(1): 1335.
doi: 10.1038/s41467-022-28940-2 |
[27] | 王瑞娴, 徐建红. 基因组DNA甲基化及组蛋白甲基化[J]. 遗传, 2014, 36(3): 191-199. |
Wang RX, Xu JH. Genomic DNA methylation and histone methylation[J]. Hereditas, 2014, 36(3): 191-199. | |
[28] |
张淼, 杨露露, 贾岩龙, 等. DNA甲基化和组蛋白甲基化修饰的表观遗传调控作用研究进展[J]. 生物技术通报, 2022, 38(7): 23-30.
doi: 10.13560/j.cnki.biotech.bull.1985.2021-1054 |
Zhang M, Yang LL, Jia YL, et al. Research progress in the roles of DNA and histone methylations in epigenetic regulation[J]. Biotechnol Bull, 2022, 38(7): 23-30.
doi: 10.13560/j.cnki.biotech.bull.1985.2021-1054 |
|
[29] |
Zhang HM, Lang ZB, Zhu JK. Dynamics and function of DNA methylation in plants[J]. Nat Rev Mol Cell Biol, 2018, 19(8): 489-506.
doi: 10.1038/s41580-018-0016-z |
[30] | 甄艳, 郑秀化, 施季森. 植物细胞分化过程中DNA甲基化及组蛋白修饰调控研究[J]. 基因组学与应用生物学, 2016, 35(11): 3194-3198. |
Zhen Y, Zheng XH, Shi JS. DNA methylation and histone modification regulation of plant celluar differentiation[J]. Genom Appl Biol, 2016, 35(11): 3194-3198. | |
[31] |
Niazi F, Valadkhan S. Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs[J]. RNA, 2012, 18(4): 825-843.
doi: 10.1261/rna.029520.111 pmid: 22361292 |
[32] |
Di C, Yuan JP, Wu Y, et al. Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features[J]. Plant J, 2014, 80(5): 848-861.
doi: 10.1111/tpj.2014.80.issue-5 URL |
[33] |
Ding YL, Tang Y, Kwok CK, et al. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features[J]. Nature, 2014, 505(7485): 696-700.
doi: 10.1038/nature12756 |
[34] |
Song YP, Tian M, Ci D, et al. Methylation of microRNA genes regulates gene expression in bisexual flower development in andromonoecious poplar[J]. J Exp Bot, 2015, 66(7): 1891-1905.
doi: 10.1093/jxb/eru531 pmid: 25617468 |
[35] |
Jones PA. Functions of DNA methylation: Islands, start sites, gene bodies and beyond[J]. Nat Rev Genet, 2012, 13(7): 484-492.
doi: 10.1038/nrg3230 pmid: 22641018 |
[36] |
Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals[J]. Nat Rev Genet, 2010, 11(3): 204-220.
doi: 10.1038/nrg2719 pmid: 20142834 |
[37] |
Cubas P, Vincent C, Coen E. An epigenetic mutation responsible for natural variation in floral symmetry[J]. Nature, 1999, 401(6749): 157-161.
doi: 10.1038/43657 |
[38] |
Ong-Abdullah M, Ordway JM, Jiang N, et al. Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm[J]. Nature, 2015, 525(7570): 533-537.
doi: 10.1038/nature15365 |
[39] | 王子成, 聂丽娟, 何艳霞. 离体条件下5-氮杂胞嘧啶核苷对菊花DNA甲基化和表型性状的影响[J]. 园艺学报, 2009, 36(12): 1783-1790. |
Wang ZC, Nie LJ, He YX. The effect of 5-azacytidine to the DNA methylation and morphogenesis character of Chrysanthemum during in vitro growth[J]. Acta Hortic Sin, 2009, 36(12): 1783-1790. | |
[40] |
Teyssier E, Bernacchia G, Maury S, et al. Tissue dependent variations of DNA methylation and endoreduplication levels during tomato fruit development and ripening[J]. Planta, 2008, 228(3): 391-399.
doi: 10.1007/s00425-008-0743-z pmid: 18488247 |
[41] |
Walker J, Gao HB, Zhang JY, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis[J]. Nat Genet, 2018, 50(1): 130-137.
doi: 10.1038/s41588-017-0008-5 pmid: 29255257 |
[42] |
Manning K, Tör M, Poole M, et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening[J]. Nat Genet, 2006, 38(8): 948-952.
doi: 10.1038/ng1841 pmid: 16832354 |
[43] |
Wang L, Xie JH, Hu JT, et al. Comparative epigenomics reveals evolution of duplicated genes in potato and tomato[J]. Plant J, 2018, 93(3): 460-471.
doi: 10.1111/tpj.2018.93.issue-3 URL |
[44] |
Johannes F, Schmitz RJ. Spontaneous epimutations in plants[J]. New Phytol, 2019, 221(3): 1253-1259.
doi: 10.1111/nph.15434 pmid: 30216456 |
[45] |
You Y, Sawikowska A, Neumann M, et al. Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering[J]. Nat Commun, 2017, 8: 15120.
doi: 10.1038/ncomms15120 URL |
[46] |
Liu GL, Yang WY, Zhang XJ, et al. Cystathionine beta-lyase is crucial for embryo patterning and the maintenance of root stem cell niche in Arabidopsis[J]. Plant J, 2019, 99(3): 536-555.
doi: 10.1111/tpj.v99.3 URL |
[47] |
Hossain MS, Kawakatsu T, Kim KD, et al. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs[J]. New Phytol, 2017, 214(2): 808-819.
doi: 10.1111/nph.14421 pmid: 28106918 |
[48] |
Zicola J, Liu LY, Tänzler P, et al. Targeted DNA methylation represses two enhancers of FLOWERING LOCUS T in Arabidopsis thaliana[J]. Nat Plants, 2019, 5(3): 300-307.
doi: 10.1038/s41477-019-0375-2 pmid: 30833712 |
[49] |
Miyashima S, Roszak P, Sevilem I, et al. Mobile PEAR transcription factors integrate positional cues to prime cambial growth[J]. Nature, 2019, 565(7740): 490-494.
doi: 10.1038/s41586-018-0839-y |
[50] |
Peng ZH, Lu Y, Li LB, et al. The draft genome of the fast-growing non-timber forest species moso bamboo(Phyllostachys heterocycla)[J]. Nat Genet, 2013, 45(4): 456-461.
doi: 10.1038/ng.2569 |
[51] | Zhao HS, Gao ZM, Wang L, et al. Chromosome-level reference genome and alternative splicing atlas of moso bamboo(Phyllostachys edulis)[J]. GigaScience, 2018, 7(10): giy115. |
[52] | 谢佳敏, 周明兵. 毛竹Mariner-like element自主转座子的鉴定与生物信息学分析[J]. 林业科学, 2022, 58(1): 175-184. |
Xie JM, Zhou MB. Identification and bioinformatics analysis of mariner-like element autonomous transposons in Phyllostachys edulis[J]. Sci Silvae Sin, 2022, 58(1): 175-184. | |
[53] | 虞莹玉, 汤定钦, 周明兵. 毛竹微型颠倒重复序列的鉴定及分子标记开发[J]. 中国细胞生物学学报, 2021, 43(2): 273-283. |
Yu YY, Tang DQ, Zhou MB. Identification of miniature inverted-repeat transposable elements and development of molecular markers in Phyllostachys edulis[J]. Chin J Cell Biol, 2021, 43(2): 273-283. | |
[54] | 蒋政勤, 周明兵, 郑浩, 等. 毛竹Phyllostachys edulis retrotransposon 7(PHRE7) 转座子的克隆与鉴定[J]. 浙江农林大学学报, 2019, 36(5): 917-927. |
Jiang ZQ, Zhou MB, Zheng H, et al. Cloning and characterization of a long terminal repeat retrotransposon(Phyllostachys edulis retrotransposon 7)in Phyllostachys edulis[J]. J Zhejiang A & F Univ, 2019, 36(5): 917-927. | |
[55] |
Liu ZH, Tang SJ, Hu WT, et al. Precise editing of methylated cytosine in Arabidopsis thaliana using a human APOBEC3Bctd-Cas9 fusion[J]. Sci China Life Sci, 2022, 65(1): 219-222.
doi: 10.1007/s11427-021-1970-x |
[56] |
Tang SJ, Yang C, Wang D, et al. Targeted DNA demethylation produces heritable epialleles in rice[J]. Sci China Life Sci, 2022, 65(4): 753-756.
doi: 10.1007/s11427-021-1974-7 |
[57] | 卢雅薇, 沈文涛, 唐清杰, 等. 植物病毒载体系统研究进展[J]. 遗传, 2007, 29(1): 29-36. |
Lu YW, Shen WT, Tang QJ, et al. Recent advances in plant virus vector systems[J]. Hereditas, 2007, 29(1): 29-36. | |
[58] |
孙敬爽, 胡瑞阳, 郑广顺, 等. 纳米载体介导的植物遗传转化研究现状和前景[J]. 生物技术通报, 2021, 37(2): 162-173.
doi: 10.13560/j.cnki.biotech.bull.1985.2020-0521 |
Sun JS, Hu RY, Zheng GS, et al. Research progress and prospect of plant genetic transformation mediated by nano-gene vector[J]. Biotechnol Bull, 2021, 37(2): 162-173. |
[1] | ZHANG Miao, YANG Lu-lu, JIA Yan-long, WANG Tian-yun. Research Progress in the Roles of DNA and Histone Methylations in Epigenetic Regulation [J]. Biotechnology Bulletin, 2022, 38(7): 23-30. |
[2] | WANG Chen-chen, ZHANG Fan-li, CHEN Pei-qi, WENG Si-yao, WANG Hui-fang, CUI Xiao-juan. Research Progress in the Structural and Functional Analysis of Mammalian DNA Methyltransferase DNMT1 and DNMT3 [J]. Biotechnology Bulletin, 2022, 38(7): 31-39. |
[3] | WANG Jian-yong, ZOU Yong-mei, GE Yan-bin, WANG Kai, XI Meng-li. Advance on Epigenetic Modification During Plant Callus Induction [J]. Biotechnology Bulletin, 2021, 37(8): 253-262. |
[4] | TANG De-ping, YAO Hui-hui, TANG Jin-zhou, MAO Ai-hong. Mutual Regulation of microRNAs and Epigenetics in Human Cancers [J]. Biotechnology Bulletin, 2020, 36(8): 194-200. |
[5] | LIU Zhi-min, YANG Zhi-yi, JI Feng-dan, MEI Zhi-chao, YU Jia-hui, XIE Li-nan. Research Progress of Plant DNA Methylation Under Abiotic Stress [J]. Biotechnology Bulletin, 2020, 36(11): 122-132. |
[6] | JIANG Rui, LÜ Ke-nao, PAN Xue-feng, CUI Xin-xia, SHEN Shi-gang, DING Liang. Current Status and Challenges of Epigenetic Drug Research and Development [J]. Biotechnology Bulletin, 2019, 35(8): 213-225. |
[7] | XUE Jing-jing, CHEN Song-bi. Variation Analysis of DNA Methylation in Different Development Stages of Cassava [J]. Biotechnology Bulletin, 2018, 34(5): 117-123. |
[8] | AO Xu-dong SA Ru-la WANG Jie WANG Hui-min YU Hai-quan. Expression of AID and Dynamic Changes of Its DNA Methylation in Regulation Region During Bovine Early Embryonic Development [J]. Biotechnology Bulletin, 2016, 32(7): 242-249. |
[9] | ZHAO Qian, WANG Wei ,SUN Ye-qing. Review on the Correlation between DNA Methylation and Gene Expression in Plant [J]. Biotechnology Bulletin, 2016, 32(4): 16-23. |
[10] | YANG Wei,PAN Yu,SU Cheng-gang,ZHANG Xing-guo,LI Jin-hua. Analysis of the DNA Methylation of SlGLD1 Regulated by JMJ524 in Tomato [J]. Biotechnology Bulletin, 2016, 32(12): 79-85. |
[11] | ZHAO Jing, LI Nan, WU Ru, YANG Zhan-wei, HU Wen-bing, WANG Wen-jun. Research Advance on the Effect of Food Functional Components on Animal Genomic DNA Methylation [J]. Biotechnology Bulletin, 2016, 32(1): 15-19. |
[12] | Liu Ying, Tang Yongzheng, Gao Li. Research Progress on Invertebrates DNA Methylation [J]. Biotechnology Bulletin, 2015, 31(8): 17-23. |
[13] | Ma Langlang, Liang Zhenjuan, Xian Xin, Luo Shiwen, Li Qingchao, Liang Qianyun. Detection Methods of Genome-wide DNA Methylation Level Based on High-throughput Sequencing Technology [J]. Biotechnology Bulletin, 2015, 31(7): 45-50. |
[14] | Jiang Nan, Pan Xuefeng. The Developments of Epigenetics and Epigenetics-based Modern Biomedicine and Pharmaceutics [J]. Biotechnology Bulletin, 2015, 31(4): 105-119. |
[15] | Huang Xinfeng, Ye Jinbo, Liu Jianjun. Application of Mass Spectrometric Technology in DNA Methylation Study [J]. Biotechnology Bulletin, 2015, 31(11): 112-120. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||