| 265 | 1 | 28 |
| 下载次数 | 被引频次 | 阅读次数 |
组蛋白修饰是表观遗传学领域中一种重要的修饰方式,可经多种组蛋白修饰酶类催化产生。为了研究谷子(Setaria italica L.)基因组中组蛋白修饰酶类基因的特征,本研究利用比较基因组学的方法,以水稻(Oryza sativa)基因组注释信息为参考,对谷子的组蛋白修饰酶类基因进行挖掘,共发现80个谷子组蛋白修饰酶类相关基因,并根据组蛋白乙酰化酶/去乙酰化酶、甲基化酶/去甲基化酶绘制系统进化树,每部分都能根据其行使的功能聚类。组蛋白修饰酶类基因的鉴定是阐明不同生物表观遗传调控机制的重要步骤。本研究为详细探讨这些基因在谷子表观遗传修饰中的功能和作用提供初步的理论依据和参考。
Abstract：Histone modification is an important epigenetic mechanism, which can be catalyzed by a variety of histone modification enzymes. In order to study the characteristics of histone modification-related genes in foxtail millet(Setaria italic L.) genome, genes were excavated in foxtail millet by comparative genomics with reference information of rice(Oryza sativa) genome. We got 80 genes related to histone modification enzymes in foxtail millet,and phy-logenetic trees were constructed according to histone acetylase/deacetylase, and methylase/demethylase,each part of which could be clustered according to their function. Identification of histone modification-related genes is an important step in elucidating the epigenetic regulation mechanism in different organisms. This study provided a preliminary theoretical basis and reference for the further study of functions and roles of these epigenetic modification-related genes in foxtail millet.
Banerjee A.,and Roychoudhury A.,2018,The gymnastics of epigenomics in rice,Plant Cell.Rep.,37(1):25-49.
Berr A.,Shafiq S.,and Shen W.H.,2011,Histone modifications in transcriptional activation during plant development,Biochim.Biophys.Acta.,1809(10):567-576.
Bird A.P.,1986,CpG-rich islands and the function of DNA methylation,Nature,321(6067):209-213.
Chen X.S.,Hu Y.F.,and Zhou D.X.,2011,Epigenetic gene regulation by plant Jumonji group of histone demethylase,Biochim.Biophys Acta,1809(8):421-426.
Chowrasia S.,Pand A.K.,Rawal H.C.,Kaur H.,and Mondal T.K.,2018,Identification of jumonjiC domain containing gene family among the Oryza species and their expression analysis in FL478,a salt tolerant rice genotype,Plant Physiol.Biochem.,130:43-53.
Deng X.,Song X.W.,Wei L.Y.,Liu C.Y.,and Cao X.F.,2016,Epigenetic regulation and epigenomic landscape in rice,Natl.Sci.Rev.,3(3):309-327.
Dong Y.R.,Du J.X.,Chen C.J.,Zhao D.X.,and Wang Z.H.,2016,Histone deacetylases and its roles in plants,Shengwu Jishu Tongbao (Biotechnology Bulletin),32(9):44-49.(董亚茹,杜建勋,陈传杰,赵东晓,王照红,2016,组蛋白去乙酰化酶(HDACs)及其在植物中的作用,生物技术通报,32(9):44-49.)
Fang H.,Liu X.,Thorn G.,Duan J.,and Tian L.N.,2014,Expression analysis of histone acetyltransferases in rice under drought stress,Biochem.Biophys.Res.Commun.,443(2):400-405.
Gendler K.,Paulsen T.,and Napoli C.,2008,ChromDB:the chromatin database,Nucleic Acids Res.,36(D):298-302.
Hu Y.F.,Qin F.J.,Huang L.M.,Sun Q.W.,Li C.,Zhao Y.,and Zhou D.X.,2009,Rice histone deacetylase genes display specific expression patterns and developmental functions,Biochem.Biophys.Res.Commun.,388(2):266-271.
Huang L.M.,Sun Q.W.,Qin F.J.,Li C.,Zhao Y.,and Zhou D.X.,2007,Down-regulation of a SILENT INFORMATION RE-GULATOR2-related histone deacetylase gene,Os SRT1,induces DNA fragmentation and cell death in rice,Plant Physiol.,144(3):1508-1519.
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.
Jia G.Q.,and Diao X.M.,2017,Current status and perspectives of researches on foxtail millet (Setaria italica (L.) P.Beauv.):a potential model of plant functional genomics studies,Shengming Kexue (Chinese Bulletin of Life Sciences),29(3):292-301.(贾冠清,刁现民,2017,谷子(Setaria italica (L.) P.Beauv.)作为功能基因组研究模式植物的发展现状及趋势,生命科学,29(3):292-301.)
Jiang P.F.,Wang S.L.,Ikram A.U.,Xu Z.T.,Jiang H.Y.,Cheng B.J.,and Ding Y.,2018a,SDG721 and SDG705 are required for rice growth,J.Integr.Plant Biol.,60(7):530-535.
Jiang P.F.,Wang S.L.,Zheng H.,Li H.,Zhang F.,Su Y.H.,Xu Z.T.,Lin H.Y.,Qian Q.,and Ding Y.,2018b,SIP1 participates in regulation of flowering time in rice by recruiting Os Trx1 to Ehd1,New Phytol.,219(1):422-435.
Kuroki S.,Okashita N.,Baba S.,Maeda R.,Miyawaki S.,Yano M.,Yamaguchi M.,Kitano S.,Miyachi H.,Itoh A.,Yoshida M.,and Tachibana M.,2017,Rescuing the aberrant sex development of H3K9 demethylase Jmjd1a-deficient mice by modulating H3K9 methylation balance,PLoS Genet.,13(9):e1007034.
Li D.D.,Zhang M.,and Kong Q.S.,2019,Histone deacetylases and schizophrenia,Jining Yixueyuan Xuebao (Journal of Jining Medical University),42(1):37-41.(李丹丹,张萌,孔庆胜,2019,组蛋白去乙酰化酶与精神分裂症,济宁医学院学报,42(1):37-41.)
Liu B.,Wei G.,Shi J.L.,Jin J.,Shen T.,Ni T.,Shen W.H.,Yu Y.,and Dong A.W.,2016,SET DOMAIN GROUP 708,a histone H3 lysine 36-specific methyltransferase,controls flowering time in rice (Oryza sativa),New Phytol.,210 (2):577-588.
Liu K.P.,Yu Y.,Dong A.W.,and Shen W.H.,2017,SET DOM-AIN GROUP701 encodes a H3K4-methytransferase and regulates multiple key processes of rice plant development,New Phytol.,215(2):609-623.
Liu X.,Luo M.,Zhang W.,Zhao J.H.,Zhang J.X.,Wu K.Q.,Tian L.N.,and Duan J.,2012,Histone acetyltransferases in rice(Oryza sativa L.):phylogenetic analysis,subcellular localization and expression,BMC Plant Biol.,12(1):145.
Lkhagva B.,Kao Y.H.,Chen Y.C.,Chao T.F.,Chen S.A.,and Chen Y.J.,2016,Targeting histone deacetylases:a novel therapeutic strategy for atrial fibrillation,Eur.J.Pharmacol.,781:250-257.
Ma H.,Wang Y.F.,and Li W.,2014,Advance in foxtail millet mutant,Guangdong Nongye Kexue (Guangdong Agricultural Sciences),41(4):23-27.(马宏,王永芳,李伟,2014,谷子突变体研究进展,广东农业科学,41(4):23-27.)
Ma X.J.,LüS.B.,Zhang C.,and Yang C.P.,2013,Histone deacetylases and their functions in plants,Plant Cell Rep.,32(4):465-478.
Ng W.K.,Wang T.,Chandrasekharan M.B.,Aramayo R.,Kertbundit S.,and Hall T.C.,2007,Plant SET domain-containing proteins:structure,function and regulation,Biochim.Biophys.Acta,1769(5-6):316-329.
Oki M.,Aihara H.,and Ito T.,2007,Role of histone phosphorylation in chromatin dynamics and its implications in diseases,Subcell.Biochem.,41:319-336.
Pikaard C.S.,and Scheid O.M.,2014,Epigenetic regulation in plants,Cold Spring Harb Perspect.Biol.,6(12):a019315.
Qin F.J.,Sun Q.W.,Huang L.M.,Chen X.S.,and Zhou D.X.,2010,Rice SUVH histone methyltransferase genes display specific functions in chromatin modification and retrotransposon repression,Mol.Plant,3(4):773-782.
Reik W.,2007,Stability and flexibility of epigenetic gene regula tion in mammalian development,Nature,447(7143):425-432.
Soares L.M.,He P.C.,Chun Y.,Suh H.,Kim T.S.,and Buratowski S.,2017,Determinants of histone H3K4 methylation patterns,Mol.Cell,68(4):773-785.
Song X.J.,Kuroha T.,Ayanoa M.,Furuta T.,Nagai K.,Komeda N.,Segami S.,Miura K.,Ogawa D.,Kamura T.,Suzuki T.,Higashiyama T.,Yamasaki M.,Mori H.,Inukai Y.,Wu J.,Kitano H.,Sakakibara H.,Jacobsen S.E.,and Ashikari M.,2015,Rare allele of a previously unidentified histone H4acetyltransferase enhances grain weight,yield,and plant biomass in rice,Proc.Natl.Acad.Sci.USA,112(1):76-81.
Sui P.F.,Shi J.L.,Gao X.Y.,Shen W.H.,and Dong A.W.,2013,H3K36 methylation is involved in promoting rice flowering,Mol.Plant,6(3):975-977.
Sun C.H.,Fang J.,Zhao T.L.,Xu B.,Zhang F.T.,Liu L.C.,Tang J.Y.,Zhang G.F.,Deng X.J.,Chen F.,Qian Q.,Cao X.F.,and Chu C.C.,2012,The histone methyltransferase SDG724 mediates H3K36me2/3 deposition at MADS50 and RFT1 and promotes flowering in rice,Plant Cell,24(8):3235-3247.
Sun Q.,and Zhou D.X.,2008,Rice jmj C domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development,Proc.Natl.Acad.Sci.USA,105 (36):13679-13684.
Torres-Padilla M.E.,Parfitt D.E.,Kouzarides T.,and ZernickaGoetz M.,2007,Histone arginine methylation regulates pluripotency in the early mouse embryo,Nature,445 (7124):214-218.
Wagner E.J.,and Carpenter P.B.,2012,Understanding the language of Lys36 methylation at histone H3,Nat.Rev.Mol.Cell Biol.,13(2):115-126.
Yoon S.,and Eom G.H.,2016,HDAC and HDAC inhibitor:from cancer to cardiovascular diseases,Chonnam Med.J.,52(1):1-11.
Zhang G.Y.,Liu X.,Quan Z.W.,Cheng S.F.,Xu X.,Pan S.K.,Xie M.,Zeng P.,Yue Z.,Wang W.L.,Tao Y.,Bian C.,Han C.L.,Xia Q.J.,Peng X.H.,Cao R.,Yang X.H.,Zhan D.L.,Hu J.C.,Zhang Y.X.,Li H.N.,Li H.,Li N.,Wang J.Y.,Wang C.C.,Wang R.Y.,Guo T.,Cai Y.J.,Liu C.Z.,Xiang H.T.,Shi Q.X.,Huang P.,Chen Q.C.,Li Y.R.,Wang J.,Zhao Z.H.,and Wang J.,2012,Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential,Nat.Biotechnol.,30(6):549-554.
Zhao J.H.,Li M.Z.,Gu D.C.,Liu X.C.,Zhang J.X.,Wu K.L.,Zhang X.H.,Teixeira da Silva J.A.,and Duan J.,2016,Involvement of rice histone deacetylase HDA705 in seed germination and in response to ABA and abiotic stresses,Biochem.Biophys.Res.Commun.,470(2):439-444.
Zhao C.,Li B.,Zhang Y.X.,Xue M.M.,Wang J.J.,Wang Y.X.,and Wang H.Y.,2019,Evolution and expression analysis of genes associated with DNA methylation modification of foxtail millet (Setaria italica),Fenzi Zhiwu Yuzhong (Molecular Plant Breeding),17(10):3115-3124.(赵宸,李博,张雨欣,薛敏敏,王晶晶,王宇昕,王红艳,2019,谷子(Setaria italica) DNA甲基化修饰相关酶类基因的进化及表达分析,分子植物育种,17(10):3115-3124.)
Zheng B.L.,and Chen X.M.,2011,Dynamics of histone H3 lysine 27 trimethylation in plant development,Curr.Opin.Plant Biol.,14(2):123-129.
基本信息:
DOI：10.13417/j.gab.040.001725
中图分类号:S515
引用信息:
[1]李博,邓欣,张司雯,等.谷子(Setaria italica L.)组蛋白修饰酶类基因的挖掘[J].基因组学与应用生物学,2021,40(04):1725-1736.DOI:10.13417/j.gab.040.001725.
基金信息:
辽宁省自然科学基金指导项目(20180550686); 辽宁省教育厅科学研究经费项目(LJC201909); 辽宁大学青年科研基金项目(LDQN2019011)共同资助
2019-12-19
2019-12-19
2019-12-19