白菜和甘蓝基因组转座子表达及其对基因调控的潜在影响
收稿日期: 2013-03-11
修回日期: 2013-04-16
网络出版日期: 2013-08-25
基金资助
国家自然科学基金项目(编号：30671119)资助
Transposon expression and potential effects on gene regulation of Brassica rapa and B. oleracea genomes
Received date: 2013-03-11
Revised date: 2013-04-16
Online published: 2013-08-25
转座子或转座元件是大多数真核生物基因组的主要组成成分。甘蓝(Brassica oleracea)基因组比白菜(B. rapa)大主要是转座子的扩增差异造成的。然而, 这两个芸薹属近缘物种转座子表达水平以及对基因的调控和功能的影响目前还不清楚。文章对白菜和甘蓝叶、根、茎3个器官的转录组数据进行了初步分析。结果显示, 转座子的表达量很低, 转录组reads中有1%来自转座子的转录本; 转座子的表达存在器官差异, 且不同类别和家族的转座子表达量相差很大, 相同类别和同一家族的转座子在白菜和甘蓝基因组中的表达活性也不相同。进一步鉴定到转录读出的LTR反转座子, 其与下游基因距离小于2 kb的有41个, 小于100 bp的有9个, 这些LTR的转录读出很可能通过正义或反义的转录本激活或干扰下游基因的表达。同时, 具有转录读出的intact LTR比solo LTR具有更强的读出活性。通过深入分析转座子的插入位点发现, 白菜基因组中转座子插入基因内部的频率比甘蓝基因组中的高; 与反转座子相比, DNA转座子更偏向于插入或保留在基因的内含子当中。这些结果为认识转座子对其他蛋白编码基因的影响提供了基础。
赵美霞 张彪 刘胜毅 马渐新 . 白菜和甘蓝基因组转座子表达及其对基因调控的潜在影响[J]. 遗传, 2013 , 35(8) : 1014 -1022 . DOI: 10.3724/SP.J.1005.2013.01014
Transposons or transposable elements (TEs) are ubiquitous and most abundant DNA components in higher eukaryotes. Recent sequencing of the Brassica rapa and B. oleracea genomes revealed that the amplification of TEs is one of the main factors inducing the difference in genome size. However, the expressions of TEs and the TE effects on gene regulation and functions of these two Brassica diploid species were unclear. Here, we analyzed the RNA sequencing data of leaves, roots, and stems from B. rapa and B. oleracea. Our data showed that overall TEs in either genome expressed at very low levels, and the expression levels of different TE categories and families varied among different organs. Moreover, even for the same TE category or family, the expression activities were distinct between the two Brassica diploids. Forty-one and nine LTR retrotransposons with the transcripts that read into their adjacent sequences have the distances shorter than 2 kb and 100 bp compared to the downstream genes. These LTR retrotransposon readout transcriptions may produce sense or antisense transcripts of nearby genes, with the effects on activating or silencing corresponding genes. Meanwhile, intact LTRs were detected at stronger readout activities than solo LTRs. Of the TEs inserted into genes, the frequencies were ob-served at a higher level in B. rapa than in B. oleracea. In addition, DNA transposons were prone to insert or retain in the intronic regions of genes in either Brassica genomes. These results revealed that the TEs may have potential effects on regulating protein coding genes.
Key words： Brassica rapa; transcriptome; transcription readout; B. oleracea; TE insertion; transposon
[1] Nagaharu U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jap J Bot, 1935, 7: 389-452.
[2] 刘后利. 几种芸薹属油菜的起源和进化. 作物学报, 1984, 10(1): 9-17.
[3] Beilstein MA, Al-Shehbaz IA, Kellogg EA. Brassicaceae phylogeny and trichome evolution. Am J Bot, 2006, 93(4): 607-619.
[4] Finnegan DJ. Eukaryotic transposable elements and genome evolution. Trends Genet, 1989, 5(4): 103-107.
[5] Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH. A unified classification system for eukaryotic transposable elements. Nat Rev Genet, 2007, 8(12): 973-982.
[6] Kapitonov VV, Jurka J. Rolling-circle transposons in eu-karyotes. Proc Natl Acad Sci USA, 2001, 98(15): 8714-8719.
[7] Kashkush K, Feldman M, Levy AA. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet, 2003, 33(1): 102-106.
[8] Kashkush K, Khasdan V. Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics, 2007, 177(4): 1975-1985.
[9] White SE, Habera LF, Wessler SR. Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression. Proc Natl Acad Sci USA, 1994, 91(25): 11792-11796.
[10] Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal en-hancer and an ultraconserved exon are derived from a novel retroposon. Nature, 2006, 441(7089): 87-90.
[11] Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science, 2008, 319(5869): 1527-1530.
[12] Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka T, Wessler SR. Un-expected consequences of a sudden and massive transpo-son amplification on rice gene expression. Nature, 2009, 461(7267): 1130-1134.
[13] 廖鸣娟, 董爱华, 王正栋, 朱睦元. 植物转座子及其在功能基因组学中的应用. 遗传, 2000, 22(5): 345-348.
[14] Zabala G, Vodkin L. A putative autonomous 20.5 kb- CACTA transposon insertion in an F3'H allele identifies a new CACTA transposon subfamily in Glycine max. BMC Plant Biol, 2008, 8: 124.
[15] Xu M, Brar HK, Grosic S, Palmer RG, Bhattacharyya MK. Excision of an active CACTA-Like transposable element from DFR2 causes variegated flowers in soybean
[Glycine max (L.) Merr.]. Genetics, 2010, 184(1): 53-63.
[16] Masson P, Surosky R, Kingsbury JA, Fedoroff NV. Genetic and molecular analysis of the Spm-dependent a-m2 alleles of the maize a locus. Genetics, 1987, 177(1): 117-137.
[17] Martienssen R, Barkan A, Taylor WC, Freeling M. Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize. Genes Dev, 1990, 4(3): 331-343.
[18] Puig M, Cáceres M, Ruiz A. Silencing of a gene adjacent to the breakpoint of a widespread Drosophila inversion by a transposon-induced antisense RNA. Proc Natl Acad Sci USA, 2004, 101(24): 9013-9018.
[19] The Brassica rapa Genome Sequencing Project Consor-tium, Wang XW, Wang HZ, Wang J, Sun RF, Wu J, Liu SY, Bai YQ, Mun JH, Bancroft I, Cheng F, Huang SW, Li XX, Hua W, Wang JY, Wang XY, Freeling M, Pires JC, Pater-son AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong CB, Song C, Duran CF, Peng CF, Geng CY, Koh C, Lin CY, Edwards D, Mu DS, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang HB, Wang HP, Belcram H, Zhou HL, Hirakawa H, Abe H, Guo H, Wang H, Jin HZ, Parkin IA, Batley J, Kim JS, Just J, Li JW, Xu JH, Deng J, Kim JA, Li JP, Yu JY, Meng JL, Wang JP, Min JM, Poula
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