玉米苗期干旱胁迫下可变剪接及其调控因子的研究
|
摘要
本文以对干旱胁迫敏感的Ye478(选自8112和5003的二环系,我国玉米单交种推广的优良自交系,Ye478)和耐早的H21(选自美国先锋种子公司杂交种P78599,我国西北干旱和半干旱地区骨干系,H21)玉米自交系为材料,在苗期进行干旱胁迫处理,对利用solexa高通量测序获得的转录组数据进行基因表达的可变剪接分析,通过对比干旱胁迫与正常对照植株基因可变剪接方式与程度的差异,了解发生可变剪接事件的基因参与的生物学途经；通过反转录PCR等手段扩增出一些基因的部分剪接变体；通过高通量测序分析和qRT-PCR分析了解玉米可变剪接重要的调控者SR蛋白基因家族干旱胁迫下表达规律,筛选干旱胁迫相关的候选SR成员,揭示其与玉米干旱胁迫应答基因表达调控的内在联系。通过对比我们发现：
1.总体上,干旱逆境会诱导部分基因的可变剪接,并通过可变剪接反映玉米的受旱程度。干旱逆境会对植物的各种生理状态有所影响,植物体内的各种与水分相关的生理生化反应会发生改变。由于Ye478的耐旱能力远低于H21,所以其在干旱胁迫下发生的可变剪接数目远多于耐旱品系H21。受干旱程度的影响,植物可变剪接数目会出现上升受环境逆境影响植物会增加基因组的多样性大大增加此外,可变剪接多样性的改变一定程度上反映了玉米受胁迫影响的程度；耐早品系H21在干旱条件下所发生的可变剪接改变要小于Ye478,由于可变剪接可以影响基因转录后的命运,这可以理解为Ye478受干旱影响更严重,关闭了大量非生活所必需的基因的表达。
2.可变剪接对玉米干旱逆境适应性有一定的影响。H21和Ye478两个品系在干旱逆境下可变剪接的差异表明：部分基因的可变剪接可以增加玉米的耐旱能力在H21对照和Ye478、H21干旱胁迫下发生类似可变剪接的基因,可能与玉米干旱适应性相关。
3.在所有两个玉米自交系中,发生的可变剪接的基因大部分在干旱和非干旱胁迫下均发生可变剪接。H21中2/3和Ye478中4/5在正常水分条件下发生可变剪接的基因在干旱胁迫下仍然发生可变剪接。由干旱诱导而发生可变剪接的基因占Ye478和H21干旱中所有发生可变剪接的基因中1/3左右,表明一部分基因可变剪接是玉米行使生理功能所必需的,不会受干旱等环境因素的影响。
4.在干旱胁迫下发生可变剪接的基因多数集中在NTP结合、糖代谢以及蛋白合成转运等相关途径中这表明,玉米干旱胁迫下发生可变剪接的基因主要为能量和蛋白代谢相关基因。这表明蛋白和能量的代谢是玉米在干旱逆境下最主要的生理途径,其可能与玉米在干旱胁迫下抗旱性相关的重要通路。
5.镁离子结合蛋白是H21在干旱胁迫特异发生可变剪接的重要蛋白成员,这表明镁离子结合蛋白的可变剪接可能与H21的干旱抗逆性相关。
6.ABA信号转导通路是玉米干旱胁迫下重要的通路,是触发植物逆境胁迫反应主要传递者。ABA诱导蛋白对植物逆境胁迫具有重要作用。ABA诱导蛋白,不论在H21还是在Ye478中都由于干旱而发生大量的可变剪接。多种转录因子和在H21和Ye478干旱条件下出现相似的可变剪接变化。此外R蛋白及部分剪接因子家族也发生可变剪接,这些可变剪接已被实验验证。
7.SR蛋白是玉米中最重要的剪接因子之一,大量SR剪接因子表达量的总体趋势与全基因组可变剪接事件变化的趋势基本一致；可以用大量SR剪接因子的表达量的改变趋势来反应全基因组可变剪接的改变,因而可以用大量剪接因子的表达量变化来表示玉米干旱耐受性。
8.部分SR蛋白家族成员与玉米的逆境胁迫应答密切相关。RSZ. ASF/SF2等家族可能与玉米细胞凋亡相关能够在一定程度上反映玉米受胁迫的程度,而SC35亚家族的部分成员在各个转录组中的不同表达显示了其与玉米干旱耐受性的亲密关系。
In this manuscript we will to explain the alternative splicing of the whole transcriptomes in seedling stage.under drought stress in two maize (zea mays sp. L) inbred lines, the sensitivity to drought stress inbred lines Ye478(from8112and5003of the system, the most popular inbred line in China) and drought tolerance oneH21(from the P78599, pioneer Seed Company, USA, widely plant in Northwest China and half arid zones).Drought stress treatment is in the seedling stage, analysis the data of alternative splicing in whole transcnptomeobtained using high-throughput Solexa sequencing for gene expression, through the comparison of differences of genes alternative splicing events and degree under drought stress and normal condtion, to understand the variable shear biological and molecular pathway; by means of reverse transcription PCR amplified part of splice variants of some genes; by high-throughput sequencing analysis and qRT-PCR analysis to understand the expression of corn important regulatorsof alternative splicing, SR protein gene family. Screening of drought related candidate SR members, and reveal the internal relationship between its response gene expression and regulation of maize drought stress. The follows are the result:
1. Overall, drought stress will be alternative splicing induced gene reflect the drought degree of Maize.Drought stress physiological state of the plant will have an impact, all kinds of plant body and water related physiological and biochemical changes. Ye478because of the drought resistance ability is far lower than the H21, so the number of alternative splicing occurs under drought stress than drought tolerant lines H21. Affected by drought, plant alternative splicing number will rise by environmental stresses affecting plant will increase the diversity of genome is greatly increased in addition, alternative splicing diversity variable change to some extent reflects the corn stress influence degree; alternative splicing drought-tolerant strains H21occurred in drought conditions change to less than Ye478, due to alternative splicing can influence gene transcription of the fate, it can be understood as Ye478affected by drought is more serious, shut down the expression of a large number of required for non housekeeping genes.
2. Alternative splicing has certain influence on maize drought adaptability. There are some difference variable under the condition of drought stress between H21and Ye478:alternative splicing genes could increase maize drought tolerance similar alternative splicing genes in H21and Ye478drought stress while it occurs alternative splicing in H21control group, may be associated with Maize Drought adaptability.
3. In all two maize inbred lines, most alternatively splicedgenes occurAlternative splicingin both drought and non-drought stress occurred alternative splicing.2/3in H21and4/5in Ye478alternatively spliced genesin normal moisture conditions still alternative splicing under drought stress. Induced by drought and alternatively spliced genes accounted for about Ye478and H21drought all alternatively spliced genes in1/3, shows a portion of a gene alternative splicing is maize physiological functions necessary, are not affected by the drought and other environmental factors.
4. The majority of the alternatively spliced genes under drought stress related pathways in NTP binding, sugar metabolism and protein synthesis, suggesting that transport, alternative splicing occurs in Maize under drought stress genes were mainly protein and energy metabolism related genes. This indicates that the protein and energy metabolism is the main physiological pathway in Maize under drought stress, the stress of drought resistance of important pathways associate with Maize under drought stress.
5. Magnesium ion binding protein is an important member of H21under drought stress specific alternatively spliced proteins, suggesting that the magnesium ion binding splicing protein may be associated with drought resistance for H21.
6. The ABA signal transduction pathway of Maize under drought stress, is triggering main transmission of the plant stress response. Induction of ABA protein plays an important role in plant abiotic stress. ABA induced protein, either in H21or in Ye478ocurrs a large number of alternative splicing due to drought. Many transcription factorshave similar alternative splicing changes in the H21and Ye478under drought condition. In addition, R protein and splicing factor family also have alternative splicing, these alternative splicing has been verified by experiment.
7. The SR protein is one of the most important splicing factors in maize, the change trend of whole genome alternative splicing, is consistent with the trend of SR splicing factors expression; whole genome splicing changes can be replaced by the expression of a large number of SR splicing factors, so it can be used to change the amount of splicing factor expression to express the maize drought tolerance.
8. The SR protein family member and the stress response is closely related to maize. RSZ, ASF/SF2families may be associated with maize cell apoptosis can reflect the corn stress to a certain extent, and the different expression of some members of the SC35subfamily of transcription in each group shows its close relationship with maize drought tolerance.
1.总体上,干旱逆境会诱导部分基因的可变剪接,并通过可变剪接反映玉米的受旱程度。干旱逆境会对植物的各种生理状态有所影响,植物体内的各种与水分相关的生理生化反应会发生改变。由于Ye478的耐旱能力远低于H21,所以其在干旱胁迫下发生的可变剪接数目远多于耐旱品系H21。受干旱程度的影响,植物可变剪接数目会出现上升受环境逆境影响植物会增加基因组的多样性大大增加此外,可变剪接多样性的改变一定程度上反映了玉米受胁迫影响的程度；耐早品系H21在干旱条件下所发生的可变剪接改变要小于Ye478,由于可变剪接可以影响基因转录后的命运,这可以理解为Ye478受干旱影响更严重,关闭了大量非生活所必需的基因的表达。
2.可变剪接对玉米干旱逆境适应性有一定的影响。H21和Ye478两个品系在干旱逆境下可变剪接的差异表明：部分基因的可变剪接可以增加玉米的耐旱能力在H21对照和Ye478、H21干旱胁迫下发生类似可变剪接的基因,可能与玉米干旱适应性相关。
3.在所有两个玉米自交系中,发生的可变剪接的基因大部分在干旱和非干旱胁迫下均发生可变剪接。H21中2/3和Ye478中4/5在正常水分条件下发生可变剪接的基因在干旱胁迫下仍然发生可变剪接。由干旱诱导而发生可变剪接的基因占Ye478和H21干旱中所有发生可变剪接的基因中1/3左右,表明一部分基因可变剪接是玉米行使生理功能所必需的,不会受干旱等环境因素的影响。
4.在干旱胁迫下发生可变剪接的基因多数集中在NTP结合、糖代谢以及蛋白合成转运等相关途径中这表明,玉米干旱胁迫下发生可变剪接的基因主要为能量和蛋白代谢相关基因。这表明蛋白和能量的代谢是玉米在干旱逆境下最主要的生理途径,其可能与玉米在干旱胁迫下抗旱性相关的重要通路。
5.镁离子结合蛋白是H21在干旱胁迫特异发生可变剪接的重要蛋白成员,这表明镁离子结合蛋白的可变剪接可能与H21的干旱抗逆性相关。
6.ABA信号转导通路是玉米干旱胁迫下重要的通路,是触发植物逆境胁迫反应主要传递者。ABA诱导蛋白对植物逆境胁迫具有重要作用。ABA诱导蛋白,不论在H21还是在Ye478中都由于干旱而发生大量的可变剪接。多种转录因子和在H21和Ye478干旱条件下出现相似的可变剪接变化。此外R蛋白及部分剪接因子家族也发生可变剪接,这些可变剪接已被实验验证。
7.SR蛋白是玉米中最重要的剪接因子之一,大量SR剪接因子表达量的总体趋势与全基因组可变剪接事件变化的趋势基本一致；可以用大量SR剪接因子的表达量的改变趋势来反应全基因组可变剪接的改变,因而可以用大量剪接因子的表达量变化来表示玉米干旱耐受性。
8.部分SR蛋白家族成员与玉米的逆境胁迫应答密切相关。RSZ. ASF/SF2等家族可能与玉米细胞凋亡相关能够在一定程度上反映玉米受胁迫的程度,而SC35亚家族的部分成员在各个转录组中的不同表达显示了其与玉米干旱耐受性的亲密关系。
In this manuscript we will to explain the alternative splicing of the whole transcriptomes in seedling stage.under drought stress in two maize (zea mays sp. L) inbred lines, the sensitivity to drought stress inbred lines Ye478(from8112and5003of the system, the most popular inbred line in China) and drought tolerance oneH21(from the P78599, pioneer Seed Company, USA, widely plant in Northwest China and half arid zones).Drought stress treatment is in the seedling stage, analysis the data of alternative splicing in whole transcnptomeobtained using high-throughput Solexa sequencing for gene expression, through the comparison of differences of genes alternative splicing events and degree under drought stress and normal condtion, to understand the variable shear biological and molecular pathway; by means of reverse transcription PCR amplified part of splice variants of some genes; by high-throughput sequencing analysis and qRT-PCR analysis to understand the expression of corn important regulatorsof alternative splicing, SR protein gene family. Screening of drought related candidate SR members, and reveal the internal relationship between its response gene expression and regulation of maize drought stress. The follows are the result:
1. Overall, drought stress will be alternative splicing induced gene reflect the drought degree of Maize.Drought stress physiological state of the plant will have an impact, all kinds of plant body and water related physiological and biochemical changes. Ye478because of the drought resistance ability is far lower than the H21, so the number of alternative splicing occurs under drought stress than drought tolerant lines H21. Affected by drought, plant alternative splicing number will rise by environmental stresses affecting plant will increase the diversity of genome is greatly increased in addition, alternative splicing diversity variable change to some extent reflects the corn stress influence degree; alternative splicing drought-tolerant strains H21occurred in drought conditions change to less than Ye478, due to alternative splicing can influence gene transcription of the fate, it can be understood as Ye478affected by drought is more serious, shut down the expression of a large number of required for non housekeeping genes.
2. Alternative splicing has certain influence on maize drought adaptability. There are some difference variable under the condition of drought stress between H21and Ye478:alternative splicing genes could increase maize drought tolerance similar alternative splicing genes in H21and Ye478drought stress while it occurs alternative splicing in H21control group, may be associated with Maize Drought adaptability.
3. In all two maize inbred lines, most alternatively splicedgenes occurAlternative splicingin both drought and non-drought stress occurred alternative splicing.2/3in H21and4/5in Ye478alternatively spliced genesin normal moisture conditions still alternative splicing under drought stress. Induced by drought and alternatively spliced genes accounted for about Ye478and H21drought all alternatively spliced genes in1/3, shows a portion of a gene alternative splicing is maize physiological functions necessary, are not affected by the drought and other environmental factors.
4. The majority of the alternatively spliced genes under drought stress related pathways in NTP binding, sugar metabolism and protein synthesis, suggesting that transport, alternative splicing occurs in Maize under drought stress genes were mainly protein and energy metabolism related genes. This indicates that the protein and energy metabolism is the main physiological pathway in Maize under drought stress, the stress of drought resistance of important pathways associate with Maize under drought stress.
5. Magnesium ion binding protein is an important member of H21under drought stress specific alternatively spliced proteins, suggesting that the magnesium ion binding splicing protein may be associated with drought resistance for H21.
6. The ABA signal transduction pathway of Maize under drought stress, is triggering main transmission of the plant stress response. Induction of ABA protein plays an important role in plant abiotic stress. ABA induced protein, either in H21or in Ye478ocurrs a large number of alternative splicing due to drought. Many transcription factorshave similar alternative splicing changes in the H21and Ye478under drought condition. In addition, R protein and splicing factor family also have alternative splicing, these alternative splicing has been verified by experiment.
7. The SR protein is one of the most important splicing factors in maize, the change trend of whole genome alternative splicing, is consistent with the trend of SR splicing factors expression; whole genome splicing changes can be replaced by the expression of a large number of SR splicing factors, so it can be used to change the amount of splicing factor expression to express the maize drought tolerance.
8. The SR protein family member and the stress response is closely related to maize. RSZ, ASF/SF2families may be associated with maize cell apoptosis can reflect the corn stress to a certain extent, and the different expression of some members of the SC35subfamily of transcription in each group shows its close relationship with maize drought tolerance.
引文
[1]Mcguire A M, Pearson M D, Neafsey D E, et al. Cross-kingdom patterns of alternative splicing and splice recognition[J]. Genome Biol,2008,9(3):R50.
[2]Carvalho R F, Feijao C V, Duque P. On the physiological significance of alternative splicing events in higher plants[J]. Protoplasma,2012.
[3]Pan Q, Shai O, Lee L J, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing[J]. Nat Genet,2008,40(12):1413-1415.
[4]English A C, Patel K S, Loraine A E. Prevalence of alternative splicing choices in Arabidopsis thaliana[J]. BMC Plant Biol,2010,10:102.
[5]Mastrangelo A M, Marone D, Laido G, et al. Alternative splicing:enhancing ability to cope with stress via transcriptome plasticity [J]. Plant Sci,2012,185-186:40-49.
[6]Filichkin S A, Mockler T C. Unproductive alternative splicing and nonsense mRNAs:a widespread phenomenon among plant circadian clock genes[J]. Biol Direct,2012,7:20.
[7]Keren-Shaul H, Lev-Maor G, Ast G. Pre-mRNA splicing is a determinant of nucleosome organization[J]. PLoS One,2013,8(l):e53506.
[8]Yap K, Makeyev E V. Regulation of gene expression in mammalian nervous system through alternative pre-mRNA splicing coupled with RNA quality control mechanisms[J]. Mol Cell Neurosci,2013.
[9]Horiuchi T, Aigaki T. Alternative trans-splicing:a novel mode of pre-mRNA processing[J]. Biol Cell,2006,98(2):135-140.
[10]Huelga S C, Vu A Q, Arnold J D, et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins[J]. Cell Rep,2012,1 (2):167-178.
[11]Barta A, Kalyna M, Reddy A S. Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants[J]. Plant Cell,2010,22(9):2926-2929.
[12]Guerra-Peraza O, Nguyen H T, Stamp P, et al. ZmCOI6.1, a novel, alternatively spliced maize gene, whose transcript level changes under abiotic stress[J]. Plant Science,2009,176(6):783-791.
[13]Li J, Li X, Guo L, et al. A subgroup of M Y B transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice[J]. J Exp Bot,2006,57(6):1263-1273.
[14]Du H, Yang S S, Liang Z, et al. Genome-wide analysis of the MYB transcription factor superfamily in soybean[J]. BMC Plant Biol,2012,12:106.
[15]Koo S C, Yoon H W, Kim C Y, et al. Alternative splicing of the OsBWMKl gene generates three transcript variants showing differential subcellular localizations[J]. Biochem Biophys Res Commun,2007,360(1):188-193.
[16]Kalyna M, Simpson C G, Syed N H, et al. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis[J]. Nucleic Acids Res,2012,40(6):2454-2469.
[17]Palusa S G, Reddy A S. Extensive coupling of alternative splicing of pre-mRNAs of serine/arginine (SR) genes with nonsense-mediated decay[J]. New Phytol,2010,185(1):83-89.
[18]Zhang J, Liao B, Craik D J, et al. Identification of two suites of cyclotide precursor genes from metallophyte Viola baoshanensis:cDNA sequence variation, alternative RNA splicing and potential cyclotide diversity[J]. Gene,2009,431(1-2):23-32.
[19]Zhang X C, Gassmann W. Alternative splicing and mRNA levels of the disease resistance gene RPS4 are induced during defense responses[J]. Plant Physiol,2007,145(4):1577-1587.
[20]Seo P J, Hong S Y, Kim S G, et al. Competitive inhibition of transcription factors by small interfering peptides[J]. Trends Plant Sci,2011,16(10):541-549.
[21]Wang X, Ma L. Unraveling the circadian clock in Arabidopsis[J], Plant Signal Behav,2012,8(2).
[22]Barta A, Kalyna M, Lorkovic Z J. Plant SR proteins and their functions[J]. Curr Top Microbiol Immunol,2008,326:83-102.
[23]Stauffer E, Westermann A, Wagner G, et al. Polypyrimidine tract-binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and downstream control[J]. Plant J,2010,64(2):243-255.
[24]Palusa S G, Ali G S, Reddy A S. Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins:regulation by hormones and stresses[J]. Plant J,2007,49(6):1091-1107.
[25]Lazar G, Goodman H M. The Arabidopsis splicing factor SRI is regulated by alternative splicing[J]. Plant Mol Biol,2000,42(4):571-581.
[26]Macknight R, Bancroft I, Page T, et al. FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains[J]. Cell,1997,89(5):737-745.
[27]Macknight R, Duroux M, Laurie R, et al. Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA[J]. Plant Cell,2002,14(4):877-888.
[28]Quesada V, Macknight R, Dean C, et al. Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time[J]. EMBO J,2003,22(12):3142-3152.
[29]Wang Z, Xiao X, Van Nostrand E, et al. General and specific functions of exonic splicing silencers in splicing control[J]. Mol Cell,2006,23(l):61-70.
[30]Matlin A J, Clark F, Smith C W. Understanding alternative splicing:towards a cellular code[J]. Nat Rev Mol Cell Biol,2005,6(5):386-398.
[31]Gromak N, Rideau A, Southby J, et al. The PTB interacting protein raver 1 regulates alpha-tropomyosin alternative splicing[J]. EMBO J,2003,22(23):6356-6364.
[32]Feng Y, Chen M, Manley J L. Phosphorylation switches the general splicing repressor SRp38 to a sequence-specific activator[J]. Nat Struct Mol Biol,2008,15(10):1040-1048.
[33]Reddy A S, Day IS, Gohring J, et al. Localization and dynamics of nuclear speckles in plants[J]. Plant Physiol,2012,158(1):67-77.
[34]Howe K J. RNA polymerase Ⅱ conducts a symphony of pre-mRNA processing activities[J]. Biochim Biophys Acta,2002,1577(2):308-324.
[35]Luco R F, Pan Q, Tominaga K, et al. Regulation of alternative splicing by histone modifications[J]. Science.2010,327(5968):996-1000.
[36]Graveley B R. Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures[J]. Cell,2005,123(1):65-73.
[37]Carrillo O F, Preibisch S, Neugebauer K M. Global analysis of nascent RNA reveals transcriptional pausing in terminal exons[J]. Mol Cell,2010,40(4):571-581.
[38]Eperon L P, Graham I R, Griffiths A D, et al. Effects of RNA secondary structure on alternative splicing of pre-mRNA:is folding limited to a region behind the transcribing RNA polymerase?[J]. Cell,1988,54(3):393-401.
[39]Witt S, Galicia L, Lisec J, et al. Metabolic and phenotypic responses of greenhouse-grown maize hybrids to experimentally controlled drought stress[J]. Mol Plant,2012,5(2):401-417.
[40]Zhao Y, Zhou Y, Jiang H, et al. Systematic analysis of sequences and expression patterns of drought-responsive members of the HD-Zip gene family in maize[J]. PLoS One,2011,6(12):e28488.
[41]Xia Z, Liu Q, Wu J, et al. ZmRFP1, the putative ortholog of SDIR1, encodes a RING-H2 E3 ubiquitin ligase and responds to drought stress in an ABA-dependent manner in maize[J]. Gene,2012,495(2):146-153.
[42]Campo S, Peris-Peris C, Montesinos L, et al. Expression of the maize ZmGF14-6 gene in rice confers tolerance to drought stress while enhancing susceptibility to pathogen infection[J]. J Exp Bot,2012,63(2):983-999.
[43]Rahman H, Pekic S, Lazic-Jancic V, et al. Molecular mapping of quantitative trait loci for drought tolerance in maize plants[J]. Genet Mol Res,2011,10(2):889-901.
[44]Zheng J, Fu J, Gou M, et al. Genome-wide transcriptome analysis of two maize inbred lines under drought stress[J]. Plant Mol Biol,2010,72(4-5):407-421.
[45]Javed N, Ashraf M, Akram N A, et al. Alleviation of adverse effects of drought stress on growth and some potential physiological attributes in maize (Zea mays L.) by seed electromagnetic treatment[J]. Photochem Photobiol,2011,87(6):1354-1362.
[46]Barbazuk W B, Fu Y, Mcginnis K M. Genome-wide analyses of alternative splicing in plants: opportunities and challenges[J]. Genome Res,2008,18(9):1381-1392.
[47]Kazan K. Alternative splicing and proteome diversity in plants:the tip of the iceberg has just emerged[J]. Trends Plant Sci,2003,8(10):468-471.
[48]Nakaminami K, Matsui A, Shinozaki K, et al. RNA regulation in plant abiotic stress responses[J]. Biochim Biophys Acta,2012,1819(2):149-153.
[49]Filichkin S A, Priest H D, Givan S A, et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana[J]. Genome Res,2010,20(l):45-58.
[50]曾纪晴,张明永.选择性剪接在植物逆境相关基因表达调控中的作用[J].植物生理学通讯,2006,42(6)：1005-1014.
[51]Akhtar M, Jaiswal A, Taj G, et al. DREB1/CBF transcription factors:their structure, function and role in abiotic stress tolerance in plants[J]. J Genet,2012,91(3):385-395.
[52]Egawa C, Kobayashi F, Ishibashi M, et al. Differential regulation of transcript accumulation and alternative splicing of a DREB2 homolog under abiotic stress conditions in common wheat[J]. Genes Genet Syst,2006,81(2):77-91.
[53]Qin F, Kakimoto M, Sakuma Y, et al. Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L[J]. Plant J,2007,50(1):54-69.
[54]Matsukura S, Mizoi J, Yoshida T, et al. Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes[J]. Mol Genet Genomics,2010,283(2):185-196.
[55]Katiyar A, Smita S, Lenka S K, et al. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis[J]. BMC Genomics,2012,13:544.
[56]Zhang X C, Gassmann W. Quantifying alternatively spliced mRNA via capillary electrophoresis[J]. Methods Mol Biol,2011,712:69-77.
[57]Del C R, Magaldi E, Podda A, et al. A stress responsive alternative splicing mechanism in Citrus clementina leaves[J]. J Plant Physiol,2011,168(9):952-959.
[58]Yan K, Liu P, Wu C A, et al. Stress-Induced Alternative Splicing Provides a Mechanism for the Regulation of MicroRNA Processing in Arabidopsis thaliana[J]. Mol Cell,2012,48(4):521-531.
[59]Severing E I, van Dijk A D, Stiekema W J, et al. Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome[J]. BMC Genomics,2009,10:154.
[60]Zou X, Jiang Y, Zheng Y, et al. Prolyl 4-hydroxylase genes are subjected to alternative splicing in roots of maize seedlings under waterlogging[J]. Ann Bot,2011,108(7):1323-1335.
[61]Lin F, Zhang Y, Jiang M Y. Alternative splicing and differential expression of two transcripts of nicotine adenine dinucleotide phosphate oxidase B gene from Zea mays[J]. J Integr Plant Biol,2009,51(3):287-298.
[62]Richardson D N, Rogers M F, Labadorf A, et al. Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes:insights into sub-family classification and extent of alternative splicing[J]. PLoS One,2011,6(9):e24542.
[63]Gao H, Gordon-Kamm W J, Lyznik L A. ASF/SF2-like maize pre-mRNA splicing factors affect splice site utilization and their transcripts are alternatively spliced[J]. Gene,2004,339:25-37.
[64]Duque P. A role for SR proteins in plant stress responses[J]. Plant Signal Behav,2011,6(1):49-54.
[65]Yoshimura K, Mori T, Yokoyama K, et al. Identification of alternative splicing events regulated by an Arabidopsis serine/arginine-like protein, atSR45a, in response to high-light stress using a tiling array[J]. Plant Cell Physiol,2011,52(10):1786-1805.
[66]Penfield S, Josse E M, Halliday K J. A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy[J]. Plant Mol Biol,2010,73(1-2):89-95.
[67]Gulledge A A, Roberts A D, Vora H, et al. Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a[J]. Am J Bot,2012,99(2):219-231.
[68]Shikata H, Shibata M, Ushijima T, et al. The RS domain of Arabidopsis splicing factor RRC1 is required for phytochrome B signal transduction[J]. Plant J,2012,70(5):727-738.
[69]Reddy A S, Shad A G. Plant serine/arginine-rich proteins:roles in precursor messenger RNA splicing, plant development, and stress responses[J]. Wiley Interdiscip Rev RNA,2011,2(6):875-889.
[70]Ali G S, Reddy A S. ATP, phosphorylation and transcription regulate the mobility of plant splicing factors[J]. J Cell Sci,2006,119(Pt 17):3527-3538.
[71]Ausin I, Greenberg M V, Li C F, et al. The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis[J]. Epigenetics,2012,7(1):29-33.
[72]Modrek B, Lee C. A genomic view of alternative splicing[J]. Nat Genet,2002,30(1):13-19.
[73]Cui Y, Han J, Zhong D, et al. A novel computational method for the identification of plant alternative splice sites[J]. Biochem Biophys Res Commun,2013,431(2):221-224.
[74]Ryan M C, Zeeberg B R, Caplen N J, et al. SpliceCenter:a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies[J]. BMC Bioinformatics,2008,9:313.
[75]Kim N, Lim D, Lee S, et al. ASePCR:alternative splicing electronic RT-PCR in multiple tissues and organs[J]. "Nucleic Acids Res,2005,33(Web Server issue):W681-W685.
[76]van der Reijden B A, Lombardo M, Dauwerse H G, et al. RT-PCR diagnosis of patients with acute nonlymphocytic leukemia and inv(16)(p13q22) and identification of new alternative splicing in CBFB-MYH11 transcripts[J]. Blood,1995,86(1):277-282.
[77]黄文强,董珍珍,邢万金.大鼠RVLG选择性剪接变异体的鉴定和分析[J].中国农业科学,2011(0).
[78]Gaveriaux-Ruff C, Peluso J, Befort K, et al. Detection of opioid receptor mRNA by RT-PCR reveals alternative splicing for the delta-and kappa-opioid receptors[J]. Brain Res Mol Brain Res,1997,48(2):298-304.
[79]Heck S, Enz R, Richter-Landsberg C, et al. Expression and mRNA splicing of glycine receptor subunits and gephyrin during neuronal differentiation of P19 cells in vitro, studied by RT-PCR and immunocytochemistry[J]. Brain Res Dev Brain Res,1997,98(2):211-220.
[80]Thomson S A, Wallace M R. RT-PCR splicing analysis of the NF1 open reading frame[J]. Hum Genet,2002,110(5):495-502.
[81]Barbieri A M, Soriani N, Ferlini A, et al. Seven novel additional small mutations and a new alternative splicing in the human dystrophin gene detected by heteroduplex analysis and restricted RT-PCR heteroduplex analysis of illegitimate transcripts[J]. Eur J Hum Genet,1996,4(3):183-187.
[82]勾文峰,杨雪,徐小燕,等.选择性剪接变异体的RT-PCR检测及结果分析[J].中国医科大学学报,2012(0).
[83]杨非,张淑琴,杜承,等.马传染性贫血病毒受体选择性剪接异构休的鉴定与分析[J].中国预防兽医学报,2012(0).
[84]程慧,张晓娟,刘海波,等.小鼠Mater基因选择性剪接变异体的鉴定和分析[J].遗传学报,2004(0).
[85]陈鑫基,胡建达,林敏辉,等.电子克隆结合RT-PCR获得两条eIF4E剪接变异体的全长cDNA[J]中国实验血液学杂志,2009(3).
[86]Szalmas A, Konya J, Sziklai I, et al. Detection and identification of CD46 splicing isoforms by nested RT-PCR[J]. Methods Mol Biol,2010,630:83-95.
[87]Caldana C, Scheible W R, Mueller-Roeber B, et al. A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors[J]. Plant Methods,2007,3:7.
[88]Tenaillon M I, Hufford M B, Gaut B S, et al. Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians[J]. Genome Biol Evol,2011,3:219-229.
[89]Avin-Wittenberg T, Tzin V, Angelovici R, et al. Deciphering energy-associated gene networks operating in the response of Arabidopsis plants to stress and nutritional cues[J]. Plant J,2012,70(6):954-966.
[90]Rasmusson A G, Fernie A R, van Dongen J T. Alternative oxidase:a defence against metabolic fluctuations?[J]. Physiol Plant,2009,137(4):371-382.
[91]Van Aken O, Giraud E, Clifton R, et al. Alternative oxidase:a target and regulator of stress responses[J]. Physiol Plant,2009,137(4):354-361.
[92]Baena-Gonzalez E, Sheen J. Convergent energy and stress signaling[J]. Trends Plant Sci,2008,13(9):474-482.
[93]Ishikawa K, Yoshimura K, Ogawa T, et al. Distinct regulation of Arabidopsis ADP-ribose/NADH pyrophosphohydrolases, AtNUDX6 and 7, in biotic and abiotic stress responses[J]. Plant Signal Behav,2010,5(7):839-841.
[94]Ogawa T, Ishikawa K, Harada K, et al. Overexpression of an ADP-ribose pyrophosphatase, AtNUDX2, confers enhanced tolerance to oxidative stress in Arabidopsis plants[J]. Plant J,2009,57(2):289-301.
[95]Liu X M, Nguyen X C, Kim K E, et al. Phosphorylation of the zinc finger transcriptional regulator ZAT6 by MPK6 regulates Arabidopsis seed germination under salt and osmotic stress[J]. Biochem Biophys Res Commun,2012.
[96]Shen H, Liu C, Zhang Y, et al. Os WRKY30 is activated by MAP kinases to confer drought tolerance in rice[J]. Plant Mol Biol,2012,80(3):241-253.
[97]Kulik A, Wawer I, Krzywinska E, et al. SnRK2 protein kinases--key regulators of plant response to abiotic stresses[J]. OMICS,2011,15(12):859-872.
[98]Farinha A P, Irar S, de Oliveira E, et al. Novel clues on abiotic stress tolerance emerge from embryo proteome analyses of rice varieties with contrasting stress adaptation[J]. Proteomics,2011,11(12):2389-2405.
[99]Liu F, Guo J, Bai P, et al. Wheat TaRab7 GTPase is part of the signaling pathway in responses to stripe rust and abiotic stimuli[J]. PLoS One,2012,7(5):e37146.
[100]Pitakrattananukool S, Kawakatsu T, Anuntalabhochai S, et al. Overexpression of OsRab7B3, a small GTP-binding protein gene, enhances leaf senescence in transgenic rice[J]. Biosci Biotechnol Biochem,2012,76(7):1296-1302.
[101]Hanstein S, Wang X, Qian X, et al. Changes in cytosolic Mg2+levels can regulate the activity of the plasma membrane H+-ATPase in maize[J]. Biochem J,2011,435(1):93-101.
[102]Hiller M, Huse K, Platzer M, et al. Non-EST based prediction of exon skipping and intron retention events using Pfam information[J]. Nucleic Acids Res,2005,33(17):5611-5621.
[103]Syed N H, Kalyna M, Marquez Y, et al. Alternative splicing in plants--coming of age[J]. Trends Plant Sci,2012,17(10):616-623.
[104]Tanabe N, Yoshimura K, Kimura A, et al. Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress[J]. Plant Cell Physiol,2007,48(7):1036-1049.
[105]Letunic I, Bork P. Interactive Tree Of Life v2:online annotation and display of phylogenetic trees made easy[J]. Nucleic Acids Res,2011,39(Web Server issue):W475-W478.
[106]Golovkin M, Reddy A S. An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein[J]. J Biol Chem,1999,274(51):36428-36438.
[107]Manley J L, Krainer A R. A rational nomenclature for serine/arginine-rich protein splicing factors (SR proteins)[J]. Genes Dev,2010,24(11):1073-1074.
[108]Pelisch F, Gerez J, Druker J, et al. The serine/arginine-rich protein SF2/ASF regulates protein sumoylation[J]. Proc Natl Acad Sci U S A,2010,107(37):16119-16124.
[109]Zienkiewicz K, Zienkiewicz A, Rodriguez-Garcia M I, et al. Transcriptional activity and distribution of splicing machinery elements during Hyacinthus orientalis pollen tube growth[J]. Protoplasma,2008,233(1-2):129-139.
[110]Day I S, Golovkin M, Palusa S G, et al. Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence:insights into regulated splicing[J]. Plant J,2012,71(6):936-947.
[111]Golovkin M, Reddy A S. An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein[J]. J Biol Chem,1999,274(51):36428-36438.
[112]Zhang X N, Mount S M. Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development[J]. Plant Physiol,2009,150(3):1450-1458.
[113]Tanabe N, Yoshimura K, Kimura A, et al. Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress[J]. Plant Cell Physiol,2007,48(7):1036-1049.
[114]Lopato S, Gattoni R, Fabini G, et al. A novel family of plant splicing factors with a Zn knuckle motif:examination of RNA binding and splicing activities[J]. Plant Mol Biol,1999,39(4):761-773.
[115]Kumar K R, Kirti P B. Novel role for a serine/arginine-rich splicing factor, AdRSZ21 in plant defense and HR-like cell death[J]. Plant Mol Biol,2012,80(4-5):461-476.
[116]Wei S, Wang L, Zhang Y, et al. Identification of early response genes to salt stress in roots of melon (Cucumis melo L.) seedlings[J]. Mol Biol Rep,2012.
[117]Blanco F J, Bernabeu C. The Splicing Factor SRSF1 as a Marker for Endothelial Senescence[J]. Front Physiol,2012,3:54.
[118]李絮花,杨守祥.玉米苗期肥水耦合效应研究[J].山东农业大学学报：自然科学版,2002,33(3)：273-280.
[119]De Block M, Verduyn C, De Brouwer D, et al. Poly(ADP-ribose) polymerase in plants affects energy homeostasis, cell death and stress tolerance[J]. Plant J,2005,41(1):95-106.
[120]Wingler A, Lea P J, Quick W P, et al. Photorespiration:metabolic pathways and their role in stress protection[J]. Philos Trans R Soc Lond B Biol Sci,2000,355(1402):1517-1529.
[121]Zadraznik T, Hollung K, Egge-Jacobsen W, et al. Differential proteomic analysis of drought stress response in leaves of common bean (Phaseolus vulgaris L.)[J]. J Proteomics,2012.
[122]Gong P, Zhang J, Li H, et al. Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato[J]. J Exp Bot,2010,61(13):3563-3575.
[123]Carvalho R F, Carvalho S D, Duque P. The plant-specific SR45 protein negatively regulates glucose and ABA signaling during early seedling development in Arabidopsis[J]. Plant Physiol,2010,154(2):772-783.
[124]Sapra A K, Arava Y, Khandelia P, et al. Genome-wide analysis of pre-mRNA splicing:intron features govern the requirement for the second-step factor, Prp17 in Saccharomyces cerevisiae and Schizosaccharomyces pombe[J]. J Biol Chem,2004,279(50):52437-52446.
[2]Carvalho R F, Feijao C V, Duque P. On the physiological significance of alternative splicing events in higher plants[J]. Protoplasma,2012.
[3]Pan Q, Shai O, Lee L J, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing[J]. Nat Genet,2008,40(12):1413-1415.
[4]English A C, Patel K S, Loraine A E. Prevalence of alternative splicing choices in Arabidopsis thaliana[J]. BMC Plant Biol,2010,10:102.
[5]Mastrangelo A M, Marone D, Laido G, et al. Alternative splicing:enhancing ability to cope with stress via transcriptome plasticity [J]. Plant Sci,2012,185-186:40-49.
[6]Filichkin S A, Mockler T C. Unproductive alternative splicing and nonsense mRNAs:a widespread phenomenon among plant circadian clock genes[J]. Biol Direct,2012,7:20.
[7]Keren-Shaul H, Lev-Maor G, Ast G. Pre-mRNA splicing is a determinant of nucleosome organization[J]. PLoS One,2013,8(l):e53506.
[8]Yap K, Makeyev E V. Regulation of gene expression in mammalian nervous system through alternative pre-mRNA splicing coupled with RNA quality control mechanisms[J]. Mol Cell Neurosci,2013.
[9]Horiuchi T, Aigaki T. Alternative trans-splicing:a novel mode of pre-mRNA processing[J]. Biol Cell,2006,98(2):135-140.
[10]Huelga S C, Vu A Q, Arnold J D, et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins[J]. Cell Rep,2012,1 (2):167-178.
[11]Barta A, Kalyna M, Reddy A S. Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants[J]. Plant Cell,2010,22(9):2926-2929.
[12]Guerra-Peraza O, Nguyen H T, Stamp P, et al. ZmCOI6.1, a novel, alternatively spliced maize gene, whose transcript level changes under abiotic stress[J]. Plant Science,2009,176(6):783-791.
[13]Li J, Li X, Guo L, et al. A subgroup of M Y B transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice[J]. J Exp Bot,2006,57(6):1263-1273.
[14]Du H, Yang S S, Liang Z, et al. Genome-wide analysis of the MYB transcription factor superfamily in soybean[J]. BMC Plant Biol,2012,12:106.
[15]Koo S C, Yoon H W, Kim C Y, et al. Alternative splicing of the OsBWMKl gene generates three transcript variants showing differential subcellular localizations[J]. Biochem Biophys Res Commun,2007,360(1):188-193.
[16]Kalyna M, Simpson C G, Syed N H, et al. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis[J]. Nucleic Acids Res,2012,40(6):2454-2469.
[17]Palusa S G, Reddy A S. Extensive coupling of alternative splicing of pre-mRNAs of serine/arginine (SR) genes with nonsense-mediated decay[J]. New Phytol,2010,185(1):83-89.
[18]Zhang J, Liao B, Craik D J, et al. Identification of two suites of cyclotide precursor genes from metallophyte Viola baoshanensis:cDNA sequence variation, alternative RNA splicing and potential cyclotide diversity[J]. Gene,2009,431(1-2):23-32.
[19]Zhang X C, Gassmann W. Alternative splicing and mRNA levels of the disease resistance gene RPS4 are induced during defense responses[J]. Plant Physiol,2007,145(4):1577-1587.
[20]Seo P J, Hong S Y, Kim S G, et al. Competitive inhibition of transcription factors by small interfering peptides[J]. Trends Plant Sci,2011,16(10):541-549.
[21]Wang X, Ma L. Unraveling the circadian clock in Arabidopsis[J], Plant Signal Behav,2012,8(2).
[22]Barta A, Kalyna M, Lorkovic Z J. Plant SR proteins and their functions[J]. Curr Top Microbiol Immunol,2008,326:83-102.
[23]Stauffer E, Westermann A, Wagner G, et al. Polypyrimidine tract-binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and downstream control[J]. Plant J,2010,64(2):243-255.
[24]Palusa S G, Ali G S, Reddy A S. Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins:regulation by hormones and stresses[J]. Plant J,2007,49(6):1091-1107.
[25]Lazar G, Goodman H M. The Arabidopsis splicing factor SRI is regulated by alternative splicing[J]. Plant Mol Biol,2000,42(4):571-581.
[26]Macknight R, Bancroft I, Page T, et al. FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains[J]. Cell,1997,89(5):737-745.
[27]Macknight R, Duroux M, Laurie R, et al. Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA[J]. Plant Cell,2002,14(4):877-888.
[28]Quesada V, Macknight R, Dean C, et al. Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time[J]. EMBO J,2003,22(12):3142-3152.
[29]Wang Z, Xiao X, Van Nostrand E, et al. General and specific functions of exonic splicing silencers in splicing control[J]. Mol Cell,2006,23(l):61-70.
[30]Matlin A J, Clark F, Smith C W. Understanding alternative splicing:towards a cellular code[J]. Nat Rev Mol Cell Biol,2005,6(5):386-398.
[31]Gromak N, Rideau A, Southby J, et al. The PTB interacting protein raver 1 regulates alpha-tropomyosin alternative splicing[J]. EMBO J,2003,22(23):6356-6364.
[32]Feng Y, Chen M, Manley J L. Phosphorylation switches the general splicing repressor SRp38 to a sequence-specific activator[J]. Nat Struct Mol Biol,2008,15(10):1040-1048.
[33]Reddy A S, Day IS, Gohring J, et al. Localization and dynamics of nuclear speckles in plants[J]. Plant Physiol,2012,158(1):67-77.
[34]Howe K J. RNA polymerase Ⅱ conducts a symphony of pre-mRNA processing activities[J]. Biochim Biophys Acta,2002,1577(2):308-324.
[35]Luco R F, Pan Q, Tominaga K, et al. Regulation of alternative splicing by histone modifications[J]. Science.2010,327(5968):996-1000.
[36]Graveley B R. Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures[J]. Cell,2005,123(1):65-73.
[37]Carrillo O F, Preibisch S, Neugebauer K M. Global analysis of nascent RNA reveals transcriptional pausing in terminal exons[J]. Mol Cell,2010,40(4):571-581.
[38]Eperon L P, Graham I R, Griffiths A D, et al. Effects of RNA secondary structure on alternative splicing of pre-mRNA:is folding limited to a region behind the transcribing RNA polymerase?[J]. Cell,1988,54(3):393-401.
[39]Witt S, Galicia L, Lisec J, et al. Metabolic and phenotypic responses of greenhouse-grown maize hybrids to experimentally controlled drought stress[J]. Mol Plant,2012,5(2):401-417.
[40]Zhao Y, Zhou Y, Jiang H, et al. Systematic analysis of sequences and expression patterns of drought-responsive members of the HD-Zip gene family in maize[J]. PLoS One,2011,6(12):e28488.
[41]Xia Z, Liu Q, Wu J, et al. ZmRFP1, the putative ortholog of SDIR1, encodes a RING-H2 E3 ubiquitin ligase and responds to drought stress in an ABA-dependent manner in maize[J]. Gene,2012,495(2):146-153.
[42]Campo S, Peris-Peris C, Montesinos L, et al. Expression of the maize ZmGF14-6 gene in rice confers tolerance to drought stress while enhancing susceptibility to pathogen infection[J]. J Exp Bot,2012,63(2):983-999.
[43]Rahman H, Pekic S, Lazic-Jancic V, et al. Molecular mapping of quantitative trait loci for drought tolerance in maize plants[J]. Genet Mol Res,2011,10(2):889-901.
[44]Zheng J, Fu J, Gou M, et al. Genome-wide transcriptome analysis of two maize inbred lines under drought stress[J]. Plant Mol Biol,2010,72(4-5):407-421.
[45]Javed N, Ashraf M, Akram N A, et al. Alleviation of adverse effects of drought stress on growth and some potential physiological attributes in maize (Zea mays L.) by seed electromagnetic treatment[J]. Photochem Photobiol,2011,87(6):1354-1362.
[46]Barbazuk W B, Fu Y, Mcginnis K M. Genome-wide analyses of alternative splicing in plants: opportunities and challenges[J]. Genome Res,2008,18(9):1381-1392.
[47]Kazan K. Alternative splicing and proteome diversity in plants:the tip of the iceberg has just emerged[J]. Trends Plant Sci,2003,8(10):468-471.
[48]Nakaminami K, Matsui A, Shinozaki K, et al. RNA regulation in plant abiotic stress responses[J]. Biochim Biophys Acta,2012,1819(2):149-153.
[49]Filichkin S A, Priest H D, Givan S A, et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana[J]. Genome Res,2010,20(l):45-58.
[50]曾纪晴,张明永.选择性剪接在植物逆境相关基因表达调控中的作用[J].植物生理学通讯,2006,42(6)：1005-1014.
[51]Akhtar M, Jaiswal A, Taj G, et al. DREB1/CBF transcription factors:their structure, function and role in abiotic stress tolerance in plants[J]. J Genet,2012,91(3):385-395.
[52]Egawa C, Kobayashi F, Ishibashi M, et al. Differential regulation of transcript accumulation and alternative splicing of a DREB2 homolog under abiotic stress conditions in common wheat[J]. Genes Genet Syst,2006,81(2):77-91.
[53]Qin F, Kakimoto M, Sakuma Y, et al. Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L[J]. Plant J,2007,50(1):54-69.
[54]Matsukura S, Mizoi J, Yoshida T, et al. Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes[J]. Mol Genet Genomics,2010,283(2):185-196.
[55]Katiyar A, Smita S, Lenka S K, et al. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis[J]. BMC Genomics,2012,13:544.
[56]Zhang X C, Gassmann W. Quantifying alternatively spliced mRNA via capillary electrophoresis[J]. Methods Mol Biol,2011,712:69-77.
[57]Del C R, Magaldi E, Podda A, et al. A stress responsive alternative splicing mechanism in Citrus clementina leaves[J]. J Plant Physiol,2011,168(9):952-959.
[58]Yan K, Liu P, Wu C A, et al. Stress-Induced Alternative Splicing Provides a Mechanism for the Regulation of MicroRNA Processing in Arabidopsis thaliana[J]. Mol Cell,2012,48(4):521-531.
[59]Severing E I, van Dijk A D, Stiekema W J, et al. Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome[J]. BMC Genomics,2009,10:154.
[60]Zou X, Jiang Y, Zheng Y, et al. Prolyl 4-hydroxylase genes are subjected to alternative splicing in roots of maize seedlings under waterlogging[J]. Ann Bot,2011,108(7):1323-1335.
[61]Lin F, Zhang Y, Jiang M Y. Alternative splicing and differential expression of two transcripts of nicotine adenine dinucleotide phosphate oxidase B gene from Zea mays[J]. J Integr Plant Biol,2009,51(3):287-298.
[62]Richardson D N, Rogers M F, Labadorf A, et al. Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes:insights into sub-family classification and extent of alternative splicing[J]. PLoS One,2011,6(9):e24542.
[63]Gao H, Gordon-Kamm W J, Lyznik L A. ASF/SF2-like maize pre-mRNA splicing factors affect splice site utilization and their transcripts are alternatively spliced[J]. Gene,2004,339:25-37.
[64]Duque P. A role for SR proteins in plant stress responses[J]. Plant Signal Behav,2011,6(1):49-54.
[65]Yoshimura K, Mori T, Yokoyama K, et al. Identification of alternative splicing events regulated by an Arabidopsis serine/arginine-like protein, atSR45a, in response to high-light stress using a tiling array[J]. Plant Cell Physiol,2011,52(10):1786-1805.
[66]Penfield S, Josse E M, Halliday K J. A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy[J]. Plant Mol Biol,2010,73(1-2):89-95.
[67]Gulledge A A, Roberts A D, Vora H, et al. Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a[J]. Am J Bot,2012,99(2):219-231.
[68]Shikata H, Shibata M, Ushijima T, et al. The RS domain of Arabidopsis splicing factor RRC1 is required for phytochrome B signal transduction[J]. Plant J,2012,70(5):727-738.
[69]Reddy A S, Shad A G. Plant serine/arginine-rich proteins:roles in precursor messenger RNA splicing, plant development, and stress responses[J]. Wiley Interdiscip Rev RNA,2011,2(6):875-889.
[70]Ali G S, Reddy A S. ATP, phosphorylation and transcription regulate the mobility of plant splicing factors[J]. J Cell Sci,2006,119(Pt 17):3527-3538.
[71]Ausin I, Greenberg M V, Li C F, et al. The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis[J]. Epigenetics,2012,7(1):29-33.
[72]Modrek B, Lee C. A genomic view of alternative splicing[J]. Nat Genet,2002,30(1):13-19.
[73]Cui Y, Han J, Zhong D, et al. A novel computational method for the identification of plant alternative splice sites[J]. Biochem Biophys Res Commun,2013,431(2):221-224.
[74]Ryan M C, Zeeberg B R, Caplen N J, et al. SpliceCenter:a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies[J]. BMC Bioinformatics,2008,9:313.
[75]Kim N, Lim D, Lee S, et al. ASePCR:alternative splicing electronic RT-PCR in multiple tissues and organs[J]. "Nucleic Acids Res,2005,33(Web Server issue):W681-W685.
[76]van der Reijden B A, Lombardo M, Dauwerse H G, et al. RT-PCR diagnosis of patients with acute nonlymphocytic leukemia and inv(16)(p13q22) and identification of new alternative splicing in CBFB-MYH11 transcripts[J]. Blood,1995,86(1):277-282.
[77]黄文强,董珍珍,邢万金.大鼠RVLG选择性剪接变异体的鉴定和分析[J].中国农业科学,2011(0).
[78]Gaveriaux-Ruff C, Peluso J, Befort K, et al. Detection of opioid receptor mRNA by RT-PCR reveals alternative splicing for the delta-and kappa-opioid receptors[J]. Brain Res Mol Brain Res,1997,48(2):298-304.
[79]Heck S, Enz R, Richter-Landsberg C, et al. Expression and mRNA splicing of glycine receptor subunits and gephyrin during neuronal differentiation of P19 cells in vitro, studied by RT-PCR and immunocytochemistry[J]. Brain Res Dev Brain Res,1997,98(2):211-220.
[80]Thomson S A, Wallace M R. RT-PCR splicing analysis of the NF1 open reading frame[J]. Hum Genet,2002,110(5):495-502.
[81]Barbieri A M, Soriani N, Ferlini A, et al. Seven novel additional small mutations and a new alternative splicing in the human dystrophin gene detected by heteroduplex analysis and restricted RT-PCR heteroduplex analysis of illegitimate transcripts[J]. Eur J Hum Genet,1996,4(3):183-187.
[82]勾文峰,杨雪,徐小燕,等.选择性剪接变异体的RT-PCR检测及结果分析[J].中国医科大学学报,2012(0).
[83]杨非,张淑琴,杜承,等.马传染性贫血病毒受体选择性剪接异构休的鉴定与分析[J].中国预防兽医学报,2012(0).
[84]程慧,张晓娟,刘海波,等.小鼠Mater基因选择性剪接变异体的鉴定和分析[J].遗传学报,2004(0).
[85]陈鑫基,胡建达,林敏辉,等.电子克隆结合RT-PCR获得两条eIF4E剪接变异体的全长cDNA[J]中国实验血液学杂志,2009(3).
[86]Szalmas A, Konya J, Sziklai I, et al. Detection and identification of CD46 splicing isoforms by nested RT-PCR[J]. Methods Mol Biol,2010,630:83-95.
[87]Caldana C, Scheible W R, Mueller-Roeber B, et al. A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors[J]. Plant Methods,2007,3:7.
[88]Tenaillon M I, Hufford M B, Gaut B S, et al. Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians[J]. Genome Biol Evol,2011,3:219-229.
[89]Avin-Wittenberg T, Tzin V, Angelovici R, et al. Deciphering energy-associated gene networks operating in the response of Arabidopsis plants to stress and nutritional cues[J]. Plant J,2012,70(6):954-966.
[90]Rasmusson A G, Fernie A R, van Dongen J T. Alternative oxidase:a defence against metabolic fluctuations?[J]. Physiol Plant,2009,137(4):371-382.
[91]Van Aken O, Giraud E, Clifton R, et al. Alternative oxidase:a target and regulator of stress responses[J]. Physiol Plant,2009,137(4):354-361.
[92]Baena-Gonzalez E, Sheen J. Convergent energy and stress signaling[J]. Trends Plant Sci,2008,13(9):474-482.
[93]Ishikawa K, Yoshimura K, Ogawa T, et al. Distinct regulation of Arabidopsis ADP-ribose/NADH pyrophosphohydrolases, AtNUDX6 and 7, in biotic and abiotic stress responses[J]. Plant Signal Behav,2010,5(7):839-841.
[94]Ogawa T, Ishikawa K, Harada K, et al. Overexpression of an ADP-ribose pyrophosphatase, AtNUDX2, confers enhanced tolerance to oxidative stress in Arabidopsis plants[J]. Plant J,2009,57(2):289-301.
[95]Liu X M, Nguyen X C, Kim K E, et al. Phosphorylation of the zinc finger transcriptional regulator ZAT6 by MPK6 regulates Arabidopsis seed germination under salt and osmotic stress[J]. Biochem Biophys Res Commun,2012.
[96]Shen H, Liu C, Zhang Y, et al. Os WRKY30 is activated by MAP kinases to confer drought tolerance in rice[J]. Plant Mol Biol,2012,80(3):241-253.
[97]Kulik A, Wawer I, Krzywinska E, et al. SnRK2 protein kinases--key regulators of plant response to abiotic stresses[J]. OMICS,2011,15(12):859-872.
[98]Farinha A P, Irar S, de Oliveira E, et al. Novel clues on abiotic stress tolerance emerge from embryo proteome analyses of rice varieties with contrasting stress adaptation[J]. Proteomics,2011,11(12):2389-2405.
[99]Liu F, Guo J, Bai P, et al. Wheat TaRab7 GTPase is part of the signaling pathway in responses to stripe rust and abiotic stimuli[J]. PLoS One,2012,7(5):e37146.
[100]Pitakrattananukool S, Kawakatsu T, Anuntalabhochai S, et al. Overexpression of OsRab7B3, a small GTP-binding protein gene, enhances leaf senescence in transgenic rice[J]. Biosci Biotechnol Biochem,2012,76(7):1296-1302.
[101]Hanstein S, Wang X, Qian X, et al. Changes in cytosolic Mg2+levels can regulate the activity of the plasma membrane H+-ATPase in maize[J]. Biochem J,2011,435(1):93-101.
[102]Hiller M, Huse K, Platzer M, et al. Non-EST based prediction of exon skipping and intron retention events using Pfam information[J]. Nucleic Acids Res,2005,33(17):5611-5621.
[103]Syed N H, Kalyna M, Marquez Y, et al. Alternative splicing in plants--coming of age[J]. Trends Plant Sci,2012,17(10):616-623.
[104]Tanabe N, Yoshimura K, Kimura A, et al. Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress[J]. Plant Cell Physiol,2007,48(7):1036-1049.
[105]Letunic I, Bork P. Interactive Tree Of Life v2:online annotation and display of phylogenetic trees made easy[J]. Nucleic Acids Res,2011,39(Web Server issue):W475-W478.
[106]Golovkin M, Reddy A S. An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein[J]. J Biol Chem,1999,274(51):36428-36438.
[107]Manley J L, Krainer A R. A rational nomenclature for serine/arginine-rich protein splicing factors (SR proteins)[J]. Genes Dev,2010,24(11):1073-1074.
[108]Pelisch F, Gerez J, Druker J, et al. The serine/arginine-rich protein SF2/ASF regulates protein sumoylation[J]. Proc Natl Acad Sci U S A,2010,107(37):16119-16124.
[109]Zienkiewicz K, Zienkiewicz A, Rodriguez-Garcia M I, et al. Transcriptional activity and distribution of splicing machinery elements during Hyacinthus orientalis pollen tube growth[J]. Protoplasma,2008,233(1-2):129-139.
[110]Day I S, Golovkin M, Palusa S G, et al. Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence:insights into regulated splicing[J]. Plant J,2012,71(6):936-947.
[111]Golovkin M, Reddy A S. An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein[J]. J Biol Chem,1999,274(51):36428-36438.
[112]Zhang X N, Mount S M. Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development[J]. Plant Physiol,2009,150(3):1450-1458.
[113]Tanabe N, Yoshimura K, Kimura A, et al. Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress[J]. Plant Cell Physiol,2007,48(7):1036-1049.
[114]Lopato S, Gattoni R, Fabini G, et al. A novel family of plant splicing factors with a Zn knuckle motif:examination of RNA binding and splicing activities[J]. Plant Mol Biol,1999,39(4):761-773.
[115]Kumar K R, Kirti P B. Novel role for a serine/arginine-rich splicing factor, AdRSZ21 in plant defense and HR-like cell death[J]. Plant Mol Biol,2012,80(4-5):461-476.
[116]Wei S, Wang L, Zhang Y, et al. Identification of early response genes to salt stress in roots of melon (Cucumis melo L.) seedlings[J]. Mol Biol Rep,2012.
[117]Blanco F J, Bernabeu C. The Splicing Factor SRSF1 as a Marker for Endothelial Senescence[J]. Front Physiol,2012,3:54.
[118]李絮花,杨守祥.玉米苗期肥水耦合效应研究[J].山东农业大学学报：自然科学版,2002,33(3)：273-280.
[119]De Block M, Verduyn C, De Brouwer D, et al. Poly(ADP-ribose) polymerase in plants affects energy homeostasis, cell death and stress tolerance[J]. Plant J,2005,41(1):95-106.
[120]Wingler A, Lea P J, Quick W P, et al. Photorespiration:metabolic pathways and their role in stress protection[J]. Philos Trans R Soc Lond B Biol Sci,2000,355(1402):1517-1529.
[121]Zadraznik T, Hollung K, Egge-Jacobsen W, et al. Differential proteomic analysis of drought stress response in leaves of common bean (Phaseolus vulgaris L.)[J]. J Proteomics,2012.
[122]Gong P, Zhang J, Li H, et al. Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato[J]. J Exp Bot,2010,61(13):3563-3575.
[123]Carvalho R F, Carvalho S D, Duque P. The plant-specific SR45 protein negatively regulates glucose and ABA signaling during early seedling development in Arabidopsis[J]. Plant Physiol,2010,154(2):772-783.
[124]Sapra A K, Arava Y, Khandelia P, et al. Genome-wide analysis of pre-mRNA splicing:intron features govern the requirement for the second-step factor, Prp17 in Saccharomyces cerevisiae and Schizosaccharomyces pombe[J]. J Biol Chem,2004,279(50):52437-52446.