黃小慶,李丹丹,吳娟
?
植物長鏈非編碼RNA研究進(jìn)展
黃小慶,李丹丹,吳娟
東北林業(yè)大學(xué)鹽堿地生物資源環(huán)境研究中心,東北油田鹽堿植被恢復(fù)與重建教育部重點(diǎn)實(shí)驗(yàn)室,哈爾濱 150040
長鏈非編碼RNA(Long non-coding RNA,lncRNA)長度大于200個(gè)核苷酸,大量存在于生物體中并具有多種生物學(xué)功能。目前,植物中發(fā)現(xiàn)的lncRNA大多由RNA聚合酶Ⅱ轉(zhuǎn)錄,并通過目標(biāo)模仿、轉(zhuǎn)錄干擾、組蛋白甲基化和DNA甲基化等多種機(jī)制介導(dǎo)基因的表達(dá),在植物開花、雄性不育、營養(yǎng)代謝、生物和非生物脅迫等生物過程中起著調(diào)節(jié)因子的作用。文章綜述了近年來發(fā)現(xiàn)的植物lncRNA數(shù)據(jù)庫、預(yù)測方法、表達(dá)及可能的生物學(xué)功能。
長鏈非編碼RNA;數(shù)據(jù)庫;基因表達(dá)調(diào)控;生物學(xué)功能
生物體內(nèi)存在著兩種不同的RNA:能翻譯成蛋白質(zhì)的編碼RNA(Coding RNA,即mRNA)和不翻譯成蛋白質(zhì)的非編碼RNA(Non-coding RNA, ncRNA)[1]。ncRNA種類繁多,目前尚無規(guī)范的命名方法。根據(jù)其表達(dá)特征,ncRNA分為持家非編碼RNA(House- keeping non-coding RNA)和調(diào)控非編碼RNA(Reg-ulatory non-coding RNA)[2]。持家非編碼RNA包括rRNA、tRNA、snRNA(Small nuclear RNA)和snoRNA (Small nucleolar RNA)等,這些 RNA在所有類型細(xì)胞中均要表達(dá)并且受環(huán)境因素影響較小,對維持細(xì)胞的基本功能是必不可少的。調(diào)控非編碼RNA在生物體的特定組織器官和發(fā)育階段表達(dá),或者對應(yīng)激環(huán)境產(chǎn)生應(yīng)答反應(yīng)后特異表達(dá),這種特異表達(dá)調(diào)控著各種生物過程[3]。調(diào)控非編碼RNA按照長度可分為短鏈非編碼RNA(Small ncRNA)和長鏈非編碼RNA(Long non-coding RNA,lncRNA)兩大類[2]。短鏈非編碼RNA長度小于200 nt,包括miRNA、siRNA和piRNA(Piwi-interacting RNA)等[4, 5]。短鏈非編碼RNA的轉(zhuǎn)錄調(diào)控和作用機(jī)制已經(jīng)比較清晰,如miRNA首先經(jīng)RNA聚合酶Ⅱ轉(zhuǎn)錄形成pri-miRNA,然后經(jīng)RNA核酸酶的剪切作用后成為20~30nt的成熟miRNA,它們在基因轉(zhuǎn)錄后水平通過與靶mRNA互補(bǔ)結(jié)合,在RNA加工、轉(zhuǎn)錄及轉(zhuǎn)錄后的基因沉默、應(yīng)激應(yīng)答、發(fā)生及發(fā)育等生物過程中起著調(diào)節(jié)因子的作用。
lncRNA是指長度在200nt以上的調(diào)控非編碼RNA[6],沒有長的開放閱讀框(ORF),不具備編碼蛋白質(zhì)的功能,但是在特定的條件下有些lncRNA可以編碼功能性寡肽[7]。lncRNA與mRNA有許多共同特征,例如由RNA聚合酶Ⅱ進(jìn)行轉(zhuǎn)錄,并有5′加帽、3′聚腺苷酸化結(jié)構(gòu)等[8]。研究表明,哺乳動(dòng)物基因組中80%的轉(zhuǎn)錄產(chǎn)物為lncRNA[9]。lncRNA的作用機(jī)制和生物學(xué)功能極其多樣,通過影響其他RNA或蛋白質(zhì)的穩(wěn)定性來調(diào)節(jié)基因的表達(dá),參與劑量補(bǔ)償、基因組印記、X染色體失活等生物過程[10, 11]。哺乳動(dòng)物中超過1000個(gè)lncRNA參與了基因表達(dá)調(diào)控,在細(xì)胞周期調(diào)控、免疫監(jiān)視和胚胎干細(xì)胞多能性等過程發(fā)揮作用[12]。大量研究證明,多種疾病與lncRNA的異常表達(dá)或突變相關(guān)[13]。lncRNA的功能已經(jīng)引起了人們廣泛的關(guān)注。
與人類和動(dòng)物相比,植物lncRNA研究仍處于起步階段。全基因組陣列分析和RNA-seq結(jié)果顯示,植物體內(nèi)存在大量lncRNA,一些通過目標(biāo)模仿、轉(zhuǎn)錄干擾、與多梳蛋白抑制復(fù)合體2(Polycomb repressive complex 2, PRC2)有關(guān)的組蛋白甲基化和DNA甲基化等機(jī)制介導(dǎo)基因表達(dá),在植物開花、雄性不育、營養(yǎng)代謝、生物和非生物脅迫等生物過程中起著調(diào)節(jié)因子作用。本文主要對植物lncRNA的最新研究進(jìn)展進(jìn)行了綜述。
真核生物基因組中非編碼部分所占比例較大,例如釀酒酵母()為29%,擬南芥()為71%,而人類基因組的非編碼部分則占98%[14]。高等生物體內(nèi)編碼蛋白質(zhì)的基因數(shù)目是相對保守的,并且一些基因的同源性很高,例如人類和小鼠有99%的蛋白質(zhì)編碼基因都是同源的[15],基因組測序發(fā)現(xiàn)人類不同個(gè)體之間的蛋白質(zhì)編碼序列可變性約為整個(gè)基因組的0.3%[16]。據(jù)上述研究結(jié)果推測,個(gè)體間和物種間的差異可能是由于非編碼序列的不同導(dǎo)致基因表達(dá)的不同而造成的[15]。
由于限制ncRNA進(jìn)化的因素較少,導(dǎo)致物種間lncRNA序列保守性低、不能形成大的同源基因家族。Ponting等[2]認(rèn)為lncRNA可能通過以下5種方式形成:(1)蛋白質(zhì)編碼基因發(fā)生閱讀框的插入,插入的閱讀框和之前的編碼序列形成新的功能性lncRNA,如在哺乳動(dòng)物進(jìn)化過程中,與雌性動(dòng)物肌肉和成骨細(xì)胞分化和發(fā)育有關(guān)的基因的部分序列形成了X染色體失活相關(guān)的lncRNA,基因啟動(dòng)子區(qū)域和4個(gè)外顯子與基因的部分外顯子同源,而其余6個(gè)外顯子則來自不同的轉(zhuǎn)座子[17~19];(2)染色體重排后,兩個(gè)不轉(zhuǎn)錄的并且之前相隔很遠(yuǎn)的序列區(qū)域并列形成一個(gè)多外顯子的lncRNA,如犬科動(dòng)物經(jīng)染色體重排形成了一個(gè)含有ESTs為BM537447、C0597044和DN744681的lncRNA[2];(3)非編碼基因通過反轉(zhuǎn)錄轉(zhuǎn)座進(jìn)行復(fù)制,形成有功能的非編碼逆基因或非功能性的非編碼反轉(zhuǎn)錄假基因,如小鼠的一個(gè)lncRNA基因家族的形成[20];(4)在ncRNA內(nèi)部出現(xiàn)鄰近的序列重復(fù)復(fù)制,兩個(gè)重復(fù)序列串聯(lián)形成新的lncRNA,如的5′區(qū)域和部分序列的形成;(5)插入轉(zhuǎn)座因子產(chǎn)生有功能的lncRNA,如分別由不同的轉(zhuǎn)座因子形成的存在于嚙齒動(dòng)物大腦細(xì)胞質(zhì)中的lncRNA和類人猿大腦細(xì)胞質(zhì)中的lncRNA。
Ponting等[2]根據(jù)lncRNA在基因組中相對于蛋白質(zhì)編碼基因的位置將其分為5種類型:(1)正義或(2)反義lncRNA,這種lncRNA分別與相同鏈或相反鏈的另一個(gè)蛋白質(zhì)編碼基因的一個(gè)或多個(gè)外顯子相重疊。小鼠lncRNA與相同鏈的蛋白質(zhì)編碼基因的幾個(gè)外顯子部分序列重疊,lncRNA形成于蛋白質(zhì)編碼基因的反義鏈上;(3)雙向(Bidirectional) lncRNA,它的轉(zhuǎn)錄起始位點(diǎn)與相反鏈上編碼蛋白質(zhì)基因的轉(zhuǎn)錄起始位點(diǎn)非常接近,但轉(zhuǎn)錄方向相反。擬南芥中最近發(fā)現(xiàn)的lncRNA形成于編碼高爾基體運(yùn)輸復(fù)合物相關(guān)蛋白基因的反義鏈上,兩者的轉(zhuǎn)錄方向相反[7];(4)內(nèi)含子(intronic) lncRNA,它來源于次級轉(zhuǎn)錄物的內(nèi)含子區(qū)域(有時(shí)可能為mRNA前體序列);(5)基因間(intergenic) lncRNA,它產(chǎn)生于兩個(gè)基因之間區(qū)域。小鼠lncRNA即在編碼基因和之間生成;酵母的lncRNA也產(chǎn)生于和編碼基因之間。
lncRNA起初被認(rèn)為是基因組轉(zhuǎn)錄的“噪音”,是RNA聚合酶Ⅱ轉(zhuǎn)錄的副產(chǎn)物,不具有生物學(xué)功能。然而,研究表明,許多l(xiāng)ncRNA具有保守的二級結(jié)構(gòu)及剪接形式[21~25]。有些lncRNA在特異的組織、細(xì)胞、發(fā)育階段表達(dá)并且表達(dá)受到調(diào)節(jié)。Dinger等[21]發(fā)現(xiàn)小鼠的胚胎干細(xì)胞中多個(gè)lncRNA有差異表達(dá),并且具有多能性;Mercer等[23]發(fā)現(xiàn)成年小鼠大腦不同區(qū)域特異表達(dá)的多個(gè)lncRNA;Sone等[24]發(fā)現(xiàn)lncRNA在小鼠神經(jīng)系統(tǒng)的神經(jīng)元中特異表達(dá)。這些特征預(yù)示著lncRNA是一種以RNA形式存在于生物體內(nèi)的功能性分子。
lncRNA功能分析表明,它們在轉(zhuǎn)錄層面上調(diào)控編碼基因的表達(dá)機(jī)制很大程度上是由其在基因組上的轉(zhuǎn)錄位點(diǎn)決定的。例如,來源于蛋白質(zhì)編碼位點(diǎn)的順式-NAT通常采取“轉(zhuǎn)錄干擾”調(diào)控目標(biāo)基因表達(dá),因?yàn)槟繕?biāo)基因的啟動(dòng)子和lncRNA很接近,兩個(gè)啟動(dòng)子轉(zhuǎn)錄起始可以被共調(diào)節(jié);同時(shí)一些lncRNA可以與目標(biāo)基因啟動(dòng)子DNA結(jié)合,形成RNA-dsDNA三聯(lián)體,阻斷轉(zhuǎn)錄起始復(fù)合物的形成。其他一些lncRNA也可以通過控制轉(zhuǎn)錄因子的亞細(xì)胞定位或抑制RNA聚合酶活性在轉(zhuǎn)錄水平調(diào)節(jié)目標(biāo)基因[8]。
lncRNA還可以通過調(diào)節(jié)pre-mRNA的可變剪接、運(yùn)輸、翻譯和降解等,在轉(zhuǎn)錄后層面調(diào)節(jié)編碼基因的表達(dá)。例如,lncRNA通過反式作用方式調(diào)節(jié)目標(biāo)mRNA的穩(wěn)定性。當(dāng)lncRNA與目標(biāo)mRNA存在堿基互補(bǔ)時(shí),它就可以與目標(biāo)mRNA形成雙鏈RNA復(fù)合體,RNA復(fù)合體可以被加工成endo-siRNA,使目標(biāo)mRNA降解[26]。
有些lncRNA能夠招募染色質(zhì)重構(gòu)復(fù)合物到特定位點(diǎn)從而介導(dǎo)相關(guān)基因的表達(dá)沉默,進(jìn)而在表觀遺傳控制基因表達(dá)中發(fā)揮重要作用,如、、和等。在人類基因組中,來源于基因座的能夠招募染色質(zhì)重構(gòu)復(fù)合物PRC2并將其定位到位點(diǎn),介導(dǎo)位點(diǎn)的表觀遺傳變化[27]。
Wilusz等[28]總結(jié)了生物體內(nèi)lncRNA的8種作用機(jī)制,包括:(1)在蛋白質(zhì)編碼基因上游的啟動(dòng)子區(qū)域發(fā)生轉(zhuǎn)錄,上調(diào)或下調(diào)下游基因的表達(dá)。酵母lncRNA在基因的啟動(dòng)子區(qū)域發(fā)生轉(zhuǎn)錄,使的表達(dá)受到抑制[29];(2)通過抑制RNA聚合酶Ⅱ活性或介導(dǎo)染色質(zhì)重構(gòu)以及組蛋白修飾,影響下游基因表達(dá)。酵母中反義RNA的表達(dá)使Hda1組蛋白產(chǎn)生脫乙酰作用,引起基因的表達(dá)沉默[30];(3)lncRNA與蛋白質(zhì)編碼基因的轉(zhuǎn)錄物形成互補(bǔ)雙鏈,阻斷剪接體對于剪接位點(diǎn)的識別,從而形成可變剪接轉(zhuǎn)錄物。如哺乳動(dòng)物的A型利尿鈉肽前體(NPPA)的反義鏈可能與NPPA mRNA形成雙鏈RNA,影響NPPA mRNA的剪接[31];(4)與正義或者反義轉(zhuǎn)錄物雜交形成互補(bǔ)雙鏈,在Dicer酶作用下產(chǎn)生內(nèi)源性的siRNA,調(diào)控基因的表達(dá)水平。在雌性哺乳動(dòng)物中,與X染色體失活相關(guān)的lncRNA和其反義鏈轉(zhuǎn)錄物可形成互補(bǔ)雙鏈,并被Dicer酶加工為siRNA,參與X染色體失活[32];(5)通過結(jié)合到特定蛋白質(zhì)上,lncRNA能夠調(diào)節(jié)相應(yīng)蛋白質(zhì)的活性。如可與轉(zhuǎn)錄因子Dlx2形成復(fù)合物,使Dlx2的活性增強(qiáng)[33];(6)作為RNA-蛋白質(zhì)復(fù)合體結(jié)構(gòu)的組成成分。Fox等[34]發(fā)現(xiàn)lncRNA與RNA結(jié)合蛋白PSP1、PSP2和p54/nrb共同構(gòu)成了一種新型核質(zhì)結(jié)構(gòu)域——paraspeckles[25, 34~36];(7)結(jié)合到特定蛋白上,改變蛋白質(zhì)在細(xì)胞中的定位。如轉(zhuǎn)錄因子NFAT位于細(xì)胞質(zhì)中,鈣依賴信號使其進(jìn)入細(xì)胞核,從而激活靶基因的轉(zhuǎn)錄,而當(dāng)lncRNA與核質(zhì)運(yùn)輸有關(guān)的蛋白結(jié)合后,抑制了NFAT向細(xì)胞核的運(yùn)輸[37, 38];(8)lncRNA能被加工產(chǎn)生小分子RNA,如miRNA、piRNA和其他小RNA[39, 40]。
植物在應(yīng)對環(huán)境變化的過程中顯示出非凡的發(fā)育可塑性。為了最大程度地減小環(huán)境的不利影響,植物與環(huán)境相互作用,逐漸形成了許多內(nèi)在生理和外在形態(tài)方面的適應(yīng)對策,出現(xiàn)了不同的植物性狀,這些特殊生理現(xiàn)象的形成與其體內(nèi)一些基因的表達(dá)調(diào)控息息相關(guān)。
植物ncRNA的研究起步較晚,且多數(shù)研究集中在短鏈非編碼RNA上,lncRNA的識別更是處于起步階段,因此植物lncRNA的研究可能揭示控制植物生長和分化的未知新機(jī)制。
在ncRNA研究過程中,隨著lncRNA的分子特征、表達(dá)模式和功能數(shù)據(jù)增多,建立了一些針對人類和動(dòng)物lncRNA的數(shù)據(jù)庫,但這些數(shù)據(jù)庫所含的植物lncRNA信息非常少。Yang等[41]首次通過收集人類、小鼠、狗、雞、果蠅和線蟲不同組織和細(xì)胞的543個(gè)ChIP-seq實(shí)驗(yàn)數(shù)據(jù)構(gòu)建了ChIPBase數(shù)據(jù)庫,主要包含了848 834個(gè)TF-lncRNA(transcription factor- lncRNA)和TF-miRNA(transcription factor-miRNA)調(diào)控關(guān)系,提供了TF-lncRNA和TF-miRNA調(diào)控關(guān)系圖譜以及轉(zhuǎn)錄因子結(jié)合位點(diǎn)(TFBSs:transcription factor binding sites)等信息。Mattick等[42]于2009年通過芯片和原位雜交數(shù)據(jù)構(gòu)建了哺乳類動(dòng)物和人類的NRED(Noncoding RNA Expression Database)數(shù)據(jù)庫,提供了lncRNA的二級結(jié)構(gòu)特征、進(jìn)化保守性和表達(dá)等信息。中國科學(xué)院計(jì)算技術(shù)研究所Zhao等[43]通過人類和小鼠芯片數(shù)據(jù)構(gòu)建了包含73 370個(gè)lncRNA表達(dá)和功能注釋的NONCODEv3數(shù)據(jù)庫。2014年,Zhao等[44]進(jìn)一步收集RNA-seq數(shù)據(jù),并更新NONCODEv3數(shù)據(jù)庫到NONCODEv4版本,其中l(wèi)ncRNA數(shù)量已經(jīng)擴(kuò)增到210 831個(gè),有56 018和46 475個(gè)lncRNA分別來自人類和小鼠。LNCipedia[45]是一個(gè)專門提供人類lncRNA序列和結(jié)構(gòu)全面注釋的數(shù)據(jù)庫。LncRNABase[46, 47]提供了miRNA調(diào)控lncRNA的互作信息。LncRNADisease[48]提供了疾病相關(guān)的lncRNA信息。
近年隨著新的高通量測序技術(shù)的開發(fā)和運(yùn)用,植物lncRNA的研究已經(jīng)取得顯著成果。擬南芥[7, 49~52]、苜蓿()[53]、玉米()[54]和小麥(L)[55]等植物全基因組范圍內(nèi)ncRNA的研究中發(fā)現(xiàn)了大量lncRNA。與人類和動(dòng)物相比,植物lncRNA相關(guān)的專門數(shù)據(jù)庫非常少,同時(shí)一些最新研究成果在公共數(shù)據(jù)庫中并沒有進(jìn)行記錄和注釋[56]。
TAIR(TheInformation Resource)是專門的擬南芥基因數(shù)據(jù)庫,是進(jìn)行擬南芥生物學(xué)和生物模型研究的重要信息來源[57]。TAIR記載了擬南芥基因組序列及基因組圖譜、各種基因的序列、結(jié)構(gòu)、表達(dá)模式和功能注釋及詳盡的各種代謝途徑,同時(shí)還有各種擬南芥種子庫存數(shù)據(jù)等信息[58]。從2000~2010年,TAIR已經(jīng)更新了10個(gè)版本。最新TAIR10中記載了擬南芥478條lncRNA信息,遺憾的是它們的生物學(xué)信息沒有被記載。
2011年,Mattick等[59]構(gòu)建了所有真核生物的lncRNAdb(lncRNAs Database)數(shù)據(jù)庫,2014年,Quek等[60]將其更新為第二版,這個(gè)數(shù)據(jù)庫包含lncRNA的序列及結(jié)構(gòu)特征、進(jìn)化保守性、表達(dá)、基因組序列、亞細(xì)胞定位、功能證據(jù)和文獻(xiàn)鏈接等其他相關(guān)信息,其中記載了擬南芥(6個(gè))、水稻(L,2個(gè))、大豆(,1個(gè))、苜蓿(3個(gè))、葡萄(,1個(gè))、蕪菁(,1個(gè))、番茄(,1個(gè))和楊樹(,1個(gè))共計(jì)16個(gè)lncRNA表達(dá)情況和可能的功能等相關(guān)信息。
PlantNATsDB[61](Plant Natural Antisense Transcripts DataBase)是首個(gè)專門用于預(yù)測、查詢植物天然反義轉(zhuǎn)錄物(Natural antisense transcript,NAT;一種產(chǎn)生于編碼基因或非編碼基因反義鏈的ncRNA,參與調(diào)節(jié)各種生物和非生物脅迫響應(yīng)過程[62~64])及其調(diào)控功能的數(shù)據(jù)庫,這個(gè)數(shù)據(jù)庫大約包含69種植物的200萬個(gè)NAT,其中包括擬南芥的7788個(gè)NAT(3005個(gè)正義-NAT,4783個(gè)反義-NAT)。但是,PlantNATsDB僅列出所有NAT對,不提供全基因組查詢。
PLncDB[56](Plant long non-coding RNA database)是目前唯一公開發(fā)表的植物lncRNA專用數(shù)據(jù)庫,該數(shù)據(jù)庫收集了EST分析、RepTAS 分析、芯片、RNA-seq分析及 TAIR中發(fā)現(xiàn)的16 227個(gè)擬南芥lncRNA的信息,記載了在不同組織、發(fā)育階段、突變體和應(yīng)激處理?xiàng)l件下這些lncRNA的表達(dá)特性,介紹了編碼lncRNA的基因座及其側(cè)翼基因組區(qū)域的DNA甲基化和組蛋白修飾等表觀遺傳變化和可能的功能,同時(shí)也收集了全基因組siRNA信息。PLncDB是目前較為全面的植物lncRNA查詢數(shù)據(jù)庫。
以上lncRNA數(shù)據(jù)庫的相關(guān)信息見表1。
植物lncRNA的預(yù)測方法主要分為計(jì)算RNA組學(xué)方法(Computational RNomics)和實(shí)驗(yàn)RNA組學(xué)方法(Experimental RNomics)[65](表2)。計(jì)算RNA組學(xué)方法是指采用計(jì)算機(jī)與生物學(xué)相結(jié)合的生物信息分析(Bioinformatic analyse)進(jìn)行l(wèi)ncRNA預(yù)測的方法。計(jì)算預(yù)測lncRNA方法中使用的原始數(shù)據(jù)可以是公開發(fā)表的cDNA序列、表達(dá)序列標(biāo)簽(EST)、各種全長cDNA克隆、tiling arrays數(shù)據(jù)、RNA-seq數(shù)據(jù)等。首先將這些數(shù)據(jù)與基因組序列進(jìn)行比對,去除蛋白質(zhì)編碼基因重疊區(qū)域,通過GeneMark.hmm[66]、GenScan[67]、ESTScan2[68]、ANGLE[69]和ORF-Pred-ictor[70]等軟件對剩余序列進(jìn)行ORF預(yù)測,根據(jù)明顯開放閱讀框(ORF)存在與否,區(qū)分mRNA和ncRNA,保留下來的ncRNA序列長度>200 nt的被認(rèn)為是lncRNA。此外,預(yù)測RNA序列是否具有編碼蛋白質(zhì)能力的生物信息學(xué)軟件(如CRITICA[71]、DIANA- EST[72]、CSTminer[73]、CONC[74]、Coding Potential Calculator[75]、integrated ncRNA finder[76]和RNA-code[77])也已經(jīng)被用于動(dòng)、植物lncRNA探索研究中。
表2 植物lncRNA的預(yù)測
實(shí)驗(yàn)RNA組學(xué)方法是通過RNA-seq、構(gòu)建cDNA數(shù)據(jù)庫、微陣列分析和基因組SELEX等發(fā)現(xiàn)lncRNA[65]。高通量測序技術(shù)特別是RNA-seq技術(shù)是發(fā)現(xiàn)lncRNA的有效方法,可以直接、快速地發(fā)現(xiàn)低豐度、新的lncRNA。目前研究中更廣泛采用了計(jì)算與實(shí)驗(yàn)相結(jié)合的方法,這種結(jié)合可以更準(zhǔn)確、有效地預(yù)測lncRNA。
Ben等[7]通過對擬南芥基因組全長cDNA數(shù)據(jù)庫進(jìn)行生物信息學(xué)分析,發(fā)現(xiàn)了76個(gè)ncRNA基因,其中14個(gè)為NAT,5個(gè)是siRNA前體;22個(gè)lncRNA與非生物應(yīng)激應(yīng)答相關(guān),其中2個(gè)lncRNA在非生物應(yīng)激環(huán)境中異常表達(dá)影響了擬南芥的生長和分化。
最近,Liu等[78]開發(fā)了RepTAS(Reproduci-bility-based tiling array analysis strategy)生物信息學(xué)方法,并對公開發(fā)表的200個(gè)擬南芥tiling array數(shù)據(jù)進(jìn)行了全基因組范圍綜合分析,發(fā)現(xiàn)了6480個(gè)基因間長鏈非編碼RNA(Long intergenic non-coding RNA, lincRNA),后續(xù)的RNA-seq結(jié)果表明其中的2708個(gè)表現(xiàn)出組織特異性和非生物脅迫應(yīng)答特性。Wang等[79]利用RepTAS生物信息學(xué)方法分析了公開發(fā)表的來自擬南芥不同器官、組織、不同激素處理、生物和非生物脅迫的200個(gè)tiling array數(shù)據(jù),發(fā)現(xiàn)大量的新lncRNA。這些lncRNA平均長度約731nt,包括基因內(nèi)轉(zhuǎn)錄物和37 238個(gè)NAT正義-反義對,實(shí)驗(yàn)分析證明大量光應(yīng)答NAT對與組蛋白修飾有關(guān)。
Xin等[55]利用微陣列分析和高通量SBS測序相結(jié)合的方法確定了小麥中125個(gè)lncRNA(其中部分為小RNA前體),它們具有組織特異性表達(dá)特征并對白粉病和熱脅迫產(chǎn)生應(yīng)激應(yīng)答反應(yīng)。
Shuai等[80]采用RNA測序方法在三角葉楊()中識別出2542個(gè)lincRNA候選基因,其中504個(gè)對干旱脅迫產(chǎn)生應(yīng)激應(yīng)答。
為了研究擬南芥對尖孢鐮刀菌感染的應(yīng)激應(yīng)答反應(yīng),Zhu等[81]對來自感染細(xì)菌的擬南芥RNA進(jìn)行深度測序,發(fā)現(xiàn)15個(gè)長鏈非編碼NAT和20個(gè)新的lincRNA的表達(dá)受尖孢鐮刀菌感染的調(diào)節(jié),部分基因?qū)φ婢腥井a(chǎn)生防御作用,表明某些lncRNA是擬南芥中抗真菌網(wǎng)絡(luò)中的重要節(jié)點(diǎn)。
Wu等[22]側(cè)重于Pol Ⅲ的Ⅲ型啟動(dòng)子結(jié)構(gòu)特點(diǎn),對擬南芥基因組進(jìn)行計(jì)算檢索,發(fā)現(xiàn)了20種可能的ncRNA候選基因,通過體外無細(xì)胞轉(zhuǎn)錄系統(tǒng)活性檢測,發(fā)現(xiàn)了lncRNA(約260nt),其在擬南芥幼苗中表現(xiàn)了低氧應(yīng)激應(yīng)答特性。
Boerner等[54]開發(fā)并優(yōu)化了Python Pipeline計(jì)算機(jī)語言,采用Python Pipeline與SVM(Support Vector Machine)相結(jié)合的生物信息分析方法篩選了玉米全長cDNA序列,發(fā)現(xiàn)2492個(gè)lncRNA候選基因,其中19個(gè)為miRNA前體,237個(gè)為shRNA(short hairpin)前體,1225個(gè)siRNA前體,1011個(gè)為lncRNA,這些lncRNA中572個(gè)位于編碼基因內(nèi),439個(gè)位于基因間區(qū)域。
Li等[82]對已經(jīng)發(fā)表的30個(gè)不同實(shí)驗(yàn)組玉米EST數(shù)據(jù)和玉米全基因組序列注釋及RNA-seq數(shù)據(jù)進(jìn)行生物信息學(xué)分析,首次發(fā)現(xiàn)玉米中的1704個(gè)lncRNA,平均長度為463nt,表達(dá)分析顯示近50%的lncRNA具有組織特異性,其中一些來自于、和(與玉米生長發(fā)育和農(nóng)業(yè)性狀相關(guān)的關(guān)鍵基因)的調(diào)控區(qū)域。
研究表明,一些重要的ncRNA在許多生物基因組中是保守的?;谛蛄斜J匦缘谋容^基因組學(xué)方法也是預(yù)測ncRNA的生物信息學(xué)方法[52, 83]。Song等[52]運(yùn)用比較基因組學(xué)方法比對了擬南芥、水稻、三角葉楊、木瓜()、葡萄的全基因組序列,確定了擬南芥中16個(gè)基因家族的21個(gè)新ncRNA基因。
基因組SELEX方法已成功運(yùn)用在mRNA結(jié)合蛋白篩選中,但ncRNA研究中的應(yīng)用目前未見報(bào)道[84]。
關(guān)于植物lncRNA的預(yù)測總結(jié)于表2。
2.3.1 植物長鏈非編碼RNA的轉(zhuǎn)錄
真核生物細(xì)胞核中的RNA聚合酶分為三類:RNA聚合酶Ⅰ(Pol Ⅰ:RNA polymeraseⅠ)、RNA聚合酶Ⅱ(Pol Ⅱ:RNA polymeraseⅡ)和RNA聚合酶Ⅲ(Pol Ⅲ:RNA polymeraseⅢ)。Pol Ⅰ位于核仁中,合成rRNA,如28S rRNA、18S rRNA和5.8S rRNA,這些rRNA是細(xì)胞中主要的核糖核酸之一,與多種核糖體蛋白質(zhì)共同構(gòu)成核糖體,在蛋白質(zhì)合成過程中起重要作用。除上述幾種持家非編碼RNA外,目前還沒有發(fā)現(xiàn)Pol Ⅰ合成的其他ncRNA。Pol Ⅱ位于核質(zhì)中,除合成編碼蛋白質(zhì)的mRNA外,還合成許多ncRNA,如snRNA、snoRNA和microRNA。此外,一些lncRNA也由Pol Ⅱ合成,如大豆、苜蓿和水稻中保守的[85~87]、黃瓜(L)中的[88]、玉米中的[89]、擬南芥中的[90]、及[7]和油菜(L)中的[91]等。Pol Ⅲ位于核質(zhì)中,合成tRNA、5S rRNA、snoRNA及microRNA等ncRNA。最近研究發(fā)現(xiàn),Pol Ⅲ也合成調(diào)節(jié)編碼基因表達(dá)的新ncRNA[92]。另外擬南芥中Pol Ⅲ的Ⅲ型啟動(dòng)子合成了低氧應(yīng)激應(yīng)答型lncRNA[22]。Wierzbicki等[93]發(fā)現(xiàn),擬南芥中Pol Ⅱ進(jìn)化而來的RNA聚合酶IV和V(Pol IV/V)參與了短鏈非編碼RNA的合成;同時(shí)Pol V也合成一類擬南芥lncRNA,它們可以和一些抑制染色質(zhì)修飾的沉默因子結(jié)合導(dǎo)致基因沉默[94]。此外,擬南芥和玉米中Pol IV和Pol V可能也合成一類與RNA介導(dǎo)的DNA甲基化有關(guān)的lncRNA[54, 95]。
2.3.2 植物長鏈非編碼RNA的表達(dá)及可能的生物學(xué)功能
lncRNA的研究成果主要集中在人類和動(dòng)物中。近年,隨著對植物ncRNA研究的不斷深入,發(fā)現(xiàn)了一些植物特有的lncRNA。
是一個(gè)磷酸鹽饑餓條件下表達(dá)被高度誘導(dǎo)的lncRNA家族[8]。這類lncRNA除了具有短的、不保守的開放閱讀框外,還具有23nt長度的保守核苷酸序列,根據(jù)上述特征推測它們可能作為核糖核酸調(diào)節(jié)子或編碼一些信號肽在生物體內(nèi)起作用[96, 97]。番茄的是家族中最早被發(fā)現(xiàn)的成員,其在基因組中為單拷貝,并且磷酸鹽饑餓條件下在根和葉中被迅速誘導(dǎo),表明可能與番茄中早期磷酸鹽饑餓反應(yīng)機(jī)制有關(guān)[98]。苜蓿[99~101]序列中含有許多短的開放閱讀框,其中一個(gè)開放閱讀框的部分序列與番茄中的開放閱讀框重合。在磷酸鹽饑餓條件下在苜蓿的根中被大量誘導(dǎo),但在磷酸鹽充足的條件下幾乎不被轉(zhuǎn)錄。是在水稻中發(fā)現(xiàn)的家族成員,磷酸鹽饑餓時(shí)在根和葉部被誘導(dǎo)表達(dá),但在根中的誘導(dǎo)尤為顯著[102]。(Induced by phosphate starvation 1)是擬南芥中發(fā)現(xiàn)的又一個(gè)家族成員,在高度磷酸鹽饑餓條件下,在葉和根部大量積累[96]。是擬南芥中同樣被磷酸鹽饑餓誘導(dǎo)積累于地上部分和根中的miRNA,它通過與的5′UTR區(qū)域的部分序列堿基互補(bǔ)配對介導(dǎo)()mRNA的斷裂,在轉(zhuǎn)錄后水平降低的表達(dá)[97, 103]。研究發(fā)現(xiàn),序列中23個(gè)核苷酸保守區(qū)域與的部分序列也存在堿基互補(bǔ),通過模仿的靶基因,與競爭結(jié)合,抑制的活性,使mRNA的積累增加,維持磷酸鹽饑餓條件下擬南芥的正常生長[96, 97]。通過“目標(biāo)模仿”機(jī)制抑制miRNA的活性[8],是首個(gè)明確作用機(jī)制的家族成員。作用機(jī)制表明,一些lncRNA可以通過自身部分序列與功能性miRNA堿基互補(bǔ)配對,從而模仿miRNA的靶基因,減弱miRNA的調(diào)節(jié)因子作用,在生物學(xué)過程中發(fā)揮重要作用。這為今后未知功能的lncRNA作用靶元件預(yù)測提供了一個(gè)新思路。
染色質(zhì)修飾對動(dòng)、植物發(fā)育過程中組織特異性基因的表達(dá)和基因組重組具有重要作用。lncRNA和染色質(zhì)重構(gòu)復(fù)合物之間的相互作用是動(dòng)物基因表觀遺傳沉默的普遍機(jī)制[104]。植物開花調(diào)控基因(FLOWERING LOCUS C)可以通過染色質(zhì)修飾影響植物開花時(shí)間。研究表明,冷處理誘導(dǎo)(Vernalization insensitive 3)的表達(dá),可以招募染色質(zhì)重構(gòu)復(fù)合物PRC2到基因座產(chǎn)生抑制型H3K27me3組蛋白修飾,從而改變?nèi)旧|(zhì)活性狀態(tài),引起基因的表觀遺傳沉默,調(diào)控植物開花時(shí)間[8]。Swiezewski等[105]采用Single Nucleotide Resolution Array技術(shù)對雙鏈及側(cè)翼50 kb區(qū)域進(jìn)行研究,發(fā)現(xiàn)了多個(gè)來自基因座的冷誘導(dǎo)反義轉(zhuǎn)錄物,即(Cold induced antisense intragenic RNA)。具有5¢端加帽及3¢端聚腺苷酸化結(jié)構(gòu),并可進(jìn)行剪接。的冷應(yīng)激反應(yīng)比發(fā)生得更早,并且表達(dá)不受缺失影響。冷誘導(dǎo)條件下對的表達(dá)有抑制作用,但環(huán)境條件由寒冷變?yōu)闇嘏瘯r(shí),的抑制作用變得可逆,這表明只能暫時(shí)抑制表達(dá),而基因失活的表觀遺傳模式是調(diào)控植物開花的必要途徑。因?yàn)楹偷谋磉_(dá)水平呈相反趨勢,并且在發(fā)生轉(zhuǎn)錄情況下,基因座上的Pol II含量減少,這意味著通過轉(zhuǎn)錄干擾的方式抑制表達(dá)。所以冷脅迫下的表達(dá)調(diào)控可能通過下面模式進(jìn)行:冷脅迫誘導(dǎo)的表達(dá),瞬時(shí)抑制的轉(zhuǎn)錄,進(jìn)一步冷脅迫處理誘導(dǎo)了的表達(dá),招募染色質(zhì)重構(gòu)復(fù)合物PRC2到基因上,產(chǎn)生抑制型H3K27me3組蛋白修飾,引起基因的表觀遺傳沉默,進(jìn)而調(diào)控植物開花[8]。另外,新的研究表明不是抑制表達(dá)所必須的ncRNA[106]。
(Cold assisted intronic noncoding RNA)是來自擬南芥基因第一個(gè)內(nèi)含子的正義轉(zhuǎn)錄物,是不同于的又一類Pol Ⅱ轉(zhuǎn)錄的lncRNA[107]。長約1100nt,具有Pol IV和V轉(zhuǎn)錄的lncRNA結(jié)構(gòu)特點(diǎn),如5¢端加帽,但3¢端沒有聚腺苷酸化等特征。冷處理誘導(dǎo)表達(dá),冷處理20 d后的表達(dá)達(dá)到峰值,冷處理30 d后其表達(dá)降到冷處理前水平。雖然的表達(dá)模式和相似,但它的表達(dá)峰值比滯后10 d。研究表明,缺失型擬南芥植株表現(xiàn)出冷處理后開花延遲現(xiàn)象,這可能是由于的缺失導(dǎo)致基因的染色質(zhì)沒有富集抑制型H3K27me3組蛋白引起的。RNA結(jié)合實(shí)驗(yàn)也進(jìn)一步表明,特異地與CLF(Curly Leaf,與H3K27me3修飾有關(guān)的PRC2復(fù)合體的重要組成成分)相互作用。因此,冷處理?xiàng)l件下,可能通過募集PRC2到染色質(zhì)引起表觀遺傳修飾,構(gòu)建了基因沉默機(jī)制,即通過Polycomb-依賴模式負(fù)調(diào)控的表達(dá)。是首次發(fā)現(xiàn)的參與基因染色質(zhì)表觀遺傳學(xué)修飾的植物lncRNA[8]。
Nongken 58S(NK 58S)是水稻Nongken 58N (NK 58N)的自然突變品種,其光敏感引起雄性不育(Photoperiod-sensitivemalesterility, PSMS)。NK 58S在長日照條件下花粉完全不育,短日照則不會(huì)引起不育。Ding等[108]采用位置克隆方法(Position cloning strategy)發(fā)現(xiàn)長約1236nt的lncRNA,即(Long-day-specific male-fertility-associated RNA)。長日照條件下,NK 58N和NK 58S花粉的發(fā)育需要大量,而調(diào)查發(fā)現(xiàn)長日照條件下NK 58S的積累量少于NK 58N,并且NK 58S啟動(dòng)子區(qū)域甲基化程度高于NK 58N。進(jìn)一步研究表明,這個(gè)現(xiàn)象是由于NK 58S序列的一個(gè)堿基C突變成G引起了二級結(jié)構(gòu)產(chǎn)生變化,導(dǎo)致啟動(dòng)子區(qū)域的甲基化,抑制了NK 58S表達(dá),使長日照條件下NK 58S雄花不育。同時(shí),來自啟動(dòng)子區(qū)域正義鏈的siRNA,即也對啟動(dòng)子區(qū)域的甲基化起調(diào)節(jié)作用[109]。Zhou等[110]證明中136nt長度的小RNA是引起PSMS的重要序列。遺憾的是,基因和小RNA是否調(diào)控雄性花粉不育目前仍未闡明[111]。
是最初在豆科植物中發(fā)現(xiàn)的根瘤特異性表達(dá)并與共生固氮根瘤形成有關(guān)的lncRNA[86,112],之后分別在水稻及苜蓿中發(fā)現(xiàn)了的同源基因[87]和[113]。在水稻莖中特異表達(dá),對水稻的器官分化和維管束組織發(fā)育發(fā)揮關(guān)鍵作用[87]。酵母三雜交實(shí)驗(yàn)發(fā)現(xiàn)苜蓿中與一種持續(xù)表達(dá)的RNA結(jié)合蛋白MtRBP1產(chǎn)生相互作用,使細(xì)胞質(zhì)中MtRBP1產(chǎn)生移位,這種RNA結(jié)合蛋白的亞細(xì)胞定位改變可能代表lncRNA在細(xì)胞中的某種新功能[85]。最近,酵母三雜交實(shí)驗(yàn)進(jìn)一步發(fā)現(xiàn)與兩個(gè)結(jié)瘤素酸性RNA結(jié)合蛋白MtSNARP1和MtSNARP2相互作用[114]。上述結(jié)果表明,酵母三雜交技術(shù)可以有效應(yīng)用于與lncRNA相互作用的生物大分子篩選研究。番茄ENOD40-GUS轉(zhuǎn)基因植株的GUS表達(dá)模式顯示,番茄中可能與消除乙烯的刺激反應(yīng)有關(guān)[115]。此外,在大豆中編碼12和24個(gè)氨基酸長度的短肽,這些短肽特定地與蔗糖合成酶結(jié)合,表明與根瘤中蔗糖利用率的調(diào)節(jié)有關(guān)。苜蓿編碼13和27個(gè)氨基酸長度的短肽,這兩個(gè)短肽與生物活性相關(guān)[116, 117]。但是,的作用機(jī)制可能只是通過的RNA分子本身而不是短肽起作用[27]。
(1517nt)是在黃瓜中發(fā)現(xiàn)的一種lncRNA[88],其在黃瓜的不同組織、不同發(fā)育階段和不同光照周期都有差異表達(dá),可能與黃瓜的雌雄分化有關(guān)。以前的研究表明,、和這3種ncRNA是生物脅迫信號中至關(guān)重要的基因[118]。與、和有179nt的保守區(qū)域,推測可能調(diào)節(jié)某些生物應(yīng)激應(yīng)答基因的表達(dá)。
Dai等[119]發(fā)現(xiàn)玉米中(1149nt)是一種花粉特異性表達(dá)的lncRNA,在單子葉植物中有高度保守的序列和穩(wěn)定的RNA二級結(jié)構(gòu)。能調(diào)節(jié)、、這3種與玉米花粉發(fā)育有關(guān)的關(guān)鍵基因的表達(dá),抑制或者過表達(dá)該基因都會(huì)影響雄蕊和花藥的生長發(fā)育,引起玉米小孢子空癟、變形,絨氈層出現(xiàn)退化延遲,使花粉形態(tài)異常,可用于玉米雄性不育植株的制作[89]。在煙草(L.)的研究中也得到了相似的結(jié)果,煙草中的異常表達(dá)擾亂了花的生長發(fā)育,約有80%轉(zhuǎn)基因煙草的花蕾在開花前花軸變黃,最終大多數(shù)脫落[120]。
Song等[91]發(fā)現(xiàn)了在油菜花粉發(fā)育的各個(gè)階段持續(xù)表達(dá)的花粉特異基因(828nt)。在轉(zhuǎn)基因油菜中,雌花發(fā)育正常,而雄花產(chǎn)生不育的花粉。研究結(jié)果顯示過表達(dá)植株的絨氈層和小孢子發(fā)育異常,使花藥發(fā)育不全,顏色變?yōu)楹稚虬咨?,形態(tài)干癟,甚至不產(chǎn)生花粉,引起油菜雄花不育[91,121]。
Ben等確定了擬南芥中76個(gè)lncRNA[7]:14個(gè)為蛋白質(zhì)編碼基因的反義轉(zhuǎn)錄物,它們可能起著反式調(diào)控作用;5個(gè)是24nt siRNA的前體;經(jīng)DCL4加工后形成;22個(gè)lncRNA受非生物脅迫調(diào)節(jié)。生物學(xué)功能研究發(fā)現(xiàn),過量表達(dá)改變了積累并導(dǎo)致擬南芥出現(xiàn)鋸齒狀葉和開花延遲現(xiàn)象;鹽脅迫下過量表達(dá)調(diào)節(jié)了擬南芥根的生長。
Wu等[22]用計(jì)算檢索方法發(fā)現(xiàn)了Pol Ⅲ合成的lncRNA,其在擬南芥根中及擬南芥由來的MM2d細(xì)胞的細(xì)胞質(zhì)中特異地大量表達(dá),且在甘藍(lán)()和蘿卜(L.)等十字花科植物中發(fā)現(xiàn)了它的同源物。低氧應(yīng)激處理抑制表達(dá),表明它是低氧應(yīng)激應(yīng)答型lncRNA。目前,的作用機(jī)制尚不清楚。
植物中的lncRNA總結(jié)于表3。
表3 植物中的lncRNA
ncRNA具有明確的生理功能,但卻不編碼任何蛋白質(zhì),僅以RNA分子形式發(fā)揮作用。從ncRNA在不同生物體細(xì)胞的所有轉(zhuǎn)錄物中所占的比例可以看出,RNA的數(shù)量和多樣性似乎與物種的復(fù)雜性密切相關(guān),其普遍性及重要性遠(yuǎn)遠(yuǎn)超出人們的想象,在生物體的多種生命活動(dòng)中起著至關(guān)重要的作用。到目前為止,人們只看到部分ncRNA所具有的功能,如果能進(jìn)一步確定ncRNA的結(jié)構(gòu)特征將會(huì)有更大的發(fā)現(xiàn)。
隨著被發(fā)現(xiàn)的ncRNA增多,越來越多的相關(guān)研究涉及到植物lncRNA,但目前植物lncRNA的研究仍處在初級階段,且研究主要集中在擬南芥、水稻、小麥和玉米這幾種植物中,已經(jīng)發(fā)現(xiàn)的部分lncRNA不能被確定是功能性轉(zhuǎn)錄物還是轉(zhuǎn)錄“噪音”,未知的lncRNA的詳細(xì)數(shù)量仍不清楚。同時(shí),預(yù)測植物lncRNA作用靶元件的生物信息學(xué)工具相對較少,這為準(zhǔn)確推測其可能的作用機(jī)制增加了難度。目前,已經(jīng)證明了某些lncRNA是microRNA的前體,部分lncRNA可以調(diào)節(jié)microRNA或蛋白質(zhì)編碼基因的功能,但對其詳細(xì)作用機(jī)制所知甚少,而且不同lncRNA適用的研究方法很少可以相互借鑒。這些因素限制了植物lncRNA研究進(jìn)展。在以后的研究中,有必要開發(fā)針對植物lncRNA的研究方法,從而更好地預(yù)測植物中l(wèi)ncRNA和其作用靶目標(biāo),識別更多符合已知功能模式或未知功能模式的lncRNA,并闡明其作用機(jī)制,為植物ncRNA研究提供新思路。
[1] Eddy SR. Non-coding RNA genes and the modern RNA world., 2001, 2(12): 919–929.
[2] Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs., 2009, 136(4): 629–641.
[3] Stoughton RB. Applications of DNA microarrays in biology., 2005, 74: 53–82.
[4] Carthew RW, Sontheimer EJ. Origins and Mechanisms of miRNAs and siRNAs., 2009, 136(4): 642–655.
[5] Malone CD, Hannon GJ. Small RNAs as guardians of the genome., 2009, 136(4): 656–668.
[6] Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions., 2009, 10(3): 155–159.
[7] Ben Amor B, Wirth S, Merchan F, Laporte P, d'Aubenton-Carafa Y, Hirsch J, Maizel A, Mallory A, Lucas A, Deragon JM, Vaucheret H, Thermes C, Crespi M. Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses., 2009, 19(1): 57–69.
[8] Zhang J, Mujahid H, Hou YX, Nallamilli BR, Peng ZH. Plant long ncRNAs: a new frontier for gene regula-tory control., 2013, 4: 1038–1045.
[9] Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR. RNA maps reveal new RNA classes and a possible function for pervasive transcription., 2007, 316(5830): 1484– 1488.
[10] Prasanth KV, Spector DL. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum., 2007, 21(1): 11–42.
[11] Amaral PP, Dinger ME, Mercer TR, Mattick JS. The eukaryotic genome as an RNA machine., 2008, 319(5871): 1787–1789.
[12] Cao XW, Yeo G, Muotri AR, Kuwabara T, Gage FH. Noncoding RNAs in the mammalian central nervous system., 2006, 29: 77–103.
[13] Wapinski O, Chang HY. Long noncoding RNAs and human disease., 2011, 21(6): 354–361.
[14] 鄭曉飛. 非編碼RNA. 北京: 化學(xué)工業(yè)出版社, 2008: 2–3.
[15] Mattick JS. Non-coding RNAs: the architects of eukaryotic complexity., 2001, 2(11): 986–991.
[16] Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang JH, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C,Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R,Chaturvedi K, Deng ZM, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan WN, Ge WM, Gong FC, Gu ZP, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke ZX, Ketchum KA, Lai ZW, Lei YD, Li ZY, Li JY, Liang Y, Lin XY, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK,Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun JT, Wang ZY, Wang AH, Wang X, Wang J, Wei MH, Wides R, Xiao CL, Yan CH, Yao A, Ye J, Zhan M, Zhang WQ, Zhang HY, Zhao Q, Zheng LS, Zhong F, Zhong WY, Zhu SC, Zhao SY, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An HJ, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D,Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N,Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R,Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J,Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K,Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L,Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C,Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D,Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu XJ, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu XH. The sequence of the human genome., 2001, 291(5507): 1304–1351.
[17] Duret L, Chureau C, Samain S, Weissenbach J, Avner P. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene., 2006, 312(5780): 1653–1655.
[18] Elisaphenko EA, Kolesnikov NN, Shevchenko AI, Rogozin IB, Nesterova TB, Brockdorff N, Zakian SM. A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements., 2008, 3(6): e2521.
[19] Flynn M, Saha O, Young P. Molecular evolution of the LNX gene family., 2011, 11: 235.
[20] Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M, Okunishi R, Fukuda S, Ru K, Frith MC, Gongora MM, Grimmond SM, Hume DA, Hayashizaki Y, Mattick JS. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome., 2006, 16(1): 11–19.
[21] Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Soldà G, Simons C, Sunkin SM, Crowe ML, Grimmond SM, Perkins AC, Mattick JS. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation., 2008, 18(9): 1433–1445.
[22] Wu J, Okada T, Fukushima T, Tsudzuki T, Sugiura M, Yukawa Y. A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis., 2012, 9(3): 302–313.
[23] Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. Specific expression of long noncoding RNAs in the mouse brain., 2008, 105(2): 716–721.
[24] Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons., 2007, 120(Pt 15): 2498–2506.
[25] Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, Lawrence JB. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles., 2009, 33(6): 717–726.
[26] Golden DE, Gerbasi VR, Sontheimer EJ. An inside job for siRNAs., 2008, 31(3): 309–312.
[27] Zhu QH, Wang MB. Molecular functions of long non- coding RNAs in plants., 2012, 3(1): 176– 190.
[28] Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world., 2009, 23(13): 1494–1504.
[29] Martens JA, Laprade L, Winston F. Intergenic tran-scription is required to repress the Saccharomyces cerevi-siae SER3 gene., 2004, 429(6991): 571–574.
[30] Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in., 2007, 131(4): 706–717.
[31] Annilo T, Kepp K, Laan M. Natural antisense transcript of natriuretic peptide precursor A (): structural organization and modulation ofexpression., 2009, 10: 81.
[32] Ogawa Y, Sun BK, Lee JT. Intersection of the RNA interference and X-inactivation pathways., 2008, 320(5881): 1336–1341.
[33] Feng JC, Bi CM, Clark BS, Mady R, Shah P, Kohtz JD. Thenoncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 tran-scriptional coactivator., 2006, 20(11): 1470– 1484.
[34] Fox AH, Lam YW, Leung AKL, Lyon CE, Andersen J, Mann M, Lamond AI. Paraspeckles: a novel nuclear domain., 2002, 12(1): 13–25.
[35] Sasaki YTF, Ideue T, Sano M, Mituyama T, Hirose T. MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles., 2009, 106(8): 2525–2530.
[36] Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL. MEN epsilon/beta nuclear-retained non-cod-ing RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles., 2009, 19(3): 347–359.
[37] Hogan PG, Chen L, Nardone J, Rao A. Transcriptional regulation by calcium, calcineurin, and NFAT., 2003, 17(18): 2205–2232.
[38] Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT., 2005, 309(5740): 1570–1573.
[39] Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants., 2002, 16(13): 1616–1626.
[40] Hirsch J, Lefort V, Vankersschaver M, Boualem A, Lucas A, Thermes C, d'Aubenton-Carafa Y, Crespi M. Characterization of 43 non-protein-coding mRNA genes in, including the-derived transcripts., 2006, 140(4): 1192–1204.
[41] Yang JH, Li JH, Jiang S, Zhou H, Qu LH. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP- Seq data., 2013, 41(Database issue): D177–D187.
[42] Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS. NRED: a database of long noncoding RNA expression., 2009, 37(Database issue): D122–D126.
[43] Bu D, Yu K, Sun S, Xie C, Skogerb? G, Miao R, Xiao H, Liao Q, Luo H, Zhao G, Zhao H, Liu Z, Liu C, Chen R, Zhao Y. NONCODE v3.0: integrative annotation of long noncoding RNAs., 2012, 40(Database issue): D210–D215.
[44] Xie C, Yuan J, Li H, Li M, Zhao G, Bu D, Zhu W, Wu W, Chen R, Zhao Y. NONCODEv4: exploring the world of long non-coding RNA genes., 2014, 42(Database issue): D98–D103.
[45] Volders PJ, Helsens K, Wang XW, Menten B, Martens L, Gevaert K, Vandesompele J, Mestdagh P. LNCipedia: a database for annotated human lncRNA transcript sequen-ces and structures., 2013, 41(Database issue): D246–D251.
[46] Li JH, Liu S, Zhou H, Qu LH, Yang JH. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein- RNA interaction networks from large-scale CLIP-Seq data., 2014, 42(Database issue): D92–D97.
[47] Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. starBase: a database for exploring microRNA-mRNA inter-action maps from Argonaute CLIP-Seq and Degradome- Seq data., 2011, 39(Database issue): D202–D209.
[48] Chen G, Wang ZY, Wang DQ, Qiu CX, Liu MX, Chen X, Zhang QP, Yan GY, Cui QH. LncRNADisease: a database for long-non-coding RNA-associated diseases., 2013, 41(Database issue): D983–D986.
[49] MacIntosh GC, Wilkerson C, Green PJ. Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs., 2001, 127(3): 765–776.
[50] Marker C, Zemann A, Terh?rst T, Kiefmann M, Kastenmayer JP, Green P, Bachellerie JP, Brosius J, Hüttenhofer A. Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana., 2002, 12(23): 2002–2013.
[51] Rymarquis LA, Kastenmayer JP, Hüttenhofer AG, Green PJ. Diamonds in the rough: mRNA-like non-coding RNAs., 2008, 13(7): 329–334.
[52] Song D, Yang Y, Yu B, Zheng B, Deng Z, Lu BL, Chen X, Jiang T. Computational prediction of novel non-coding RNAs in Arabidopsis thaliana., 2009, 10(Suppl 1): S36.
[53] Wen J, Parker BJ, Weiller GF. In Silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula., 2007, 7(4–5): 485–505.
[54] Boerner S, McGinnis KM. Computational identification and functional predictions of long noncoding RNA in., 2012, 7(8): e43047.
[55] Xin MM, Wang Y, Yao YY, Song N, Hu ZR, Qin DD, Xie CJ, Peng HR, Ni ZF, Sun QX. Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing., 2011, 11: 61.
[56] Jin JJ, Liu J, Wang H, Wong L, Chua NH. PLncDB: plant long non-coding RNA database., 2013, 29(8): 1068–1071.
[57] Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E. The Arabidopsis Information Resource (TAIR): gene structure and function annotation., 2008, 36(Database issue): D1009–D1014.
[58] Lamesch P, Berardini TZ, Li DH, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools., 2012, 40(Database issue): D1202–D1210.
[59] Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs., 2011, 39(Database issue): D146–D151.
[60] Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs., 2015,43(Database issue): D168–D173.
[61] Chen DJ, Yuan CH, Zhang J, Zhang Z, Bai L, Meng YJ, Chen LL, Chen M. PlantNATsDB: a comprehensive database of plant natural antisense transcripts., 2012, 40(Database issue): D1187–D1193.
[62] Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G. In search of antisense., 2004, 29(2): 88–94.
[63] Werner A. Natural antisense transcripts., 2005, 2(2): 53–62.
[64] Charon C, Moreno AB, Bardou F, Crespi M. Non-protein- coding RNAs and their interacting RNA-binding proteins in the plant cell nucleus., 2010, 3(4): 729–739.
[65] Hüttenhofer A. RNomics: identification and function of small non-protein-coding RNAs in model organisms., 2006, 71: 135–140.
[66] Lukashin AV, Borodovsky M. GeneMark.hmm: new solutions for gene finding., 1998, 26(4): 1107–1115.
[67] Burge CB, Karlin S. Finding the genes in genomic DNA., 1998, 8(3): 346–354.
[68] Lottaz C, Iseli C, Jongeneel CV, Bucher P. Modeling sequencing errors by combining Hidden Markov models., 2003, 19(Suppl 2): ii103-ii112.
[69] Shimizu K, Adachi J, MuraokaY. ANGLE: a sequencing errors resistant program for predicting protein coding regions in unfinished cDNA., 2006, 4(3): 649–664.
[70] Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L. Genome-wide computational identification and manual annotation of human long noncoding RNA genes., 2010, 16(8): 1478–1487.
[71] Badger JH, Olsen GJ. CRITICA: coding region identifi-cation tool invoking comparative analysis., 1999, 16(4): 512–524.
[72] Hatzigeorgiou AG, Fiziev P, Reczko M. DIANA-EST: a statistical analysis., 2001, 17(10): 913–919.
[73] Mignone F, Grillo G, Liuni S, Pesole G. Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis., 2003, 31(15): 4639–4645.
[74] Liu J, Gough J, Rost B. Distinguishing protein-coding from non-coding RNAs through support vector machines., 2006, 2(4): e29.
[75] Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei LP, Gao G. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine., 2007, 35(Web Server issue): W345– W349.
[76] Lu ZJ, Yip KY, Wang GL, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB. Prediction and characterization of noncod-ing RNAs inby integrating conservation, secondary structure, and high-throughput sequencing and array data., 2011, 21(2): 276–285.
[77] Washietl S, Findeiβ S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data., 2011, 17(4): 578–594.
[78] Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, Arenas-Huertero C, Chua NH. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis., 2012, 24(11): 4333–4345.
[79] Wang H, Chung PJ, Liu J, Jang IC, Kean MJ, Xu J, Chua NH. Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in., 2014, 24(3): 444–453.
[80] Shuai P, Liang D, Tang S, Zhang ZJ, Ye CY, Su YY, Xia XL, Yin WL. Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in., 2014, 65(17): 4975–4983.
[81] Zhu QH, Stephen S, Taylor J, Helliwell CA, Wang MB. Long noncoding RNAs responsive toinfection in., 2014, 201(2): 574–584.
[82] Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MM, Scanlon MJ, Yu J, Schnable PS, Timmermans MC, Springer NM, Muehlbauer GJ. Genome-wide discovery and characterization of maize long non-coding RNAs., 2014, 15(2): R40.
[83] McCutcheon JP, Eddy SR. Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics., 2003, 31(14): 4119–4128.
[84] Hüttenhofer A, Vogel J. Experimental approaches to identify non-coding RNAs., 2006, 34(2): 635–646.
[85] Campalans A, Kondorosi A, Crespi M., a short open reading frame-containing mRNA, induces cytopla-smic localization of a nuclear RNA binding protein in., 2004, 16(4): 1047–1059.
[86] van de Sande K, Pawlowski K, Czaja I, Wieneke U, Schell J, Schmidt J, Walden R, Matvienko M, Wellink J, van Kammen A, Franssen H, Bisseling T. Modification of phytohormone response by a peptide encoded byof legumes and a nonlegume., 1996, 273(5273): 370–373.
[87] Kouchi H, Takane K, So RB, Ladha JK, Reddy PM. Rice: isolation and expression analysis in rice and transgenic soybean root nodules., 1999, 18(2): 121–129.
[88] Cho J, Koo DH, Nam YW, Han CT, Lim HT, Bang JW, Hur Y. Isolation and characterization of cDNA clones expressed under male sex expression conditions in a monoecious cucumber plant (L. cv. Winter Long)., 2005, 146(3): 271–281.
[89] Ma JX, Yan BX, Qu YY, Qin FF, Yang YT, Hao XJ, Yu JJ, Zhao Q, Zhu DY, Ao GM., a short-open reading-frame mRNA or noncoding RNA, is essential for tapetum and microspore development and can regulate the floret formation in maize., 2008, 105(1): 136–146.
[90] Shin H, Shin HS, Chen RJ, Harrison MJ. Loss offunction impacts phosphate distribution between the roots and the shoots during phosphate starvation., 2006, 45(5): 712–726.
[91] Song JH, Cao JS, Yu XL, Xiang X. BcMF11, a putative pollen-specific non-coding RNA fromssp. chinensis., 2007, 164(8): 1097–1100.
[92] Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A. The expanding RNA polymerase III transcriptome., 2007, 23(12): 614–622.
[93] Wierzbicki AT, Haag JR, Pikaard CS. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes., 2008, 135(4): 635–648.
[94] Rowley MJ, B?hmdorfer G, Wierzbicki AT. Analysis of long non-coding RNAs produced by a specialized RNA polymerase in., 2013, 63(2): 160–169.
[95] Haag JR, Pikaard CS. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing., 2011, 12(8): 483–492.
[96] Martín AC, del Pozo JC, Iglesias J, Rubio V, Solano R, de La Pe?a A, Leyva A, Paz-Ares J. Influence of cytokinins on the expression of phosphate starvation responsive genes in., 2000, 24(5): 559–567.
[97] Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, García JA, Paz-Ares J. Target mimicry provides a new mechanism for regulation of microRNA activity., 2007, 39(8): 1033–1037.
[98] Liu CM, Muchhal US, Raghothama KG. Differential expression of TPS11, a phosphate starvation-induced gene in tomato., 1997, 33(5): 867–874.
[99] Burleigh SM, Harrison MJ. Characterization of the Mt4 gene from., 1998, 216(1): 47–53.
[100]Burleigh SH, Harrison MJ. The down-regulation of-like genes by phosphate fertilization occurs systemically and involves phosphate translocation to the shoots., 1999, 119(1): 241–248.
[101]Burleigh SH, Harrison MJ. A novel gene whose expression in Medicago truncatula roots is suppressed in response to colonization by vesicular-arbuscular mycorrhizal (VAM) fungi and to phosphate nutrition., 1997, 34(2): 199–208.
[102]Wasaki J, Yonetani R, Shinano T, Kai M, Osaki M. Expression of thegene, cloned from rice roots using cDNA microarray, rapidly responds to phosphorus status., 2003, 158(2): 239–248.
[103]Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK. A miRNA involved in phosphate-starvation response in., 2005, 15(22): 2038–2043.
[104]Nagano T, Fraser P. Emerging similarities in epigenetic gene silencing by long noncoding RNAs., 2009, 20(9–10): 557–562.
[105]Swiezewski S, Liu FQ, Magusin A, Dean C. Cold-induced silencing by long antisense transcripts of anPolycomb target., 2009, 462(7274): 799–802.
[106]Helliwell CA, Robertson M, Finnegan EJ, Buzas DM, Dennis ES. Vernalization-repression of Arabidopsis FLC requires promoter sequences but not antisense transcripts., 2011, 6(6): e21513.
[107]Heo JB, Sung S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA., 2011, 331(6013): 76–79.
[108] Ding JH, Lu Q, Ouyang YD, Mao HL, Zhang PB, Yao JL, Xu CG, Li XH, Xiao JH, Zhang QF. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice., 2012, 109(7): 2654–2659.
[109] Ding JH, Shen JQ, Mao HL, Xie WB, Li XH, Zhang QF. RNA-directed DNA methylation is involved in regulating photoperiod-sensitive male sterility in rice., 2012, 5(6): 1210–1216.
[110]Zhou H, Liu QJ, Li J, Jiang DG, Zhou LY, Wu P, Lu S, Li F, Zhu LY, Liu ZL, Chen LT, Liu YG, Zhuang CX. Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA., 2012, 22(4): 649–660.
[111]Zhu DM, Deng XW. A non-coding RNA locus mediates environment-conditioned male sterility in rice., 2012, 22(5): 791–792.
[112]Yang WC, Katinakis P, Hendriks P, Smolders A, de Vries F, Spee J, van Kammen A, Bisseling T, Franssen H. Characterization of, a gene showing novel patterns of cell-specific expression during soybean nodule development., 1993, 3(4): 573–585.
[113]Crespi MD, Jurkevitch E, Poiret M, d'Aubenton-Carafa Y, Petrovics G, Kondorosi E, Kondorosi A. enod40, a gene expressed during nodule organogenesis, codes for a non-translatable RNA involved in plant growth., 1994, 13(21): 5099–5112.
[114]Laporte P, Satiat-Jeunema?tre B, Velasco I, Csorba T, Van de Velde W, Campalans A, Burgya J, Arevalo-Rodriguez M, Crespi M. A novel RNA-binding peptide regulates the establishment of the-nitrogen-fixing symbiosis., 2010, 62(1): 24–38.
[115]Vleghels I, Hontelez J, Ribeiro A, Fransz P, Bisseling T, Franssen H. Expression ofduring tomato plant development., 2003, 218(1): 42–49.
[116]Rohrig H, Schmidt J, Miklashevichs E, Schell J, John M. Soybean ENOD40 encodes two peptides that bind to sucrose synthase., 2002, 99(4): 1915–1920.
[117]Sousa C, Johansson C, Charon C, Manyani H, Sautter C, Kondorosi A, Crespi M. Translational and structural requirements of the early nodulin gene, a short-open reading frame-containing RNA, for elicitation of a cell-specific growth response in the alfalfa root cortex., 2001, 21(1): 354–366.
[118]Erdmann VA, Szymanski M, Hochberg A, de Groot N, Barciszewski J. Non-coding, mRNA-like RNAs database Y2K., 2000, 28(1): 197–200.
[119]Dai XY, Yu JJ, Zhao Q, Zhu DY, Ao GM. Non-coding RNA for, a pollen-specific gene of., 2004, 46(4): 497–504.
[120]Ma JX, Zhao Q, Yu JJ, Ao GM. Ectopic expression of a maize pollen specific gene,, results in aberrant anther development in tobacco., 2005, 144(1-2): 133–140.
[121]Song JH, Cao JS, Wang CG., a novel non-coding RNA gene from, is required for pollen development and male fertility., 2013, 32(1): 21–30.
(責(zé)任編委: 張憲省)
Long non-coding RNAs in plants
Xiaoqing Huang, Dandan Li, Juan Wu
Long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides in length, widely exist in organisms and function in a variety of biological processes. Currently, most of lncRNAs found in plantsare transcribed by RNA polymerase Ⅱ and mediate gene expression through multiple mechanisms, such as target mimicry, transcription interference, histone methylation and DNA methylation, and play important roles in flowering, male sterility, nutrition metabolism, biotic and abiotic stress and other biological processes as regulators in plants. In this review, we summarize the databases, prediction methods, and possible functions of plant lncRNAs discovered in recent years.
long non-coding RNAs (lncRNAs); database; gene expression regulation; biological function
2014-12-04;
2015-01-27
東北林業(yè)大學(xué)中央高校基本科研業(yè)務(wù)費(fèi)專項(xiàng)資金項(xiàng)目(編號: DL12BA38),長江學(xué)者和創(chuàng)新團(tuán)隊(duì)發(fā)展計(jì)劃資助(編號: IRT13053),東北林業(yè)大學(xué)中央高校基本科研業(yè)務(wù)費(fèi)專項(xiàng)資金項(xiàng)目(編號: DL13EA04 - 02)和教育部留學(xué)回國人員科研啟動(dòng)基金(第47批)資助
黃小慶,碩士研究生,專業(yè)方向:生物化學(xué)與分子生物學(xué)。E-mail: huangxiaoqing85@163.com
吳娟,博士,副教授,研究方向:植物生理學(xué)和RNA分子生物學(xué)。E-mail: wuj1970@163.com
10.16288/j.yczz.14-432
2015-3-3 16:58:43
http://www.cnki.net/kcms/detail/11.1913.R.20150303.1658.002.html