長鏈非編碼核糖核酸

長鏈非編碼核糖核酸（英語：long non-coding RNAs，簡稱為lncRNA）指的是長於200核苷酸的不編碼蛋白質的轉錄物（Perkel 2013）。該有些武斷的界定將長鏈非編碼核糖核酸與較小的調控核糖核酸區分開來，後者如微核糖核酸（miRNAs）、小干擾核糖核酸（siRNAs）、Piwi互作核糖核酸類（piRNAs）、小核仁核糖核酸（snoRNAs）及其它短核糖核酸（Ma 2013）。

長鏈非編碼核糖核酸的豐度

近年研究顯示人類基因組中的轉錄只有五分之一與蛋白編碼基因有關（Kapranov 2007），這說明至少有較編碼核糖核酸序列四倍多的長鏈非編碼核糖核酸。而像FANTOM（哺乳動物cDNA功能注釋）等的大規模互補脫氧核糖核酸（cDNA）測序計劃揭示了轉錄的複雜性（Carninci 2005）。FANTOM3計劃從約一萬個不同的基因座中鑑定出了約三萬五千條非編碼轉錄物它們有着與mRNA類類似的特徵，包括5'端有帽、受到剪接及多聚腺苷酸化，但只有很小的開放閱讀框（ORF）或根本沒有（Carninci 2005）。然而長鏈非編碼RNA的豐度是意料之外的，其數目代表的是保守估計的最低值，因為這種方法忽略了許多單獨的轉錄物及非多腺苷酸化的轉錄物（瓦片陣列數據顯示出40%以上的轉錄物是非多腺苷酸化的）（Cheng 2005）。儘管如此，在這些cDNA文庫中明確鑑定非編碼RNA類仍是充滿挑戰的，因為該方法無法區分非編碼轉錄物及蛋白編碼轉錄物。

長鏈非編碼核糖核酸的基因組組織

目前將哺乳動物基因組的全景描繪為：長段的基因間空間將多個轉錄「焦點」分割開（Carninci 2005）。然而長鏈非編碼核糖核酸正位於這些基因間區段中並由此轉錄出來，其中大多數是與其它轉錄物之間呈錯綜複雜的正義或反義重疊，這些轉錄物往往包括了蛋白編碼基因（Kapranov 2007）。在正義或反義鏈上的多個不同的編碼或非編碼轉錄物共享這些轉錄焦點中的基因組序列（Birney 2007），使得這些重疊的亞型之間產生複雜的層次結構。例如，8961個cDNA中的3012個曾被FANTOM2計劃注釋為編碼序列中的一段截短序列，但後來又重新被指定為蛋白編碼cDNA中的新非編碼RNA變異體（Carninci 2005）。儘管編碼RNA及非編碼RNA的交錯排列具備一定的豐度和保守性，並可能意味着它們兩者之間具有某些生物學關聯性，但仍無法對這些複雜的焦點結構進行簡單的評價。

GENCODE共同體已綜合性整理及分析了一些人類長鏈非編碼RNA的注釋及它們的基因組結構、修飾、細胞定位及組織表達譜（Derrien 2012）。他們的分析結果說明人類長鏈非編碼RNA易形成具有兩個外顯子的轉錄物（Derrien 2012）。

長鏈非編碼核糖核酸的保守性

如微核糖核酸及小核仁核糖核酸等的眾多小型核糖核酸都顯現出了跨多物種的保守性（Bentwich 2005）。與之相反，大多數長鏈非編碼核糖核酸則保守性不強，這一點常被引用為其不具備功能的證據（Brosius 2005；Struhl 2007）。然而，如Air及Xist等經過詳細研究的長鏈非編碼RNA，它們的保守性也很差（Nesterova 2001），這意味着非編碼RNA類可能受到不同的選擇壓力（Pang 2006）。mRNA必須保守密碼子的正常用法並防止單個長ORF中出現移碼突變，然而對長鏈非編碼RNA的選擇壓力可能只會令其保守其中的較短區域，這些較短區域對於結構或序列特異性相互作用較為關鍵。因此，我們可見選擇壓力只會作用於長鏈非編碼RNA轉錄物的小塊區域。仍然要看到：儘管長鏈非編碼RNA總體來說保守性較低，但仍可見許多長鏈非編碼RNA具有較強的保守元件。例如，高度保守的phastCons元件中有19%存在於已知的內含子中，而其它32%存在於未注釋的區域之中（Siepel 2005）。此外，人類長鏈非編碼RNA中的具有代表性的一類長鏈非編碼RNA在鹼基取代和插入/缺失速率方面顯現出較小但顯著的降低，這一現象指示了淨化選擇壓力使得轉錄物的完整性得到保守，這在序列、啟動子及剪接三種水平上體現出來（Ponjavic 2007）。

非編碼核糖核酸的保守性差可能是近期且快速的適應性選擇的結果。例如，非編碼核糖核酸較蛋白編碼基因可能對進化壓力可塑性更強，如Xist或Air等的許多世系特異性非編碼RNA的存在可以證明這一點（Pang 2006）。相對於黑猩猩基因組來說人類基因組中經受近期進化改變的保守區域確實主要存在於非編碼區域，其中很多已有詳盡描述（Pollard 2006；Pollard 2006）。其中包括一條名為HAR1F的非編碼RNA，該基因在人類中經歷了快速的進化變化，且特異性地在人類新皮質的卡哈爾-雷濟厄斯氏細胞中特異性表達（Pollard 2006）。現有報道稱許多功能已確定的RNA進化速率也很快（Pang 2006；Smith 2004），這可能由於這些序列受到結構-功能約束時表現得更靈活，我們可以期待在這些序列中發現新的進化方式。人類基因組中有數千條序列的一級序列保守性較差，但有證據顯示它們RNA二級結構卻存在着保守性（Torarinsson 2006；Torarinsson 2008），這支持了上述論點。

長鏈非編碼核糖核酸的功能

cDNA文庫的大規模測序及更先進的基於下一代測序的轉錄組測序表明哺乳動物中長鏈非編碼核糖核酸的數量大約是幾萬條。然而，雖然越來越多的證據提示大多數長鏈非編碼核糖核酸具有功能（Mercer 2009；Dinger 2009），但相對只有一小部分已被證明有生物學重大意義。截至2012年十二月，約有127條長鏈非編碼RNA在LncRNAdb（一個描述長鏈非編碼RNA的文獻數據庫）中有功能注釋（Amral 2011）。

長鏈非編碼RNA類在基因轉錄調控中的作用

長鏈非編碼RNA類在基因特異性轉錄中的作用

RNA轉錄在真核生物中是一個受到嚴密調控的過程。非編碼RNA可以靶向該進程的多個方面，包括靶向轉錄激活因子或轉錄抑制因子、如RNA聚合酶（RNAP）Ⅱ等轉錄反應中的各組分、甚至是DNA雙螺旋結構，以達到調控基因轉錄及表達的目的（Goodrich 2006）。非編碼RNA將這些機制結合在一起可以組成為一個包括轉錄因子在內的調控網絡，可以精細地調控複雜真核生物的基因表達。

非編碼RNA通過多種不同的機制調節轉錄因子的功能，包括充當共調控因子的角色、修飾轉錄因子的活性或是調控共調控因子的活性。例如，非編碼RNA Evf-2作為同源異形框轉錄因子Dlx2的共激活因子，Dlx2在前腦發育及神經發生中起到重要作用（Feng 2006；Panganiban 2002）。Evf-2轉錄自位於Dlx5與Dlx6基因之間的超保守元件，音蝟因子在前腦發育過程中誘導該長鏈的轉錄（Feng 2006）。Evf-2接着將Dlx2轉錄因子招募到同一個超保守元件處，Dlx2在此處誘導Dlx5的表達。哺乳動物基因組中存在其它一些可轉錄且執行增強子功能的超級保守或高度保守元件，這提示Evf-2可作為範例闡述脊椎動物生長過程中以複雜表達的形式嚴密調控重要發育基因的普遍機制（Pennacchio 2006；Visel 2008）。近期研究也確實發現與之類似的其它非編碼超保守元件的轉錄及表達在人類白血病中出現異常，且促進結腸癌細胞的凋亡，這提示了它們涉及到腫瘤形成（Calin 2007）。

局部的非編碼RNA類可以招募轉錄機制對附近蛋白編碼基因的轉錄加以調控。TLS（英語：translocated in liposarcoma）是一種結合RNA的蛋白，它結合到CREB結合蛋白和組蛋白乙酰基轉移酶p300上並抑制這兩者在靶基因周期蛋白D1上的活性，從而起到抑制後者的作用。作為DNA受損信號的響應，長鏈非編碼RNA以低水平表達出來並拴在周期蛋白D1基因的5'調控區域上，這指導了TLS招募到周期蛋白D1啟動子上（Wang 2008）。除此之外，這些局部的非編碼RNA作為配體調控TLS的活性。從更廣泛的層面上說，這一機制使得細胞可以利用RNA結合蛋白（它們組成了哺乳動物蛋白質組中的最龐大的種類之一）並在轉錄程序控制中整合它們的功能。

在X染色體失活的情況下一些基因仍可以轉錄，近期對逃避染色體失活控制的染色體區域進行研究，發現其中表達的長鏈非編碼RNA可能介導了這一過程（Reinius 2010）。

長鏈非編碼RNA調控基礎轉錄機器

非編碼RNA還可以靶向通用轉錄因子，後者是RNAPⅡ轉錄所有基因所必需的（Goodrich 2006）。這些通用因子包括了起始複合體中組裝在啟動子上或涉及轉錄延伸的部件。轉錄自二氫葉酸還原酶（DHFR）基因上游次要啟動子的一條非編碼RNA進入DHFR主要啟動子，形成穩定的RNA-DNA三股螺旋以阻止轉錄輔因子TFⅡB結合到其上（Martianov 2007）。已知真核染色體上存在着數千個三股螺旋（Lee 1987），這一調控基因表達的新機制可能事實上代表這些三股螺旋在控制啟動子上起到的廣泛作用。U1非編碼RNA通過結合到TFⅡH上並刺激其對RNAPⅡ的C-端以實現誘導轉錄起始（Kwek 2002）。相反，非編碼RNA 7SK可通過下列方式起到抑制轉錄延伸的作用：7SK首先與HEXIM1/2結合，形成抑制性複合物，該複合物阻止PTEFb通用轉錄因子去磷酸化RNAPⅡ的C-端結構域（Kwek 2002；Yang 2001；Yik 2003），當細胞處於應激狀況下可以抑制全局延伸。這些例子中的機制可以繞開單個啟動子上特異性的調控模式，介導起始及延伸轉錄機器工作水平發生直接改變，提供了迅速影響基因表達全局改變的方法。

現也證明非編碼重複序列有着介導全局調控的能力。人類的短散在核內（SINE）Alu元件及小鼠中同源的B1和B2元件是基因組中豐度最高的可移動性元件，分別組成了人類和小鼠基因組的約10%和約6%（Lander 2001；Waterston 2002）。在如熱休克等環境應激情況下這些元件被RNAPⅢ轉錄為非編碼RNA（Liu 1995），後者接下來會以高親和度的方式與RNAPⅡ結合併阻止其形成為有活性的前起始複合物（Allen 2004；Espinoza 2004；Espinoza 2007；Mariner & Walters 2008）。這使得在響應應激的情況下可以大範圍並迅速抑制基因的表達（Allen 2004；Mariner & Walters 2008）。

對Alu元件的RNA轉錄物中的功能序列進行分析後，發現其亦有類似於蛋白質轉錄因子中結構域的模塊化結構（Shamovsky 2008）。Alu元件RNA包括兩個「臂」，每個臂都可以結合到一個RNAPⅡ分子上；體外實驗表明該RNA還具有兩個調控結構域，起到抑制RNAPⅡ轉錄活性的作用（Mariner 2008）。 These two loosely-structured domains may even be concatenated to other ncRNAs such as B1 elements to impart their repressive role (Mariner & Walters 2008). The abundance and distribution of Alu elements and similar repetitive elements throughout the mammalian genome may be partly due to these functional domains being co-opted into other long ncRNAs during evolution, with the presence of functional repeat sequence domains being a common characteristic of several known long ncRNAs including Kcnq1ot1, Xlsirt and Xist (Mattick 2003; Mohammad 2008; Wutz 2002; Zearfoss 2003).

除了熱休克外，如病毒感染、, the expression of SINE elements (including Alu, B1, and B2 RNAs) increases during cellular stress such as viral infection (Singh 1985) in some cancer cells (Tang 2005) where they may similarly regulate global changes to gene expression. The ability of Alu and B2 RNA to bind directly to RNAP II provides a broad mechanism to repress transcription (Espinoza 2004; Mariner & Walters 2008). Nevertheless, there are specific exceptions to this global response where Alu or B2 RNAs are not found at activated promoters of genes undergoing induction, such as the heat shock genes (Mariner & Walters 2008). This additional hierarchy of regulation that exempts individual genes from the generalised repression also involves a long ncRNA, heat shock RNA-1 (HSR-1). It was argued that HSR-1 is present in all cells in an inactive state, but upon stress is activated to induce the expression of heat shock genes (Shamovsky 2006). The authors found that this activation involves a conformational alteration to the structure of HSR-1 in response to rising temperatures, thereby permitting its interaction with the transcriptional activator HSF-1 that subsequently undergoes trimerisation and induces the expression of heat shock genes (Shamovsky 2006). In the broad sense, these examples illustrate a regulatory circuit nested witin ncRNAs whereby Alu or B2 RNAs repress general gene expression, while other ncRNAs activate the expression of specific genes.

長鏈非編碼RNA類在基因轉錄後調控中的作用

除了在轉錄水平上調控，ncRNAs 也在轉錄後水平調控mRNA加工的不同方面。與小調控RNAs，例如微小RNAs和小核仁RNAs，類似，ncRNAs 的功能包括與目標mRNA進行互補鹼基配對。互補ncRNA和mRNA形成的RNA雙鏈可能為需要結合反式作用因子的mRNA募集關鍵因子，可能影響轉錄後水平基因表達的每一步，包括前體mRNA加工，剪接，運輸，翻譯以及降解。

長鏈非編碼RNA類在剪接調控中的作用

The splicing of mRNA can induce its translation and functionally diversify the repertoire of proteins it encodes. The Zeb2 mRNA, which has a particularly long 5』UTR, requires the retention of a 5』UTR intron that contains an internal ribosome entry site for efficient translation (Beltran 2008). However, retention of the intron is dependent on the expression of an antisense transcript that complements the intronic 5』 splice site (Beltran 2008). Therefore, the ectopic expression of the antisense transcript represses splicing and induces translation of the Zeb2 mRNA during mesenchymal development. Likewise, the expression of an overlapping antisense Rev-ErbAα2 transcript controls the alternative splicing of the thyroid hormone receptor ErbAα2 mRNA to form two antagonistic isoforms (Munroe 1991).

長鏈非編碼RNA類在翻譯調控中的作用

NcRNA may also apply additional regulatory pressures during translation, a property particularly exploited in neurons where the dendritic or axonal translation of mRNA in response to synaptic activity contributes to changes in synaptic plasticity and the remodelling of neuronal networks. The RNAP III transcribed BC1 and BC200 ncRNAs, that previously derived from tRNAs, are expressed in the mouse and human central nervous system, respectively (Tiedge 1993; Tiedge 1991). BC1 expression is induced in response to synaptic activity and synaptogenesis and is specifically targeted to dendrites in neurons (Muslimov 1998). Sequence complementarity between BC1 and regions of various neuron-specific mRNAs also suggest a role for BC1 in targeted translational repression (Wang 2005). Indeed it was recently shown that BC1 is associated with translational repression in dendrites to control the efficiency of dopamine D2 receptor-mediated transmission in the striatum (Centonze 2007) and BC1 RNA-deleted mice exhibit behavioural changes with reduced exploration and increased anxiety (Lewejohann 2004).

長鏈非編碼RNA類在siRNA導向的基因調控中的作用

In addition to masking key elements within single-stranded RNA, the formation of double-stranded RNA duplexes can also provide a substrate for the generation of endogenous siRNAs (endo-siRNAs) in Drosophila and mouse oocytes (Golden 2008). The annealing of complementary sequences, such as antisense or repetitive regions between transcripts, forms an RNA duplex that may be processed by Dicer-2 into endo-siRNAs. Also, long ncRNAs that form extended intramolecular hairpins may be processed into siRNAs, compellingly illustrated by the esi-1 and esi-2 transcripts (Czech 2008). Endo-siRNAs generated from these transcripts seem particularly useful in suppressing the spread of mobile transposon elements within the genome in the germline. However, the generation of endo-siRNAs from antisense transcripts or pseudogenes may also silence the expression of their functional counterparts via RISC effector complexes, acting as an important node that integrates various modes of long and short RNA regulation, as exemplified by the Xist and Tsix (see above) (Ogawa 2008).

長鏈非編碼RNA類在表觀遺傳調控中的作用

包括組蛋白和DNA甲基化、組蛋白乙酰化和SUMO化等在內的表觀遺傳修飾影響了染色體生物學的眾多方面，主要包括通過對廣大染色質區域進行重塑從而調控大量基因（Kiefer 2007；Mikkelsen 2007）。一段時間以來，RNA作為染色質的有機組成部分已被人知曉（Nickerson 1989；Rodriguez-Campos 2007），但現在我們才開始認識到RNA在涉及到染色質修飾通路上的意義（Chen 2008；Rinn 2007；Sanchez-Elsner 2006）。

果蠅屬中的長鏈非編碼RNA類通過將三胸蛋白Ash1募集到同源異形調控元件並指導其發揮染色質修飾作用的方式誘導同源異形基因Ubx的表達（Sanchez-Elsner 2006）。後來發現哺乳動物中也存在着相似的調控模式：認為強大的表觀遺傳機制奠定了胚胎同源異形基因家族的表達譜，而同源異形基因家族是貫穿整個人體發育過程中持續發揮作用的重要因子（Mazo 2007；Rinn 2007）。人類同源異形基因家族確實與數百個非編碼RNA之間有着相關性，這些非編碼RNA在人體發育的時空軸上按順序表達，這些非編碼RNA也定義染色質各區域中組蛋白甲基化程度的差異以及RNA聚合酶可進入染色質的程度（Rinn 2007）。其中一條名為HOTAIR的轉錄自HOXC基因座的非編碼RNA通過改變組蛋白三甲基化狀態從而使HOXD基因座中長約40kb的區域發生轉錄沉默。目前認為HOTAIR執行的作用機制是：多梳染色質重塑複合物具有操縱細胞表觀遺傳狀態的功能，而HOTAIR以反式調控的方式指導該功能的發揮並繼而影響基因的表達。多梳複合物中的成員包括SUZ12、EZH2和EED等，它們具有RNA結合結構域並可能結合HOTAIR及其它類似的非編碼RNA類（Denisenko 1998；Katayama 2005）。該例子極好地描繪出了這樣一個更廣泛的主題：非編碼RNA類招募一系列染色質修飾蛋白到特定基因組基因座上並發揮功能，這更加突出了目前所繪製基因組圖譜的複雜性（Mikkelsen 2007）。發育時期中調控基因表達的染色質修飾有着區域化的模式，大量長鏈非編碼與蛋白編碼基因的聯繫確實幫助塑造了這種模式。例如，大多數蛋白編碼基因都具有配對的反義基因，許多抑癌基因在癌症中常受到沉默，一些反義基因使用表觀遺傳機制使這些抑癌基因沉默（Yu 2008）。近期研究發現：在白血病中p15基因和一條反義非編碼RNA的表達此消彼長（Yu 2008）。經過詳細分析發現：p15的反義非編碼RNA（CDKN2BAS）可通過一種未知機制誘導p15的異染色質和DNA甲基化狀態發生改變，因而調控了p15基因的表達（Yu 2008）。因此，相關的反義非編碼RNA類表達發生異常可能繼而沉默了抑癌基因，從而走向癌症發生。

基因印記

最近非編碼RNA指導的染色質修飾主題最初是從基因組印記的現象中引出的，基因組印記是僅從母系或父系染色體兩者中的一個表達出等位基因的現象。一般來說，印記基因是呈簇狀排列於染色體上，這提示：印記的機制是作用於局部的染色質區域上而不是針對單個基因。這些基因簇常常與長鏈非編碼RNA相關：長鏈非編碼RNA的表達量與在相同等位上相連鎖的蛋白編碼基因受到抑制的程度呈正相關（Pauler 2007）。詳細分析確實顯示出非編碼RNA Kcnqot1和Igf2r/Air在指導基因印記上發揮着重要作用（Braidotti 2004）。

幾乎所有位於Kcnq1基因座Almost all the genes at the Kcnq1 loci are maternally inherited, except the paternally expressed antisense ncRNA Kcnqot1 (Mitsuya 1999). Transgenic mice with truncated Kcnq1ot fail to silence the adjacent genes, suggesting that Kcnqot1 is crucial to the imprinting of genes on the paternal chromosome (Mancini-Dinardo 2006). It appears that Kcnqot1 is able to direct the trimethylation of lysine 9 (H3K9me3) and 27 of histone 3 (H3K27me3) to an imprinting centre that overlaps the Kcnqot1 promoter and actually resides within a Kcnq1 sense exon (Umlauf 2004). Similar to HOTAIR (see above), Eed-Ezh2 Polycomb complexes are recruited to the Kcnq1 loci paternal chromosome, possibly by Kcnqot1, where they may mediate gene silencing through repressive histone methylation (Umlauf 2004). A differentially methylated imprinting centre also overlaps the promoter of a long antisense ncRNA Air that is responsible for the silencing of neighbouring genes at the Igf2r locus on the paternal chromosome (Sleutels 2002; Zwart 2001). The presence of allele-specific histone methylation at the Igf2r locus suggests Air also mediates silencing via chromatin modification (Fournier 2002).

Xist與X-染色體失活

The inactivation of a X-chromosome in female placental mammals is directed by one of the earliest and best characterized long ncRNAs, Xist (Wutz 2007). The expression of Xist from the future inactive X-chromosome, and its subsequent coating of the inactive X-chromosome, occurs during early embryonic stem cell differentiation. Xist expression is followed by irreversible layers of chromatin modifications that include the loss of the histone (H3K9) acetylation and H3K4 methylation that are associated with active chromatin, and the induction of repressive chromatin modifications including H4 hypoacetylation, H3K27 trimethylation (Wutz 2007), H3K9 hypermethylation and H4K20 monomethylation as well as H2AK119 monoubiquitylation. These modifications coincide with the transcriptional silencing of the X-linked genes (Morey 2004). Xist RNA also localises the histone variant macroH2A to the inactive X–chromosome (Costanzi 1998). There are additional ncRNAs that are also present at the Xist loci, including an antisense transcript Tsix, which is expressed from the future active chromosome and able to repress Xist expression by the generation of endogenous siRNA (Ogawa 2008). Together these ncRNAs ensure that only one X-chromosome is active in female mammals.

端粒非編碼RNA類

Telomeres form the terminal region of mammalian chromosomes and are essential for stability and aging and play central roles in diseases such as cancer (Blasco 2007). Telomeres have been long considered transcriptionally inert DNA-protein complexes until it was recently shown that telomeric repeats may be transcribed as telomeric RNAs (TelRNAs) (Schoeftner 2008) or telomeric repeat-containing RNAs (Azzalin 2007). These ncRNAs are heterogeneous in length, transcribed from several sub-telomeric loci and physically localise to telomeres. Their association with chromatin, which suggests an involvement in regulating telomere specific heterochromatin modifications, is repressed by SMG proteins that protect chromosome ends from telomere loss (Azzalin 2007). In addition, TelRNAs block telomerase activity in vitro and may therefore regulate telomerase activity (Schoeftner 2008). Although early, these studies suggest an involvement for telomeric ncRNAs in various aspects of telomere biology.

長鏈非編碼RNA類在衰老與疾病中的作用

外部連結

• LncRNAWiki （頁面存檔備份，存於網際網路檔案館）: a wiki-based database for management of human lncRNAs.
• ChIPBase database^{[永久失效連結]}: decodes the transcriptional regulation of lncRNAs from ChIP-Seq and provides expression profiles of lncRNAs (lincRNAs) from RNA-Seq data across 22 tissues.
• lncRNAdb database （頁面存檔備份，存於網際網路檔案館）: providing comprehensive annotations of functional long non-coding RNAs (lncRNAs).
• Long RNA Synthesis （頁面存檔備份，存於網際網路檔案館）: chemical long RNA synthesis and long RNA synthesis by transcription.

另見

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