RNA中6-甲基腺嘌呤的研究进展

RNA酶促共价修饰研究, 尤其是m⁶A(6-甲基腺嘌呤), 是RNA生物学研究的一个新兴领域。m⁶A是真核生物mRNA内部序列中最常见的一种转录后修饰形式, 由包含3个独立组分的复合物mRNA: m⁶A甲基转移酶催化生成。最新研究发现肥胖相关蛋白FTO可以脱掉m⁶A上的甲基, 表明该甲基化过程是可逆的。抑制或敲除m⁶A甲基转移酶会引起重要的表型变化, 但是由于过去的检测方法受限, m⁶A确切的作用机制目前为止还不甚清楚。二代测序技术结合免疫沉淀方法为大规模检测m⁶A修饰并研究其作用机制提供了可能。文章主要综述了m⁶A的发现史、生成机制、组织和基因组分布、检测方法、生物学功能等及其最新研究进展, 并通过比较3种IP-seq技术和数据分析的异同及优缺点, 对m⁶A这种RNA表观修饰研究中尚未解决的问题进行了讨论。     

RNA m6A甲基化与神经发育

中枢神经系统控制高级神经活动,例如知觉、运动、语言和认知等。作为人体神经系统最重要的部分,其正常的发育及功能活动在人体发育过程中至关重要。更好地了解调节神经系统发育的基本分子途径以及对大脑的基本生物学理解,可以帮助诊断和治疗各种神经疾病。RNA分子m⁶A修饰状态的动态变化及其功能主要由m⁶A甲基转移酶、m⁶A去甲基化酶和m⁶A阅读蛋白等蛋白质复合物共同调控。本文对此进行了详细介绍,并详细概述m⁶A修饰对神经发育的影响,重点介绍表观转录组学在基因调控中的作用。此外,还强调m⁶A修饰在神经发育过程中的生物学意义,包括神经发生、神经分化、轴突导向、突触形成及突触可塑性等。根据不同的实验原理和实验技术,本文详细介绍了最近发展的几种检测m⁶A位点的技术,每种方法都有各自的优点,据此将能够更广泛和更深入地研究这一修饰,并选择合适的方法去研究课题。RNA m⁶A甲基化是神经科学领域的一个新前沿。近年来,随着m⁶A检测技术的发展,m⁶A甲基化在神经系统发育过程中及神经疾病发生中的作用研究逐渐成为热点,具有很大潜力,为神经发育和神经疾病的研究提供了新视角。     

Chlorella virus SC-1A encodes at least five functional and one nonfunctional DNA methyltransferases

Chlorella virus SC-1A encodes at least six DNA methyltransferases (MTases): four N⁶-methyldeoxyadenine (m⁶A) MTases, M- CviSI (TGC^mA), M· CviSII C^mATG), M· CviSIII (TCG^mA) and M^mCviSIV (G^mATC), one 5-methyldeoxycytosine (m⁵C) MTase, M· CviSV (RC^mCG), and one nonfunctional m⁵C MTase, M· CviSVI, which is homologous to the MTase M· CviJI [RG^mC(T/C/G)] produced by another chlorella virus IL-3A. Genes encoding three of the SC-1A m⁶A MTases (M·CviSI, M· CviSII, and M· CviSIII) and the nonfunctional m⁵C MTase were cloned and sequenced. Neither M· CviSI nor M· CviSIII genes hybridized to genes for their respective isomethylomers, M· CviRI and M· CviBIII, from other chlorella viruses. However, the M· CviSII gene hybridized strongly to its M· CviAII isomethylomer gene from virus PBCV-1. Like the prototype chlorella virus PBCV-1, the SC-1A genome contains inverted terminal repeats, one of which is adjacent to the nonfunctional m⁵C MTase. The three cloned m⁶A MTase genes are distributed throughout the approx. 345 kb SC-1A genome.     

水稻ECT基因家族的全基因组研究

真核生物mRNA转录后修饰可调控许多基因的遗传信息,植物m⁶A甲基化研究正成为关注的新热点。m⁶A结合蛋白 (m⁶A readers) 调节m⁶A修饰的特异性,通常具有YTH (YT521-B homology) 结构域,在拟南芥中被命名为ECT结构域 (evolutionarily conserved C-terminal region ECT domain) 。目前ECT基因已在拟南芥和水稻等植物中检测到,但该基因家族在水稻中的成员及生物学功能还缺乏研究。本研究通过水稻ECT基因家族的全基因组分析,鉴定出12个OsECT基因,具有1个保守的基序,多位于蛋白质氨基酸序列C-端。共线性分析表明,在水稻基因组内OsECT-c与OsECT-e发生了重复事件,在物种间ECT同源基因对可能是在双子叶和单子叶植物分化后形成。同源基因对OsECT的Ka/Ks < 1,表明OsECT基因家族在进化过程中可能经历了较强的纯化选择压力。表达模式分析显示,OsECT-b、OsECT-c、OsECT-e和OsECT-j在水稻生长初期各个组织均保持较高的表达水平,OsECT-g在干旱处理后表达量显著下调。因此,OsECT基因在水稻生长发育和逆境胁迫中可能发挥着重要作用。本研究为今后OsECT基因在水稻的节水抗旱机制研究和相关抗逆育种提供了重要的理论基础。     

Characterization of human AlkB homolog 1 produced in mammalian cells and demonstration of mitochondrial dysfunction in ALKBH1-deficient cells

Alkbh1 is a mammalian homolog of the Escherichia coli DNA repair enzyme AlkB, an Fe(II) and 2-oxoglutarate dependent dioxygenase that removes alkyl lesions from DNA bases. The human homolog ALKBH1 has been associated with six different enzymatic activities including DNA, mRNA, or tRNA hydroxylation, cleavage at abasic (AP) sites in DNA, as well as demethylation of histones. The reported cellular roles of this protein reflect the diverse enzymatic activities and include direct DNA repair, tRNA modification, and histone modification. We demonstrate that ALKBH1 produced in mammalian cells (ALKBH1₂₉₃) is similar to the protein produced in bacteria (ALKBH1_Ec) with regard to its m⁶A demethylase and AP lyase activities. In addition, we find that ALKBH1₂₉₃ forms a covalent adduct with the 5′ product of the lyase product in a manner analogous to ALKBH1_Ec. Localization and subcellular fractionation studies with the endogenous protein in two human cell strains confirm that ALKBH1 is primarily in the mitochondria. Two strains of CRISPR/Cas9-created ALKBH1-deficient HEK293 cells showed increases in mtDNA copy number and mitochondrial dysfunction as revealed by growth measurements and citrate synthase activity assays.     

Methylation Modifications in Eukaryotic Messenger RNA

RNA methylation modifications have been found for decades of years, which occur at different RNA types of numerous species, and their distribution is species-specific. However, people rarely know their biological functions. There are several identified methylation modifications in eukaryotic messenger RNA （mRNA）, such as NT-methylguanosine （mVG） at the cap, Nr-methyl-2＇-O-methyladenosine （m6Am）, 2＇-O-methylation （Nm） within the cap and the internal positions, and internal N6-methyladenosine （m6A） and 5-methylcytosine （mSC）. Among them, mTG cap was studied more clearly and found to have vital roles in several important mRNA processes like mRNA translation, stability and nuclear export, m6A as the most abundant modification in mRNA was found in the 1970s and has been proposed to function in mRNA splicing, translation, stability, transport and so on. mrA has been discovered as the first RNA reversible modification which is demethylated directly by human fat mass and obesity associated protein （FRO） and its homolog protein, alkylation repair ho- molog 5 （ALKBH5）. b-TO has a special demethylation mechanism that demethylases m6A to A through two over-oxidative intermediate states： N6-hydroxymethyladenosine （hm6A） and Nr-formyladenosine （frA）. The two newly discovered m6A demethylases, bTO and ALKBH5, significantly control energy homeostasis and spermatogenesis, respectively, indicating that the dynamic and reversible mrA, analogous to DNA and histone modifications, plays broad roles in biological kingdoms and brings us an emerging field ＂RNA Epige- netics＂. 5-methylcytosine （5mC） as an epigenetic mark in DNA has been studied widely, but mSC in mRNA is seldom explored. The bisulfide sequencing showed mSC is another abundant modification in mRNA, suggesting that it might be another RNA epigenetic mark. This review focuses on the main methylation modifications in mRNA to describe their formation, distribution, function and demethylation from the current knowledge and to provide future 19erspectives on functional studies.     

TMK4 receptor kinase negatively modulates ABA signaling by phosphorylating ABI2 and enhancing its activity

In plants, clade A type 2C protein phosphatases (PP2CAs) have emerged as major players in abscisic acid (ABA)-regulated stress responses by inhibiting protein kinase activity. However, how different internal and external environmental signals modulate the activity of PP2CAs are not well known. The transmembrane kinase (TMK) protein 4 (TMK4), one member of a previously identified receptor kinase subfamily on the plasma membrane that plays vital roles in plant cell growth, directly interacts with PP2CAs member (ABA-Insensitive 2, ABI2). tmk4 mutant is hypersensitive to ABA in both ABA-inhibited seed germination and primary root growth, indicating that TMK4 is a negative regulator in ABA signaling pathway. Further analyses indicate that TMK4 phosphorylates ABI2 at three conserved Ser residues, thus enhancing the activity of ABI2. The phosphorylation-mimic ABI2^{S139DS140DS266D} can complement but non-phosphorylated form ABI2^{S139AS140AS266A} cannot complement ABA hypersensitive phenotype of the loss-of-function mutant abi1-2abi2-2. This study provides a previously unidentified mechanism for positively regulating ABI2 by a plasma membrane protein kinase.     

小麦TaLCD基因的克隆及其对渗透胁迫的调节作用

半胱氨酸脱巯基酶(CDes)可催化降解半胱氨酸(Cys)生成硫化氢(H₂S)。通过克隆小麦(Triticum aestivum)中的L-半胱氨酸脱巯基酶基因TaLCD, 并将其在拟南芥(Arabidopsis thaliana)中过表达, 探讨TaLCD对渗透胁迫条件下种子萌发和根系生长的影响, 并分析其对干旱胁迫的调节作用。结果显示, 盐胁迫条件下, TaLCD过表达植株种子萌发率显著高于野生型; 甘露醇处理条件下, TaLCD过表达植株的根长也显著高于野生型, 且TaLCD过表达显著提高植株抗旱性。此外, TaLCD过表达植株对ABA更加敏感, ABA处理下TaLCD过表达植株的种子萌发率及根长均显著低于野生型。干旱胁迫下, TaLCD过表达植株胁迫响应基因(COR47、RD29A、RAB18和RD22)及ABA信号途径相关基因(NCED3、HAB1、HAB2、ABI1、ABI2和ABF2)的表达水平均显著高于野生型。因此推测, TaLCD增强植株抗旱和抗盐能力可能依赖于ABA信号途径。     

干旱胁迫下拟南芥中H_2S与ABA信号关系研究

以野生型拟南芥(WT)、硫化氢(H_2S)合成酶缺失型突变体lcd、脱落酸(ABA)合成缺失型突变体aba1实生苗为材料,以0.3 mol·L^-1甘露醇模拟干旱胁迫,研究干旱胁迫对ABA含量、H_2S含量的影响,及其在拟南芥抵抗干旱胁迫中的作用及信号关系。结果显示:干旱胁迫显著提高LCD和ABA1基因相对表达以及H_2S含量,ABA含量;干旱胁迫显著抑制突变体lcd、aba1的种子萌发;干旱胁迫下,外施NaHS促进干旱胁迫下WT、lcd和aba1中內源H_2S的产生及上调LCD、ABA1基因相对表达,而外施ABA提高干旱胁迫下WT、aba1中H_2S含量及LCD、ABA1基因相对表达,但是对lcd中H_2S含量及LCD基因相对表达没有显著影响。研究结果表明,信号分子H_2S和ABA在拟南芥的干旱胁迫响应中发挥一定的作用,且H_2S位于ABA的下游参与调控拟南芥的信号过程。     

Responses of wild type and abscisic acid mutants ofArabidopsis thaliana to cadmium

Heavy metal-induced inhibitory effects are reported to be concomitant with an increase in endogenous abscisic acid (ABA) levels in plant tissues indicating the possibility of this phytohormone mediating a part of the metal-imposed phytotoxicity. We examined this possibility by comparing the seed germination and seedling growth responses of ABA-deficient (aba-1, aba-3 and aba-4) and ABA-insensitive (abi2-1 and abi3-1) mutants of Arabidopsis thaliana to Cd with those of the wild type (Landsberg erecta, Ler). Assuming that Cd imposed a part of its toxic influence via affecting a rise in endogenous ABA level, all ABA mutants studied could be predicted to exhibit reduced responsiveness to Cd exposure in comparison to the wild type. However, the data obtained both in germination and growth assays were not consistent with this prediction. In germination assays, all ABA mutants proved consistently more sensitive than the wild type to Cd. In case of growth (root length and seedling fresh weight), the magnitude of Cd-induced inhibition in ABA mutants (aba-1, abi2-1 and abi3-1) was generally comparable to that in the wild type. Based on these observations a direct mediatory role of ABA in Cd-imposed phytotoxic effects on early growth could be excluded. The possible significance of heavy metal-dependent increase in endogenous ABA levels in plant tissues is discussed.     

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

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Highlights? ALKBH5 is a mammalian m⁶A RNA demethylase ? RNA demethylation affects mRNA export and RNA metabolism ? RNA demethylation is important for mouse fertility ? Reversible mammalian messenger RNA methylation affects gene expression