m6A修饰与植物RNA病毒侵染

N⁶-甲基腺嘌呤(N6-methyladenosine, m⁶A)是真核生物m RNA中丰度最高的RNA转录后化学修饰. RNA的m⁶A修饰主要由甲基化转移酶(writers)、去甲基化酶(erasers)以及阅读蛋白(reader proteins)共同调控.近年的研究表明, m⁶A修饰在植物病毒侵染中发挥了重要作用,相关调控机制成为植物病毒领域的研究热点.本文概述了植物RNA m⁶A修饰相关蛋白的基本组成和m⁶A修饰的检测技术,重点阐述了m⁶A修饰在植物与RNA病毒互作中的作用,并提出了今后植物RNA病毒m⁶A修饰功能研究的方向.     

基于circRNA的m6A修饰对肿瘤及免疫的调控作用

环状RNA(circular RNA,circRNA)是一类由反向剪切形成的单链共价闭合RNA分子，可通过吸附微RNA(microRNA,miRNA),结合RNA结合蛋白(RNA-binding protein, RBP),以及调控基因表达调控多种生命活动。此外，circRNA还能进行翻译活动，并被认为是一种有前景的生物标志物。N⁶-甲基腺嘌呤(N⁶-methyladenosine, m⁶A)为真核生物中广泛存在且最为常见的RNA修饰方式，通过m⁶A甲基转移酶(writers)、m⁶A去甲基化酶(erasers)和m⁶A识别蛋白(readers)3类调控因子发挥功能。近期的研究发现，m⁶A除了能在mRNA中发挥的作用外，对circRNA也具有调控作用。m⁶A修饰可调控circRNA的表达、稳定性、胞质转移、翻译及逃避非特异性免疫，已经被报道可以在直结肠癌、肝癌、非小细胞肺癌、宫颈癌、乳腺癌、骨肉瘤、下咽鳞状细胞癌...     

m6A修饰对神经干细胞分化的影响

神经干细胞是中枢神经系统中具有自我更新能力并且能够分化产生成熟脑细胞的多潜能细胞，移植神经干细胞治疗神经退行性疾病是一项新兴趋势，已被证实可恢复疾病动物的神经功能。N⁶-甲基腺苷(N⁶-methyladenosine,m⁶A)发生在RNA分子腺苷酸第六位氮原子上，m⁶A甲基转移酶(Writers)和去甲基化酶(Erasers)能够可逆性调控RNA分子的m⁶A甲基化水平，而m⁶A甲基化结合蛋白(Readers)则可以识别RNA上的m⁶A修饰，影响RNA的降解、稳定性和翻译等生物学过程。研究表明，m⁶A修饰在神经系统中含量丰富，并且随着年龄的增长、疾病的进展，其水平发生改变。m⁶A相关酶表达的差异可引起m⁶A修饰水平的改变。一些神经相关因子受到m⁶A修饰的调控，在不改变碱基序列的条件下影响着神经干细胞的分化和神经系统功能的发挥。现将m⁶     

m6A甲基转移酶METTL3在胚胎发育中的作用研究进展

胚胎发育调控机制是一个非常重要的生物学基础问题，而其中的表观遗传学机制成为最近的研究热点。研究发现，甲基转移酶样3 (methyltransferase-like 3,METTL3)催化产生的m⁶A修饰在卵母细胞成熟、母源-合子转化、胚胎干细胞命运调控以及血管生成等胚胎发育过程中发挥重要作用。同时，靶向METTL3的化合物也不断被发现与合成，有望应用于m⁶A相关疾病的靶向治疗。本文就METTL3的结构、催化机制、调控机制、在RNA代谢和胚胎发育中的作用以及METTL3靶向化合物进行介绍。     

m6A修饰调控细胞自噬参与雄性生殖疾病研究进展

N⁶-甲基腺苷(N⁶-methyladenosine, m⁶A)修饰是在腺苷核苷酸N⁶位置上发生的甲基化,在多种RNA代谢过程如m RNA剪接、翻译、运输、降解中发挥关键作用,进而对各种生命过程产生广泛影响。细胞自噬是真核细胞在自噬相关基因的调控下通过溶酶体对自身细胞质蛋白质和受损细胞器进行降解的过程。本文总结了m⁶A修饰调控细胞自噬在雄性生殖疾病发生发展过程中的研究进展,旨在为今后m⁶A修饰调节自噬水平在雄性生殖中的调控机理研究提供参考资料,为雄性生殖疾病的治疗策略提供新方向。     

m6A修饰在植物生长发育和抗逆境胁迫中的功能

真核生物mRNA存在多种甲基化修饰,其中N⁶-腺苷酸甲基化(N⁶-methyladenosine, m⁶A)修饰是最为常见的一种动态内部修饰。m⁶A是指RNA腺嘌呤的第6位氮原子上发生甲基化修饰,它能够动态的被甲基转移酶添加,被去甲基化酶去除,以及被甲基化阅读蛋白识别。近年来,植物m⁶A修饰相关的酶被陆续鉴定,研究发现m⁶A修饰调控植物胚胎发育、茎尖分生组织分化、开花等生长发育过程,在植物抗逆境胁迫响应中也具有重要调控作用。本文就m⁶A修饰相关酶的组成及其在植物生长发育和植物抗逆境胁迫过程中的功能相关研究进展进行综述,并对甘蓝型油菜中m⁶A修饰相关的酶进行了生物信息学分析。     

N6-甲基化腺嘌呤RNA甲基化修饰在中枢神经系统中的作用研究进展

mRNA存在多种转录后修饰,这些修饰调控mRNA的稳定和剪接、翻译、转运等多个过程,进而影响细胞发育、机体免疫、学习认知等重要生理功能。其中m⁶A修饰是转录后修饰中最丰富的一种,广泛存在于mRNA中,调控mRNA的代谢活动,影响基因表达。m⁶A修饰的稳态对神经系统的发育和功能维持至关重要。近年研究发现,在神经退行性疾病、精神疾病和脑肿瘤中均存在m⁶A修饰的身影。因此本文对近几年m⁶A甲基化修饰在中枢神经系统发育、功能及相关疾病中的作用进行总结,为神经系统疾病提供潜在的临床治疗靶点。     

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。     

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。     

m6A甲基化对老年神经退行性疾病的调控作用

衰老是机体对环境的生理和心理适应能力下降，最终导致死亡的自然过程，也是各种老年相关疾病发展的驱动因素，特别是神经退行性疾病。常见的老年神经退行性疾病包括阿尔兹海默病(Alzheimer’s disease, AD)、帕金森病(Parkinson’s disease, PD)、肌萎缩侧索硬化症(amyotrophic lateral sclerosis, ALS)等。而以AD和PD为代表的老年神经退行性疾病是21世纪老龄化社会面临的最大健康问题之一。m⁶A甲基化在多种修饰酶的作用下调控基因转录和翻译，也是最常见的RNA修饰类型。m⁶A修饰酶表达异常引起m⁶A甲基化水平失调，从而引起RNA表达紊乱是m⁶A甲基化参与调控疾病发展的基本机制。近期研究表明，METTL3、FTO在阿尔兹海默病、帕金森病等疾病中发生显著变化，它们通过影响神经炎症、细胞周期、氧化应激等过程参与上述疾病的发生发展。本文以AD和PD为例探讨了m⁶A修饰对老年神经退行性疾病的调控作用，这将为抗衰老和治疗老年相关疾病...     

Human METTL16 is a N6‐methyladenosine (m6A) methyltransferase that targets pre‐mRNAs and various non‐coding RNAs

N⁶‐methyladenosine (m⁶A) is a highly dynamic RNA modification that has recently emerged as a key regulator of gene expression. While many m⁶A modifications are installed by the METTL3–METTL14 complex, others appear to be introduced independently, implying that additional human m⁶A methyltransferases remain to be identified. Using crosslinking and analysis of cDNA (CRAC), we reveal that the putative human m⁶A “writer” protein METTL16 binds to the U6 snRNA and other ncRNAs as well as numerous lncRNAs and pre‐mRNAs. We demonstrate that METTL16 is responsible for N⁶‐methylation of A43 of the U6 snRNA and identify the early U6 biogenesis factors La, LARP7 and the methylphosphate capping enzyme MEPCE as METTL16 interaction partners. Interestingly, A43 lies within an essential ACAGAGA box of U6 that base pairs with 5′ splice sites of pre‐mRNAs during splicing, suggesting that METTL16‐mediated modification of this site plays an important role in splicing regulation. The identification of METTL16 as an active m⁶A methyltransferase in human cells expands our understanding of the mechanisms by which the m⁶A landscape is installed on cellular RNAs.     

m6A‐mediated alternative splicing coupled with nonsense‐mediated mRNA decay regulates SAM synthetase homeostasis

Alternative splicing of pre‐mRNAs can regulate gene expression levels by coupling with nonsense‐mediated mRNA decay (NMD). In order to elucidate a repertoire of mRNAs regulated by alternative splicing coupled with NMD (AS‐NMD) in an organism, we performed long‐read RNA sequencing of poly(A)⁺ RNAs from an NMD‐deficient mutant strain of Caenorhabditis elegans, and obtained full‐length sequences for mRNA isoforms from 259 high‐confidence AS‐NMD genes. Among them are the S‐adenosyl‐L‐methionine (SAM) synthetase (sams) genes sams‐3 and sams‐4. SAM synthetase activity autoregulates sams gene expression through AS‐NMD in a negative feedback loop. We furthermore find that METT‐10, the orthologue of human U6 snRNA methyltransferase METTL16, is required for the splicing regulation in␣vivo, and specifically methylates the invariant AG dinucleotide at the distal 3′ splice site (3′SS) in␣vitro. Direct RNA sequencing coupled with machine learning confirms m⁶A modification of endogenous sams mRNAs. Overall, these results indicate that homeostasis of SAM synthetase in C. elegans is maintained by alternative splicing regulation through m⁶A modification at the 3′SS of the sams genes.     

Activity of chimeric RNAs of U6 snRNA and (-)sTRSV in the cleavage of a substrate RNA.

U6 small nuclear RNA is one of the spliceosomal RNAs essential for pre-mRNA splicing. Discovery of mRNA-type introns in the highly conserved region of the U6 snRNA genes led to the hypothesis that U6 snRNA functions as a catalytic element during pre-mRNA splicing. The highly conserved region of U6 snRNA has a structural similarity with the catalytic domain of the negative strand of the satellite RNA of tobacco ring spot virus [(-)sTRSV], suggesting that the highly conserved region of U6 snRNA forms the catalytic center. We examined whether synthetic RNAs consisting of the sequence of the highly conserved region of U6 snRNA or various chimeric RNAs between the U6 region and the catalytic RNA of (-)sTRSV could cleave a substrate RNA that can partially base-pair with them and have a GU sequence. Chimeric RNAs with 70 to 83% sequence identity with the conserved region of S. pombe U6 snRNA cleaved the substrate RNA at the 5' side of the GU sequence, which is shared by the 5' end of an intron in a pre-mRNA. We found that the highly conserved region of U6 snRNA and the catalytic domain of (-)sTRSV are strikingly similar in structure to the catalytic core region of the group I self-splicing intron in cyanobacteria. These results suggest that U6 snRNA, (-)sTRSV and the group I self-splicing intron originated from a common ancestral RNA, and support the hypothesis that U6 snRNA catalyzes pre-mRNA splicing reaction.     

Synthesis of chimeric RNAs between U6 small nuclear RNA and (-)sTRSV and analysis of their cleavage activities against the substrate RNA.

U6 small nuclear RNA (U6 snRNA) is one of the spliceosomal RNAs essential for pre-mRNA splicing. Highly conserved region of U6 snRNA shows a structural similarity with the catalytic center of the negative strand of the satellite RNA of tobacco ring spot virus [(-)sTRSV], supporting the hypothesis that U6 snRNA has a catalytic role in pre-mRNA splicing. To test this hypothesis, we examined in vitro whether synthetic RNAs consisting of the sequence of the highly conserved region of U6 snRNA or various chimeric RNAs between the U6 region and the catalytic center of (-)sTRSV could cleave a substrate RNA that can partially base-pair with them and has a GU sequence between the pairing regions. Chimeric RNAs with 70 to 83% sequence identity with the conserved region of S. pombe U6 snRNA cleaved the substrate RNA at the 5' side of the GU sequence. In addition, we found that the highly conserved region of U6 snRNA is similar in structure to the catalytic core region of the group I self-splicing intron in cyanobacteria. These results support the hypothesis that U6 snRNA catalyzes the pre-mRNA splicing reaction and U6 snRNA may originate from the catalytic domain of an ancient self-splicing intron.     

Remodeling of U2-U6 snRNA helix I during pre-mRNA splicing by Prp16 and the NineTeen Complex protein Cwc2

Removal of intron regions from pre-messenger RNA (pre-mRNA) requires spliceosome assembly with pre-mRNA, then subsequent spliceosome remodeling to allow activation for the two steps of intron removal. Spliceosome remodeling is carried out through the action of DExD/H-box ATPases that modulate RNA–RNA and protein–RNA interactions. The ATPase Prp16 remodels the spliceosome between the first and second steps of splicing by catalyzing release of first step factors Yju2 and Cwc25 as well as destabilizing U2-U6 snRNA helix I. How Prp16 destabilizes U2-U6 helix I is not clear. We show that the NineTeen Complex (NTC) protein Cwc2 displays genetic interactions with the U6 ACAGAGA, the U6 internal stem loop (ISL) and the U2-U6 helix I, all RNA elements that form the spliceosome active site. We find that one function of Cwc2 is to stabilize U2-U6 snRNA helix I during splicing. Cwc2 also functionally cooperates with the NTC protein Isy1/NTC30. Mutation in Cwc2 can suppress the cold sensitive phenotype of the prp16-302 mutation indicating a functional link between Cwc2 and Prp16. Specifically the prp16-302 mutation in Prp16 stabilizes Cwc2 interactions with U6 snRNA and destabilizes Cwc2 interactions with pre-mRNA, indicating antagonistic functions of Cwc2 and Prp16. We propose that Cwc2 is a target for Prp16-mediated spliceosome remodeling during pre-mRNA splicing.     

Genetic and functional interaction of evolutionarily conserved regions of the Prp18 protein and the U5 snRNA

Both the Prp18 protein and the U5 snRNA function in the second step of pre-mRNA splicing. We identified suppressors of mutant prp18 alleles in the gene for the U5 snRNA (SNR7). The suppressors' U5 snRNAs have either a U4-to-A or an A8-to-C mutation in the evolutionarily invariant loop 1 of U5. Suppression is specific for prp18 alleles that encode proteins with mutations in a highly conserved region of Prp18 which forms an unstructured loop in crystals of Prp18. The snr7 suppressors partly restored the pre-mRNA splicing activity that was lost in the prp18 mutants. The close functional relationship of Prp18 and U5 is emphasized by the finding that two snr7 alleles, U5A and U6A, are dominant synthetic lethal with prp18 alleles. Our results support the idea that Prp18 and the U5 snRNA act in concert during the second step of pre-mRNA splicing and suggest a model in which the conserved loop of Prp18 acts to stabilize the interaction of loop 1 of the U5 snRNA with the splicing intermediates.     

An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene.

Splicing an mRNA precursor requires multiple factors involving five small nuclear RNA (snRNA) species called U1, U2, U4, U5, and U6. The presence of mRNA-type introns in the U6 snRNA genes of some yeasts led to the hypothesis that U6 snRNA may play a catalytic role in pre-mRNA splicing and that the U6 introns occurred through reverse splicing of an intron from an mRNA precursor into a catalytic site of U6 snRNA. We characterized the U2 snRNA gene of the yeast Rhodotorula hasegawae, which has four mRNA-type introns in the U6 snRNA gene, and found an mRNA-type intron of 60 bp. The intron of the U2 snRNA gene is present in the highly conserved region immediately downstream of the branch site recognition domain. Interestingly, we found that this region can form a novel base pairing with U6 snRNA. We discuss the possible implications of these findings for the mechanisms of intron acquisition and for the role of U2 snRNA in pre-mRNA splicing.