RNA结合蛋白调节mRNA稳定性的作用机制

免疫稳态的维持涉及多种细胞因子的基因表达调控,其中在转录后水平对mRNA稳定性的调控起重要作用。ARE(AU-rich element)位于mRNA 3'UTR(非编码区),富含AU碱基,某些RNA结合蛋白通过识别结合ARE影响mRNA的稳定性。本文综合最新研究,概述了TTP、HUR等RNA结合蛋白对mRNA稳定性的调节机制及其在信号通路中的作用。     

低分化胃腺癌组织AUF1与p16表达的负相关

RNA结合蛋白AUF1（AU-富含元件结合/降解因子）通过结合并促进抑癌基因p16 mRNA降解来抑制p16表达.然而,AUF1-p16调控过程在肿瘤发生发展过程中的意义有待探讨.本研究用Western印迹与RT-PCR技术分别检测临床50例患者低分化胃腺癌组织和癌旁组织细胞中AUF1和p16蛋白、p16 mRNA的表达情况,并分析其关联性;用RNA Pull-down技术检测其AUF1与p16 mRNA的结合情况.结果显示,低分化胃腺癌组织AUF1蛋白表达水平明显增高,且与p16蛋白和p16 mRNA相对表达水平呈负相关;RNA pull-down分析结果显示,癌组织AUF1与p16-3′UTR的结合活性明显强于癌旁组织. 提示AUF1-p16调控过程可能是低分化胃腺癌组织p16水平降低的重要机制.     

人SDCT2β3'-非翻译区基因表达负调控序列对mRNA稳定性的影响

为探索人高亲和力钠离子依赖性二羧酸转运蛋白基因(high affinity sodium-dependent dicarboxylate transporter,SDCT2)3'端非翻译区是否在基因表达调控中起作用,首先通过生物信息学分析发现,在SDCT2β mRNA的3'端非翻译区内存在585 nt的Au富含区(AU-rich region,AUR),其中包括3个AU富含元件(AU-rich element,ARE),然后将SDCT213的AU富含区DNA片段插入报告基因GFP表达载体pcDNA-GFP的下游,构建pcDNA-GFP-AUR表达载体并转染HEK293、HKC和LLC-PK1细胞系,用Western blot和流式细胞仪检测细胞中GFP的表达水平.结果显示,SDCT2β的AU富含区序列可显著降低GFP的表达水平(P＜0.01).利用放线菌素D阻断RNA转录后,每隔2 h从稳定转染的HEK293细胞中提取总RNA,用RNA印迹分析GFP mRNA的稳定性.结果显示GFP-AUR mRNA较GFP mRNA不稳定.这些结果提示,在SDCT2β3'非翻译区的AU富含区内存在基因表达负调控区,该区可降低mRNA的稳定性、促进mRNA的降解,从而在转录后水平调控基因的表达.     

人SDCT2β 3′-非翻译区基因表达负调控序列对mRNA稳定性的影响

为探索人高亲和力钠离子依赖性二羧酸转运蛋白基因（high affinity sodium-dependent dicarboxylate transporter,SDCT2）3′端非翻译区是否在基因表达调控中起作用,首先通过生物信息学分析发现,在SDCT2βmRNA的3′端非翻译区内存在585nt的AU富含区（AU-rich region,AUR）,其中包括3个AU富含元件（AU-rich element,ARE）,然后将SDCT2β的AU富含区DNA片段插入报告基因GFP表达载体pcDNA-GFP的下游,构建pcDNA-GFP-AUR表达载体并转染HEK293、HKC和LLC-PK1细胞系,用Western blot和流式细胞仪检测细胞中GFP的表达水平.结果显示,SDCT2β的AU富含区序列可显著降低GFP的表达水平（P〈0.01）.利用放线菌素D阻断RNA转录后,每隔2h从稳定转染的HEK293细胞中提取总RNA,用RNA印迹分析GFP mRNA的稳定性.结果显示GFP-AURmRNA较GFP mRNA不稳定.这些结果提示,在SDCT2β3′非翻译区的AU富含区内存在基因表达负调控区,该区可降低mRNA的稳定性、促进mRNA的降解,从而在转录后水平调控基因的表达.     

远端上游元件结合蛋白1的生物学功能

远端上游元件结合蛋白1（far upstream element binding protein 1, FUBP1）通过特异性结合远端上游元件（upstream element, FUSE）调控原癌基因c-Myc的转录。FUBP家族包括FUBP1、FUBP2、FUBP3及FUBP4,其序列具有高度同源性,但功能各不相同。FUBP1蛋白由3个结构域构成,具有两亲性螺旋结构的N端、富含酪氨酸的C端以及1个DNA结合区域。生理状态下,FUBP1蛋白定位于细胞核。除了调控c-Myc转录外,FUBP1还可结合RNA,参与调控mRNA稳定性、病毒复制及RNA的剪接。     

miRNA在细胞因子表达调控中的作用

最新研究表明miRNA在免疫系统的精细调节中发挥重要作用,本综述则重点探讨miRNA如何调节细胞因子基因的机制。细胞因子转录后水平的调节主要是通过使富含腺嘌呤/尿嘧啶元件(AU-rich element,ARE)稳定性降低,然而miRNA表达具有空间和时间上的特异性,使得其在上述过程中发挥了重要作用。深入理解miRNA调节免疫反应的机制,不仅有助于鉴定调节免疫反应的新靶标,还有助于建立基于miRNA的有效新疗法。     

MIWI/piRNA激活小鼠精子细胞mRNA翻译的新功能机制研究

哺乳动物减数分裂后期的精子发生(spermatogenesis),即精子形成(spermiogenesis),是一个剧烈的细胞形态变化过程。伴随精子细胞中细胞核压缩和染色质重构,基因转录活性将逐渐降低直至完全停止,那些为精子细胞后期阶段发育所需的基因都需要提前转录为信使核糖核酸(mRNA),然后以翻译抑制状态储存在精子细胞中,直到特定发育阶段再被激活翻译,以合成蛋白质发挥作用。这个现象被称为“转录–翻译解偶联”,是精子发生中基因表达调控的一个典型特征。然而,目前对于精子细胞中被抑制的mRNA是如何被翻译激活的还知之甚少。我们当前的这项研究发现,MIWI/piRNA通过与翻译起始因子eIF3f、RNA结合蛋白HuR等因子形成功能性翻译激活复合物,特异性地激活小鼠精子细胞中包含AU序列富含元件(AU-rich element,ARE)mRNA的翻译。此项研究揭示了PIWI/piRNA在精子细胞翻译激活中的新功能,并证明此功能为精子细胞发育和功能性精子生成所必需。     

AUF1在胞质DNA抑制细胞葡萄糖代谢中的作用研究

目的 探讨AUF1在胞质DNA引起的细胞葡萄糖代谢应答中的作用及其机制。方法 (1)用核质分离技术分离细胞核与细胞质,并通过生物素-亲和素亲和层析技术分离细胞质中与胞质DNA(ISD)结合的蛋白质,然后通过“银染-质谱”和“复合物-质谱”技术鉴定出差异蛋白——AUF1。再利用体外结合实验验证AUF1与胞质DNA的相互作用。(2)在胞质DNA刺激后,通过ATP检测试剂盒和CCK8细胞氧还活力检测试剂,比较野生型细胞和基于CRISPR/Cas9技术的AUF1基因敲除细胞中葡萄糖代谢应答情况。(3)通过半定量PCR技术,在野生型、基因敲除AUF1、基因敲除后回补AUF1或空载体的四类细胞中检测葡萄糖转运蛋白GLUTs以及葡萄糖代谢相关酶的mRNA表达情况,筛选出与细胞糖代谢相关的AUF1下游效应分子——GLUT3。进而用实时荧光定量PCR进行验证。(4)通过半定量和荧光定量PCR分析胞质DNA刺激下GLUT3的mRNA变化情况,分析胞质DNA的刺激是否影响GLUT3的mRNA表达。结果 (1)两次质谱分析均发现AUF1能与ISD结合。体外结合实验也证实,不论是原核表达的GST-AUF1还是真核细胞表达的GFP-AUF1均能与单链和双链的ISD相结合。(2)基因敲除AUF1后的HEK293细胞在用胞质DNA刺激后,胞内的ATP水平和对CCK8的还原能力都明显高于野生型细胞。提示AUF1基因敲除细胞内的葡萄糖代谢不受胞质DNA刺激所抑制,说明AUF1很可能参与了胞质DNA对细胞糖代谢的调节。(3)半定量PCR技术检测发现在AUF1敲除的细胞中GLUT3的mRNA明显减少,而其他的GLUT家族成员和代谢酶则没有显著差异。实时荧光定量PCR证实上述现象,提示AUF1很可能通过稳定GLUT3的mRNA参与葡萄糖代谢的调节。(4)无论是单链还是双链ISD刺激后的细胞中,GLUT3的mRNA均减少,说明GLUT3可能是胞质DNA对糖代谢的调节过程中的一个下游效应分子。结论 AUF1能与胞质DNA结合,很可能通过调节下游GLUT3的mRNA稳定性参与胞质DNA引起的糖代谢应答反应。     

NMD作用的顺式调控元件

真核生物利用无义介导的mRNA降解(nonsense-mediated mRNA decay,NMD),对含有提前终止密码子(premature termination codons,PTC)的异常转录产物进行快速清除,防止毒害性截短蛋白(truncatedproteins)的产生,是真核生物重要的mRNA监视机制。NMD作用的启动与多种顺式调控元件有关,它们包括：提前终止密码子的标识;PTC下游特定位置的序列元件,在酵母细胞称为DSE(downstream sequence element,DSE),在哺乳动物细胞主要为内含子剪接依赖性序列元件(exon-exon junction,EEJ);稳定作用元件(stabilizer elements,STE)对NMD作用的阻抑调节;以及其他与NMD作用相关的序列,如poly(A)延长、5’-UTR的uORF(upstream open reading frame,uORF)和程序化核糖体移码(programmed-1 ribosomal frameshift,-1PRF)信号序列等。NMD途径中的这些顺式调控元件可能是分子遗传调控的关键靶点。     

细菌脂多糖对肠道病毒71型感染影响的初步研究

肠道病毒71型(enterovirus 71, EV71)感染常导致婴幼儿手足口病(hand, foot and mouth disease, HFMD),细菌脂多糖(lipopolysaccharide, LPS)在多种肠道病毒感染过程中起重要作用。本研究旨在探讨细菌LPS对EV71感染的影响。将EV71与LPS共孵育,测定病毒被热处理后残留病毒的活力,以及病毒感染过程中病毒基因拷贝数的变化。结果显示,热处理后病毒活力逐渐丧失,而经LPS处理的病毒活力丧失的速度减缓,且残留病毒活力与LPS浓度呈正相关;LPS处理后的病毒在黏附、侵入、胞内复制及释放过程中基因拷贝数较对照组均降低;免疫印迹分析表明LPS与抗VP1单克隆抗体可竞争性结合EV71,且粪便中的EV71可被抗大肠埃希菌抗体识别。上述结果提示,LPS可增强EV71热稳定性,抑制EV71感染过程,且LPS可能与EV71结合。     

mRNA Decay Factor AUF1 Binds the Internal Ribosomal Entry Site of Enterovirus 71 and Inhibits Virus Replication

AU-rich element binding factor 1 (AUF1) has a role in the replication cycles of different viruses. Here we demonstrate that AUF1 binds the internal ribosome entry site (IRES) of enterovirus 71 (EV71) and negatively regulates IRES-dependent translation. During EV71 infection, AUF1 accumulates in the cytoplasm where viral replication occurs, whereas AUF1 localizes predominantly in the nucleus in mock-infected cells. AUF1 knockdown in infected cells increases IRES activity and synthesis of viral proteins. Taken together, the results suggest that AUF1 interacts with the EV71 IRES to negatively regulate viral translation and replication.     

HuR and Ago2 Bind the Internal Ribosome Entry Site of Enterovirus 71 and Promote Virus Translation and Replication

EV71 (enterovirus 71) RNA contains an internal ribosomal entry site (IRES) that directs cap-independent initiation of translation. IRES-dependent translation requires the host’s translation initiation factors and IRES-associated trans-acting factors (ITAFs). We reported recently that mRNA decay factor AUF1 is a negative-acting ITAF that binds IRES stem-loop II. We also reported that the small RNA-processing enzyme Dicer produces at least four small RNAs (vsRNAs) from the EV71 IRES. One of these, vsRNA1, derived from IRES stem-loop II, reduces IRES activity and virus replication. Since its mechanism of action is unknown, we hypothesized that it might control association of ITAFs with the IRES. Here, we identified the mRNA stability factor HuR and the RISC subunit Argonaute 2 (Ago2) as two ITAFs that bind stem-loop II. In contrast to AUF1, HuR and Ago2 promote EV71 IRES activity and virus replication. In vitro RNA-binding assays revealed that vsRNA1 can alter association of Ago2, HuR, and AUF1 with stem-loop II. This presents a possible mechanism by which vsRNA1 could control viral translation and replication.     

Far upstream element binding protein 2 interacts with enterovirus 71 internal ribosomal entry site and negatively regulates viral translation

An internal ribosomal entry site (IRES) that directs the initiation of viral protein translation is a potential drug target for enterovirus 71 (EV71). Regulation of internal initiation requires the interaction of IRES trans-acting factors (ITAFs) with the internal ribosomal entry site. Biotinylated RNA-affinity chromatography and proteomic approaches were employed to identify far upstream element (FUSE) binding protein 2 (FBP2) as an ITAF for EV71. The interactions of FBP2 with EV71 IRES were confirmed by competition assay and by mapping the association sites in both viral IRES and FBP2 protein. During EV71 infection, FBP2 was enriched in cytoplasm where viral replication occurs, whereas FBP2 was localized in the nucleus in mock-infected cells. The synthesis of viral proteins increased in FBP2-knockdown cells that were infected by EV71. IRES activity in FBP2-knockdown cells exceeded that in the negative control (NC) siRNA-treated cells. On the other hand, IRES activity decreased when FBP2 was over-expressed in the cells. Results of this study suggest that FBP2 is a novel ITAF that interacts with EV71 IRES and negatively regulates viral translation.     

Far upstream element binding protein 1 binds the internal ribosomal entry site of enterovirus 71 and enhances viral translation and viral growth

Enterovirus 71 (EV71) is associated with severe neurological disorders in children, and has been implicated as the infectious agent in several large-scale outbreaks with mortalities. Upon infection, the viral RNA is translated in a cap-independent manner to yield a large polyprotein precursor. This mechanism relies on the presence of an internal ribosome entry site (IRES) element within the 5'-untranslated region. Virus-host interactions in EV71-infected cells are crucial in assisting this process. We identified a novel positive IRES trans-acting factor, far upstream element binding protein 1 (FBP1). Using binding assays, we mapped the RNA determinants within the EV71 IRES responsible for FBP1 binding and mapped the protein domains involved in this interaction. We also demonstrated that during EV71 infection, the nuclear protein FBP1 is enriched in cytoplasm where viral replication occurs. Moreover, we showed that FBP1 acts as a positive regulator of EV71 replication by competing with negative ITAF for EV71 IRES binding. These new findings may provide a route to new anti-viral therapy.     

A cytoplasmic RNA virus generates functional viral small RNAs and regulates viral IRES activity in mammalian cells

The roles of virus-derived small RNAs (vsRNAs) have been studied in plants and insects. However, the generation and function of small RNAs from cytoplasmic RNA viruses in mammalian cells remain unexplored. This study describes four vsRNAs that were detected in enterovirus 71-infected cells using next-generation sequencing and northern blots. Viral infection produced substantial levels (>10⁵ copy numbers per cell) of vsRNA1, one of the four vsRNAs. We also demonstrated that Dicer is involved in vsRNA1 generation in infected cells. vsRNA1 overexpression inhibited viral translation and internal ribosomal entry site (IRES) activity in infected cells. Conversely, blocking vsRNA1 enhanced viral yield and viral protein synthesis. We also present evidence that vsRNA1 targets stem-loop II of the viral 5′ untranslated region and inhibits the activity of the IRES through this sequence-specific targeting. Our study demonstrates the ability of a cytoplasmic RNA virus to generate functional vsRNA in mammalian cells. In addition, we also demonstrate a potential novel mechanism for a positive-stranded RNA virus to regulate viral translation: generating a vsRNA that targets the IRES.     

Host factors in enterovirus 71 replication

Enterovirus 71 (EV71) infections continue to remain an important public health problem around the world, especially in the Asia-Pacific region. There is a significant mortality rate following such infections, and there is neither any proven therapy nor a vaccine for EV71. This has spurred much fundamental research into the replication of the virus. In this review, we discuss recent work identifying host cell factors which regulate the synthesis of EV71 RNA and proteins. Three of these proteins, heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), far-upstream element-binding protein 2 (FBP2), and FBP1 are nuclear proteins which in EV71-infected cells are relocalized to the cytoplasm, and they influence EV71 internal ribosome entry site (IRES) activity. hnRNP A1 stimulates IRES activity but can be replaced by hnRNP A2. FBP2 is a negative regulatory factor with respect to EV71 IRES activity, whereas FBP1 has the opposite effect. Two other proteins, hnRNP K and reticulon 3, are required for the efficient synthesis of viral RNA. The cleavage stimulation factor 64K subunit (CstF-64) is a host protein that is involved in the 3' polyadenylation of cellular pre-mRNAs, and recent work suggests that in EV71-infected cells, it may be cleaved by the EV71 3C protease. Such a cleavage would impair the processing of pre-mRNA to mature mRNAs. Host cell proteins play an important role in the replication of EV71, but much work remains to be done in order to understand how they act.