高通量测序技术分析急性髓系白血病血浆外泌体微RNA表达谱差异

急性髓系白血病（acute myeloid leukemia,AML）是一类造血干细胞的恶性克隆性疾病,目前的诊断方法不利于疾病的早期发现,且诊断结果重复性较差。已有大量研究显示,细胞外microRNA（miRNA或miR）富集在外泌体（exosome）中,且受其表面膜的保护而具有很好的稳定性,是理想的分子标志物。目前,多种实体肿瘤均已检测到肿瘤特异性外泌体miRNA(exosomal miRNA)。然而,在AML患者中未见此外泌体miRNA报道。本研究探讨急性髓系白血病血浆外泌体miRNA表达谱差异及新miRNA序列。采用solexa高通量测序技术对7例AML患者（AML组）及7例健康对照者（对照组）血浆外泌体miRNAs进行测序,利用Mireap预测软件进行新miRNAs分析,通过edger差异分析软件筛选组间差异miRNA,获得211个已知的差异表达miRNAs以及2个新miRNAs,选择4个差异表达的miRNAs：miR-155-5p、miR-335-5p、miR-451a及xxx-m0038 5p（新miRNA）,在两组（各23例）的血浆外泌体样本中,进行实时荧光定量PCR（qRT-PCR）验证,验证结果与测序结果一致。对差异表达的外泌体miRNA进行靶基因预测及其GO（Gene Ontology）和信号通路富集分析,发现靶基因聚集的生物学功能多数参与生物进展过程的调控。靶基因主要富集在FoxO、MAPK、Hippo信号通路以及HTLV-I感染等。结果显示,AML患者与健康对照者的血浆外泌体miRNA存在着差异性表达。差异性表达的miRNA特异性很高,对进一步阐明AML白血病发生与发展的分子机制、研发新的无创诊断方法、新的诊断标记物和有效治疗AML的方法具有十分重要和深远的意义。     

大乳头水螅RACE cDNA文库的构建

目的:为筛选和克隆大乳头水螅发育调控相关基因的全长cDNA,构建大乳头水螅RACE cDNA文库.方法:提取大乳头水螅总RNA后从其中分离mRNA,运用SMART技术构建RACE cDNA文库.为鉴定所构建文库的质量,根据GenBank中大乳头水螅actin基因cDNA序列设计5'RACE和3'RACE的引物及用于扩增actin基因编码区全长序列的引物.结果:琼脂糖凝胶电泳结果表明,RACE cDNA文库中全长cDNA的长度集中在500-2 000bp之间.5'RACE、3'RACE PCR及扩增actin基因编码区全长序列时均以本文构建的大乳头水螅RACE cDNA文库为模板,这3个PCR反应均能扩增出产物,产物大小与目标片段预计大小相似.PCR产物分别经T/A克隆及测序后证明为大乳头水螅actin基因cDNA的相应序列.结论:RACE cDNA文库的成功构建为通过RACE方法获得大乳头水螅功能基因cDNA全长序列奠定了基础.     

外泌体内mircoRNAs在肝癌中的作用北大核心CSCD

外泌体是细胞间重要的信息交流介质,包含多种活性分子,如蛋白质、脂类、DNA和微RNA(microRNA,miRNA)等,外泌体可从供体细胞分泌后直接或间接作用于受体细胞,进而影响细胞之间的生命活动。更有意义的是,外泌体内的miRNAs可在血液中稳定存在,且当肿瘤发生时出现异常表达,进而参与肿瘤的发生发展,影响肿瘤患者生存及预后。近年大量研究报道显示,外泌体内miRNAs可作为肝癌诊断的新生物标志物及治疗肝癌的潜在靶标。本文就近年来外泌体内miRNAs在肝癌中的表达及其临床应用进行综述。     

外泌体内mircoRNAs在肝癌中的作用

外泌体是细胞间重要的信息交流介质,包含多种活性分子,如蛋白质、脂类、DNA和微RNA（microRNA, miRNA）等,外泌体可从供体细胞分泌后直接或间接作用于受体细胞,进而影响细胞之间的生命活动。更有意义的是,外泌体内的miRNAs可在血液中稳定存在,且当肿瘤发生时出现异常表达,进而参与肿瘤的发生发展,影响肿瘤患者生存及预后。近年大量研究报道显示,外泌体内miRNAs可作为肝癌诊断的新生物标志物及治疗肝癌的潜在靶标。本文就近年来外泌体内miRNAs在肝癌中的表达及其临床应用进行综述。     

应用聚合酶链式反应扩增和光敏生物素标记的cDNA探针检测马铃薯纺锤块茎类病毒

以含马铃薯纺锤块茎类病毒(potato spindle tuber viroid,PSTV)RNA的总核酸为模板,加入人工合成的互补DNA引物,用反转录酶合成PSTV cDNA;在聚合酶链式反应系统中,用两个PSTV特异性引物进行cDNA扩增,用以制备光敏生物素标记的PSTV cDNA探针。用此探针进行斑点杂交检测含PSTV的马铃薯核酸提取液和汁液均出现阳性杂交信号,而健康马铃薯的核酸提取液和汁液的结果均为阴性。光敏生物素标记探针检测纯化PSTV的灵敏度可达5pg;检测感染PSTV的马铃薯块茎汁液的可测出最高稀释度为1:400。     

黄地老虎颗粒体病毒cDNA文库的构建

以感染黄地老虎颗粒体病毒（Agrotis segetum ganulosis virus,AsGV)黄地老虎幼虫为材料提取总RNA,分离mRNA,并反转录合成cDNA ,构建了包括黄地老虎（Agrotis segetum,As)幼虫和黄地老虎颗粒体病毒的cDNA 文库。用Eco RI和HindⅢ限制性内切酶酶切AsGV基因组DNA,制备地高辛探针,与上述总RNA,mRNA,cDNA 杂交,从文库中筛选出AsGV的阳性克隆1081个,经cDNA测序,cDNA 编码序列与基因组编码序列相符。并根据基因组阅读框序列合成引物,PCR扩增出59个阅读框的编码基因,也完全与基因组序列相符。     

猪FGL2基因cDNA末端序列检测及结构分析

检测猪FGL2基因cDNA末端序列并对该基因结构初步分析。α-32P dCTP放射性同位素标记cDNA探针筛选猪基因组DNA文库;cDNA末端快速扩增(rapid amplification of cDNA end,RACE)。以猪正常小肠及心脏组织提取新鲜总RNA,反转录后作为模板,设计基因特异性引物,采用Advantage 2 聚合酶混合物进行PCR扩增;依据猪与人FGL2基因3′端已知同源序列设计PCR上游引物,以人FGL2基因3′末端序列设计下游引物,以猪基因组DNA为模板采用Advantage 2 聚合酶混合物进行PCR反应;PCR载体重组质粒DNA亚克隆扩增。同位素探针未能筛选到特异阳性克隆,RACE反应检测到特异性转录起始位置及第一个转录终止位置,但仍未检测到第二个转录终止位置。猪基因组DNA行PCR扩增成功检测到猪FGL2基因3′末端未知序列及第二个转录终止位置。     

黄地老虎颗粒体病毒cDNA文库的构建

以感染黄地老虎颗粒体病毒(Agrotis segetum ganulosis virus,AsGV)的黄地老虎幼虫为材料提取总RNA、分离mRNA,并反转录合成cDNA,构建了包括黄地老虎(Agrotis segetura,As)幼虫和黄地老虎颗粒体病毒的cDNA文库.用EcoR Ⅰ和HindⅢ限制性内切酶酶切AsGV基因组DNA,制备地高辛探针,与上述总RNA、mR-NA、cDNA杂交,从文库中筛选出AsGV的阳性克隆1081个,经cDNA测序,cDNA编码序列与基因组编码序列相符.并根据基因组阅读框序列合成引物,PCR扩增出59个阅读框的编码基因,也完全与基因组序列相符.     

限制性内切酶介导的重叠延伸在人环氧合酶-1(COX-1)基因克隆中的应用

建立一种用于克隆全长基因的、限制性内切酶介导的重叠延伸法 .对全长基因进行分段扩增 ,并利用适当的限制性内切酶对基因序列内相应的限制性位点进行酶切 ,从而使分段扩增片段得以重叠并互为模板 ,在DNA聚合酶的作用下延伸获得全长基因 .将环氧合酶 1 (COX 1 )基因的外显子 9巧妙地拼接到了缺失外显子 9的COX 1cDNA片段中 ,获得了COX 1基因的全长cDNA .该方法分 3步进行 .首先 ,通过RT PCR分别扩增跨外显子 9的cDNA片段和缺失外显子 9的cDNA片段 ,并克隆到pMD1 8 T载体上 ;其次 ,PCR扩增外显子 9片段 ,限制性内切酶StuI酶切缺失外显子9cDNA片段的重组质粒 ,二者以一定的比例混合 ,互为模板 ,在pfuDNA聚合酶的作用下进行延伸 ,从而产生一个双链的DNA分子 .最后 ,以延伸产物为模板 ,用COX 1cDNA两端的引物进行PCR扩增 ,产生包含外显子 9的COX 1基因的全长cDNA .这种限制性内切酶介导的重叠延伸方法 ,对于克隆mRNA剪接水平上受调控的基因尤为有用 ,同时也为基因的重组和修饰提供一个新的思路     

巨型艾美耳球虫孢子化卵囊cDNA文库的构建

为构建巨型艾美耳球虫(Eimeria maxima)孢子倾卵囊cDNA表灰文库,从E.maxima孢子化卵囊中提取总RNA,以总RNA为模板、λTriplex2TM为栽体,利用SMARTTM cDNA文库构建试剂盒构建全长cDNA表达文库.经测定构建的E.maxima cDNA表达文库的原始文库容量为1×106 pfu/ml,扩增后的文库滴度为5×1010pfu/ml,重组率为95%,插入片断主要集中在0.5～1kb之间.根据已知序列设计引物,能从文库中扩增出编码E.maxima免疫球蛋白重链结合蛋白的基因序列片段.结果 表明所构建的E.maxima cDNA表达文库质量良好,为克隆、筛选E.maxima的功能性基因奠定了基础.     

Automated system for purification of dye-terminator sequencing products eliminates up-stream purification of templates.

The quality of sequencing results is to a large extent determined by the purity of the template and the purification of the sequencing products. Fragments that can act as unspecific primers and templates are removed before gel analysis, and the background of unspecific signals is highly reduced. Purification of the sequencing products is needed to remove salts, nucleotides, proteins and template DNA that can interfere with the gel separation. We have developed a product, DYNAPURE Dye Terminator Removal, that specifically isolates and purifies the sequencing products in 10 min. The method is based on biotinylated sequencing primers and super-paramagnetic streptavidin beads. A PCR product is sequenced using a biotinylated sequencing primer, and the sequencing products are then bound to streptavidin beads in a 5-min reaction. The bead-DNA complexes are magnetically separated from the rest of the solution, and the remaining buffer constituents are washed away with TE buffer or with 70% ethanol. The whole procedure can be automated on liquid-handling robots fitted with a magnet station. The method eliminates purification of templates before cycle sequencing.     

利用磁珠构建稻瘟菌cDNA文库

本文以稻瘟菌菌丝体为材料提取RNA,[目的]改进张学敏等人的方法,通过磁珠构建稻瘟菌cDNA文库,并用于下一步研究稻瘟菌与水稻之间的互作关系.[方法]通过共价键连接的寡聚oligo(dT)磁珠纯化mRNA,并以磁珠上的oligo(dT)为引物引导第一链cDNA的合成,再利用末端转移酶加尾法合成第二链cDNA.构建过程中避免使用限制酶和连接接头.[结果]用此方法构建的文库容量为8.9×107cfu,滴度为8.9×106 cfu/mL,随机挑取的25个克隆插入片断平均大小达到1380bp.[结论]实验结果表明用改进的方法可构建高质量的cDNA文库,并且方便快捷,所用材料少,构建时间短,利于大规模的功能基因分析.     

A modified cDNA subtraction to identify differentially expressed genes from plants with universal application to other eukaryotes

We have designed a simple and efficient polymerase chain reaction (PCR)-based cDNA subtraction protocol for high-throughput cloning of differentially expressed genes from plants that can be applied to any experimental system and as an alternative to DNA chip technology. Sequence-independent PCR-amplifiable first-strand cDNA population was synthesized by priming oligo-dT primer with a defined 5' heel sequence and ligating another specified single-stranded oligonucleotide primer on the 3' ends of first-strand cDNAs by T4 RNA ligase. A biotin label was introduced into the sense strands of cDNA that must be subtracted by using 5' biotinylated forward primer during PCR amplification to immobilize the sense strand onto the streptavidin-linked paramagnetic beads. The unamplified first strand (antisense) of the interrogating cDNA population was hybridized with a large excess of amplified sense strands of control cDNA. We used magnetic bead technology for the efficient removal of common cDNA population after hybridization to reduce the complexity of the cDNA prior to PCR amplification for the enrichment and sequence abundance normalization of differentially expressed genes. Construction of a subtracted and normalized cDNA library efficiently eliminates common abundant cDNA messages and also increases the probability of identifying clones differentially expressed in low-abundance cDNA messages. We used this method to successfully isolate differentially expressed genes from Pennisetum seedlings in response to salinity stress. Sequence analysis of the selected clones showed homologies to genes that were reported previously and shown to be involved in plant stress adaptation.     

Use of ‘long’ polymerase chain reaction and magnetic beads for extraction of chromosome-specific cDNAs

The detection of expressed sequences of genomic DNA is an important aspect of the human genome project. A technique is described where ‘long’ polymerase chain reaction (LPCR), which allows for extended large fragment production of > 10–20 kb, is used with Alu primers to generate a biotinylated template for cDNA hybridization. Streptavidin-coated magnetic beads are used to extract the long PCR templates and bound cDNAs, which are recovered by standard PCR. This method allows the isolation of cDNAs from virtually any human DNA source and should be valuable in expression mapping, positional cloning and gene isolation.     

Subtractive hybridization of cDNA from small amounts of plant tissue

A subtractive hybridization method is described that allows the generation of a subtractive gene library from small amounts of plant or other eukaryotic tissues. The method uses paramagnetic oligo-dT beads to capture poly-adenylated mRNA and to synthesize the complementary cDNA on a solid support. The use of magnetic beads facilitates the change of reaction buffers and the removal of primers and minimizes yield losses. Subtracted material obtained from this method can either be cloned directly or used to screen a specific library.     

Label-free DNA sequencing using Millikan detection

A label-free method for DNA sequencing based on the principle of the Millikan oil drop experiment was developed. This sequencing-by-synthesis approach sensed increases in bead charge as nucleotides were added by a polymerase to DNA templates attached to beads. The balance between an electrical force, which was dependent on the number of nucleotide charges on a bead, and opposing hydrodynamic drag and restoring tether forces resulted in a bead velocity that was a function of the number of nucleotides attached to the bead. The velocity of beads tethered via a polymer to a microfluidic channel and subjected to an oscillating electric field was measured using dark-field microscopy and used to determine how many nucleotides were incorporated during each sequencing-by-synthesis cycle. Increases in bead velocity of approximately 1% were reliably detected during DNA polymerization, allowing for sequencing of short DNA templates. The method could lead to a low-cost, high-throughput sequencing platform that could enable routine sequencing in medical applications.     

CUT&Tag产物回收和建库方法的优化

新兴的染色质靶向切割和标签化(clevage under target and tagment,CUT&Tag)技术利用转座酶在目标蛋白结合的DNA附近进行切割并对切割下的DNA片段进行标签化,通过后续的二代测序可以快速鉴定蛋白质-DNA相互作用,极大的简化了染色质免疫共沉淀测序(chromatin immunoprecipitation sequencing,ChIP-seq)的实验过程。CUT&Tag中转座酶完成标签化后需要DNA回收或其他后处理才能进行建库PCR,不同的回收方法对CUT&Tag结果有着显著的影响。通过建立生物素化转座体-链霉亲和素磁珠体系(streptavidin beads recovery CUT&Tag,srCUT&Tag),可以快速便捷地完成CUT&Tag的产物回收。本文在K562细胞中展开H3K4me3、RNA聚合酶Ⅱ(RNA polymeraseⅡ,RNAPⅡ)、转录因子CTCF和HMGA1的CUT&Tag实验,并利用现有的乙醇沉淀、片段分选(solid-phase reversible immobilization,SPRI)磁珠回收和直接PCR法,以及本研究建立的srCUT&Tag方法对产物进行回收。结果表明,从整体上看,SPRI磁珠回收和srCUT&Tag方法着较高的回收效率,而乙醇沉淀法则回收效率低下。在全部4种CUT&Tag产物回收过程中,SPRI磁珠回收均会损失大部分小于150 bp的产物片段。在CTCF和HMGA1 CUT&Tag产物的回收中,直接PCR法则损失了大部分大于300 bp的片段并与其他回收方法的结果有较大的差别。因此,srCUT&Tag能够比其他三种回收方法提供更多更完整的测序信息。综上所述,新建立srCUT&Tag回收方法相比现有的CUT&Tag产物回收方法能提高建库效率并得到更好的数据质量,为表观遗传学研究提供了更好的技术选择。