Multiplexing RT-PCR for the detection of multiple miRNA species in small samples

MicroRNAs are short (approximately 22 nucleotides), non-coding RNAs that play critical roles in gene regulation and may be used as rapid precise diagnostic indicators of early stages of cancer. The small size of these RNAs makes detection of multiple microRNA species in very small samples problematic. Here we investigate the parameters associated with multiplexing RT-PCR to obtain relative abundance profiles of multiple microRNAs in small sample sizes down to the amount of RNA found in a single cell.     

CID-miRNA: a web server for prediction of novel miRNA precursors in human genome

microRNAs (miRNA) are a class of non-protein coding functional RNAs that are thought to regulate expression of target genes by direct interaction with mRNAs. miRNAs have been identified through both experimental and computational methods in a variety of eukaryotic organisms. Though these approaches have been partially successful, there is a need to develop more tools for detection of these RNAs as they are also thought to be present in abundance in many genomes. In this report we describe a tool and a web server, named CID-miRNA, for identification of miRNA precursors in a given DNA sequence, utilising secondary structure-based filtering systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form. The web server can be accessed at http://mirna.jnu.ac.in/cidmirna/.     

Computational identification and comparative analysis of miRNA precursors in three palm species

Planta - In the present study, miRNA precursors in the genomes of three palm species were identified. Analyzes of sequence conservation and biological function of their putative targets contribute...     

Interactions between oligodendrocyte precursors control the onset of CNS myelination

The formation of CNS myelin is dependent on the differentiation of oligodendrocyte precursor cells (OPCs) and oligodendrocyte maturation. How the initiation of myelination is regulated is unclear, but it is likely to depend on the development of competence by oligodendrocytes and receptivity by target axons. Here we identify an additional level of control of oligodendrocyte maturation mediated by interactions between the different cellular components of the oligodendrocyte lineage. During development oligodendrocyte precursors mature through a series of stages defined by labeling with monoclonal antibodies A2B5 and O4. Newly differentiated oligodendrocytes begin to express galactocerebroside recognized by O1 antibodies and subsequently mature to myelin basic protein (MBP)-positive cells prior to formation of compact myelin. Using an in vitro brain slice culture system that supports robust myelination, the consequences of ablating cells at different stages of the oligodendrocyte lineage on myelination have been assayed. Elimination of all OPC lineage cells through A2B5+, O4+, and O1+ complement-mediated cell lysis resulted in a delay in development of MBP cells and myelination. Selective elimination of early OPCs (A2B5+) also unexpectedly resulted in delayed MBP expression compared to controls suggesting that early OPCs contribute to the timing of myelination onset. By contrast, elimination of differentiated (O1+) immature oligodendrocytes permanently inhibited the appearance of MBP+ cells suggesting that oligodendrocytes are critical to facilitate the maturation of OPCs. These data illuminate that the presence of intra-lineage feed-forward and feedback cues are important for timely myelination by oligodendrocytes.     

miRNA在白血病中的研究进展

microRNA(miRNA)是一种小分子非编码RNA,在细胞增殖、分化和凋亡等多种生理过程中发挥着重要作用.白血病相关miRNA研究进展迅速,并呈现了miRNA介导白血病瘤细胞增殖、分化和凋亡的调控网络.深入了解相关miRNA与白血病的发生、发展关系将为白血病的治疗开辟新途径.     

Rotaviruses code for two types of glycoprotein precursors

Rotaviruses are nonenveloped viruses that code for two glycoproteins: a structural glycoprotein (VP7) and a nonstructural glycoprotein (NS29). The precursor to VP7 (37K) was shown to contain a 1.5K cleavable signal sequence. The 37K precursor was authentically processed (signal sequence cleaved and the polypeptide "core" glycosylated) when synthesized in a cell-free system supplemented with dog pancreatic microsomes. Similar experiments were performed with the nonstructural glycoprotein precursor (20K); however, the 20K precursor contained an integral (noncleavable) signal sequence. Both precursors were inserted into membranes cotranslationally and both glycosylated products underwent posttranslational oligosaccharide processing. The results suggest a morphogenetic scheme for the simian rotavirus SA11.     

miRNA在植物重金属胁迫应答中的作用

microRNA （miRNA）是一种新型的长度为20~24 nt的非编码RNA,通过对靶基因的表达调节进而参与调控植物体的多种生理代谢活动。重金属是一类重要的环境污染物,严重危害植物的生长发育,甚至导致植物死亡。植物在长期的进化过程中形成了抵御重金属胁迫的多种机制,如miRNA对特定基因转录后水平的调控就在逆境胁迫应答中发挥重要作用。本文综述了植物中参与重金属胁迫应答miRNA的种类及作用机制,为揭示重金属胁迫条件下基因表达调控机制,以及利用基因工程手段改良植物对重金属的耐受性提供了线索和依据。     

MiRNA在乳腺癌转移中的作用

乳腺癌是女性高发的恶性肿瘤之一,远处转移是患者致死的最重要原因。目前乳腺癌转移的具体机制尚未明确。乳腺癌转移相关微RNA(microRNA,miRNA)的发现,为我们研究乳腺癌转移提供了新的思路。miRNA参与包括乳腺癌细胞的生长、凋亡、迁移、侵袭等肿瘤发生、发展过程,进而实现对乳腺癌转移的调控。有些miRNA在乳腺癌转移过程中起促进作用;有些则起抑制作用;还有一些miRNA的功能存在争议。本文将主要着眼于近年来发现的这几类miRNA在乳腺癌转移中所起的作用,并对其将来在乳腺癌诊断、预后判断及治疗中的应用做一综述。     

Distribution of miRNA genes in the pig genome

Background

Recent completion of swine genome may simplify the production of swine as a large biomedical model. Here we studied sequence and location of known swine miRNA genes, key regulators of protein-coding genes at the level of RNA, and compared them to human and mouse data to prioritize future molecular studies.

Results

Distribution of miRNA genes in pig genome shows no particular relation to different genomic features including protein coding genes - proportions of miRNA genes in intergenic regions, introns and exons roughly agree with the size of these regions in the pig genome. Our analyses indicate that host genes harbouring intragenic miRNAs are longer from other protein-coding genes, however, no important GO enrichment was found. Swine mature miRNAs show high sequence similarity to their human and mouse orthologues. Location of miRNA genes relative to protein-coding genes is also similar among studied species, however, there are differences in the precise position in particular intergenic regions and within particular hosts. The most prominent difference between pig and human miRNAs is a large group of pig-specific sequences (53% of swine miRNAs). We found no evidence that this group of evolutionary new pig miRNAs is different from old miRNAs genes with respect to genomic location except that they are less likely to be clustered.

Conclusions

There are differences in precise location of orthologues miRNA genes in particular intergenic regions and within particular hosts, and their meaning for coexpression with protein-coding genes deserves experimental studies. Functional studies of a large group of pig-specific sequences in future may reveal limits of the pig as a model organism to study human gene expression.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0166-3) contains supplementary material, which is available to authorized users.     

真核生物中的微小RNA及其功能研究进展

真核生物中存在两种主要的非编码RNA(non-coding RNA),在真核生物中发挥重要作用。一类为微小RNA(microRNA,miRNA),另一为小干扰RNA(siRNA)。miRNA大小为19～25nt,在体内与蛋白质形成核糖核蛋白复合体(miRNP),在真核基因的表达调控,生长发育中起重要作用。siRNA在RNA干扰(RNA地 interference,RNAi)途径中起定位特异mRNA的作用。miRNA与siRNA有联系也有区别。miRNA在真核生物中的调控机制具有保守性。     

microRNA在人类免疫缺陷病毒感染中的作用

microRNA(miRNA)对调控基因表达有着重要作用,病毒与宿主在miRNA水平存在着复杂的"对话"。研究显示,人类免疫缺陷病毒(HIV)可能编码病毒miRNA(vmiRNA),通过维持病毒潜伏、保护感染细胞免于凋亡或外力刺激下的细胞死亡等方式,在HIV病理过程中发挥重要作用。宿主miRNA则参与到了抗HIV的防御性机制中,但也面临HIV调控相应宿主miRNA、编码RNA沉默抑制物等多种阻力。深入研究HIV与宿主间miRNA水平上的动态相互作用,有助于进一步了解HIV的致病机理,开发新的治疗策略。     

MiRNA在特发性肺纤维化中的作用

近年来研究发现微RNA（microRNA,miRNA）与机体人部分生理、病理过程均有密切关系,如：组织的发育和分化、组织再生、病毒防御以及细胞增殖与凋亡等。miRNA在特发性肺纤维化（IPF）中的作用也日渐为研究者所重视,在IPF中有些miRNA上调（如miR-155、miR-21）,有些下调（如let-7、miR-29、miR-200）。这一发现为寻找IPF治疗方法提供了一个新的突破口。本文对近年来miRNA在IPF中作用的研究进展进行了综述,并对miRNA-21、let-7d、miRNA-155、miRNA-29以及miRNA-200在肺纤维化中的作用分别进行了阐述,为研究miRNA征IPF中的作用及机制提供一定参考。     

Caged oligonucleotides for bidirectional photomodulation of let-7 miRNA in zebrafish embryos

Many biological functions of microRNA (miRNA) have been identified in the past decade. However, a single miRNA can regulate multiple gene targets, thus it has been a challenge to elucidate the specific functions of each miRNA in different locations and times. New chemical tools make it possible to modulate miRNA activity with higher spatiotemporal resolution. Here, we describe light-activated (caged) constructs for switching let-7 miRNA ‘on’ or ‘off’ with 365 nm light in developing zebrafish embryos.     

miRNA在疼痛相关离子通道及受体中的作用研究

miRNA广泛表达于神经系统,与疼痛的发生、发展密切相关。近年来研究表明,抑制miRNA的合成调制伤害性神经元对炎症刺激的反应。疼痛时,背根神经节(DRG)上miRNA明显下调,该变化参与炎性疼痛和神经性疼痛的产生和维持。同时,miRNA也可以下调Navα亚基、ASIC3、TRPV1和P2X7mRNA的表达水平,还可以降低Kv电流。因此,miRNA可能成为疼痛治疗的新靶点。综述了miRNA的生物起源、分布,及其对痛觉相关离子通道Nav、Kv、ASICs、TRPV1以及嘌呤受体的调节作用。     

Commensalism facilitates gene flow in mountains: a comparison between two Rattus species

Small mammal dispersal is strongly affected by geographical barriers. However, commensal small mammals may be passively transported over large distances and strong barriers by humans (often with agricultural products). This pattern should be especially apparent in topographically complex landscapes, such as mountain ranges, where valleys and/or peaks can limit dispersal of less vagile species. We predict that commensal species would have lower genetic differentiation and higher migration rates than related non-commensals in such landscapes. We contrasted population genetic differentiation in two sympatric Rattus species (R. satarae and R. rattus) in the Western Ghats mountains in southern India. We sampled rats from villages and adjacent forests in seven locations (20–640 km apart). Capture-based statistics confirmed that R. rattus is abundant in human settlements in this region, whereas R. satarae is non-commensal and found mostly in forests. Population structure analyses using ~970-bp mitochondrial control region and 17 microsatellite loci revealed higher differentiation for the non-commensal species (R. satarae F-statistics=0.420, 0.065, R. rattus F-statistics=0.195, 0.034; mitochondrial DNA, microsatellites, respectively). Genetic clustering analyses confirm that clusters in R. satarae are more distinct and less admixed than those in R. rattus. R. satarae shows higher slope for isolation-by-distance compared with R. rattus. Although mode of migration estimates do not strongly suggest higher rates in R. rattus than in R. satarae, they indicate that migration over long distances could still be higher in R. rattus. We suggest that association with humans could drive the observed pattern of differentiation in the commensal R. rattus, consequently impacting not only their dispersal abilities, but also their evolutionary trajectories.