Genome-wide Analysis Of microRNAs Research Articles

Genome-Wide Analysis of microRNAs and Their Target Genes in Dongxiang Wild Rice (Oryza rufipogon Griff.) Responding to Salt Stress.

Rice (Oryza sativa) is a staple food for more than half of the world's population, and its production is critical for global food security. Moreover, rice yield decreases when exposed to abiotic stresses, such as salinity, which is one of the most detrimental factors for rice production. According to recent trends, as global temperatures continue to rise due to climate change, more rice fields may become saltier. Dongxiang wild rice (Oryza rufipogon Griff., DXWR) is a progenitor of cultivated rice and has a high tolerance to salt stress, making it useful for studying the regulatory mechanisms of salt stress tolerance. However, the regulatory mechanism of miRNA-mediated salt stress response in DXWR remains unclear. In this study, miRNA sequencing was performed to identify miRNAs and their putative target genes in response to salt stress in order to better understand the roles of miRNAs in DXWR salt stress tolerance. A total of 874 known and 476 novel miRNAs were identified, and the expression levels of 164 miRNAs were found to be significantly altered under salt stress. The stem-loop quantitative real-time PCR (qRT-PCR) expression levels of randomly selected miRNAs were largely consistent with the miRNA sequencing results, suggesting that the sequencing results were reliable. The gene ontology (GO) analysis indicated that the predicted target genes of salt-responsive miRNAs were involved in diverse biological pathways of stress tolerance. This study contributes to our understanding of DXWR salt tolerance mechanisms regulated by miRNAs and may ultimately improve salt tolerance in cultivated rice breeding using genetic methods in the future.

Genome-Wide Analysis of MicroRNAs in Relation to Pupariation in Oriental Fruit Fly.

Insect metamorphosis is a complex process involving drastic morphological and physiological changes. microRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play key roles in regulating various biological processes, including metamorphosis, by post-transcriptional repression of mRNAs. The oriental fruit fly, Bactrocera dorsalis, is one of the most destructive insect pests in many Asian countries and the Pacific Islands. The regulatory role of miRNAs in B. dorsalis metamorphosis is unclear. To better understand the molecular regulatory mechanisms of miRNAs in pupariation, Illumina sequencing of the wandering stage (WS), the late WS and the white puparium stage of B. dorsalis were performed. Two hundred forty-nine miRNAs, including 184 known miRNAs and 65 novel miRNAs, were obtained. Among these miRNAs, 19 miRNAs were differentially expressed in pupariation, and eight miRNAs showed relative high expression levels (>50 TPM), of which five differentially expressed miRNAs (DEMs) had target differentially expressed genes (DEGs) predicted by the expected miRNA–mRNA negative regulation pattern using the Illumina HiSeq data. Four sets of DEMs and their predicted target DEGs were confirmed by qPCR. Of the four miRNAs, two miRNAs were down-regulated: miR-981, which may target pdpc, and Bdo-novel-mir-55, which potentially regulates spsX1, psB/C, and chit3. The other two miRNAs were up-regulated: let-7a-3p, which possibly controls lap, and Bdo-novel-mir-24, which may regulate ipc and sp1/2. This study provides a useful resource to elucidate the regulatory role of miRNAs and understand the molecular mechanisms of metamorphosis.

Saliva a sample matrix for systemic disease diagnostics

Our current focus at AIT is to investigate saliva for its suitability for any type of circulating biomarker diagnostics. Along these lines we will present proof of concept data for salivary DNA-methylation – and autoantibody-based biomarkers in a breast cancer patient cohort. Besides reporting on the evaluation of different exosome isolation approaches we will share results from genome-wide DNA-methylation analysis in serum – and saliva-derived exosomes from healthy individuals and present data obtained along genome-wide microRNA analysis from the same sample sources using both microarrays and microRNA Sequencing.

A double negative feedback loop involving LMO2 in hematopoietic cell fate determination revealed by genome-wide analysis of micrornas and transcription factor regulatory loops

A double negative feedback loop involving LMO2 in hematopoietic cell fate determination revealed by genome-wide analysis of micrornas and transcription factor regulatory loops

Genome-wide analysis of microRNAs and their target genes related to leaf senescence of rice.

Grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human beings. One of the approaches to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. MicroRNAs (miRNAs) are key regulators of aging and cellular senescence in eukaryotes. Here, to help understand their biological role in rice leaf senescence, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). In total 372 known miRNAs, 162 miRNA candidates and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding.

Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing

MicroRNAs (miRNAs) are short RNAs with essential roles in gene regulation in various organisms including higher plants. In contrast to the vast information on miRNAs from many economically important plants, almost nothing has been reported on the identification or analysis of miRNAs from rubber tree (Hevea brasiliensis L.), the most important natural rubber-producing crop. To identify miRNAs and their target genes in rubber tree, high-throughput sequencing combined with a computational approach was performed. Four small RNA libraries were constructed for deep sequencing from mature and young leaves of two rubber tree clones, PB 260 and PB 217, which provide high and low latex yield, respectively. 115 miRNAs belonging to 56 known miRNA families were identified, and northern hybridization validated miRNA expression and revealed developmental stage-dependent and clone-specific expression for some miRNAs. We took advantage of the newly released rubber tree genome assembly and predicted 20 novel miRNAs. Further, computational analysis uncovered potential targets of the known and novel miRNAs. Predicted target genes included not only transcription factors but also genes involved in various biological processes including stress responses, primary and secondary metabolism, and signal transduction. In particular, genes with roles in rubber biosynthesis are predicted targets of miRNAs. This study provides a basic catalog of miRNAs and their targets in rubber tree to facilitate future improvement and exploitation of rubber tree.