The expression of microRNAs in embryoid bodies derived from mouse embryonic stem cells
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ABSTRACT: Mouse embryonic stem cells can spontaneously differentiate and assemble into a spherical embryoid body (EB) during suspension culture. The initial study aims to identify the up-regulated or down-regulated microRNAs during the differentiation process of pluripotent stem cells. From the microRNA profiling, we will focus on the microRNAs associated with mesodermal and endothelial differentiation of embryonic or induced pluripotent stem cells. In this study, the EBs were collected at 0 and 10-day differentiation of ESCs (ATCC: CRL-1934). The miRNA transcripts listed in Sanger miRBase Release 19.0 was detected by microarray.
Project description:For a long time, the BARD1 (BRCA1-associated RING domain 1) protein has been considered as a BRCA1 (BReast Cancer susceptibility gene 1, early onset) interactor, and tumor suppressor mutated in breast and ovarian cancers. Despite its functions in a stable heterodimer with BRCA1, there is increasing evidence for BRCA1-independent functions of BARD1. Here, we investigated BARD1 expression and function in human acute myeloid leukemias and their modulation by epigenetic mechanisms and microRNA. We show that the HDACi (histone deacetylase inhibitor) Vorinostat reduces BARD1 mRNA levels by increasing miR-19a and miR-19b expression levels. Moreover, we identify specific BARD1 isoforms that might act as tumor diagnostic and prognostic markers. Two-condition experiment: untreated NB4 cells (control) vs. NB4 cells treated with 5M-BM-5M SAHA (Vorinostat) for 6h. Biological replicates: 3 control, 3 treated, independently grown and harvested at 6 hours. One replicate per array.
Project description:Mesenchymal stem cell transplantation (MSCT) has been widely used to treat a variety of human diseases. However, the detailed mechanisms underlying its success are not fully understood. Here we show that MSCT rescues recipient bone marrow mesenchymal stem cell (BMMSC) function in Fas-deficient-MRL/lpr systemic lupus erythematosus (SLE) mice via a miR-29b/Dnmt1/Notch epigenetic cascade. Using the microRNA microarray, we found that MSCT could rescue the high level of miR-29b in the recipient BMMSCs of MRL/lpr mice. In the present study, mesenchymal stem cell transplantation (MSCT) was used to treat MRL/lpr mice. One week after the treatment, normal control MSCs from C3H/HeJ mice (C3H), recipient MSCs from untreated MRL/lpr mice (LPR) and recipient MSCs from MSCT-treated MRL/lpr mice (MSC) were used for total RNA extraction and microRNA microarray for analysis of microRNA expressions.
Project description:This study examined the expression of pig-specific microRNAs (miRNAs) at gestation day 20 (gd20) of pregnancy in Yorkshire sows. Tissue differences in miRNA expression, and miRNA differences between healthy and arresting embryo attachment sites (i.e., healthy endometrium vs. arresting endometrium; healthy trophoblast vs. arresting trophoblast), were of prime interest. For more information, please refer to the primary research paper. Paired endometrium and trophoblast samples were collected at gestation day 20 from two conceptus attachement sites (1 healthy, 1 arresting) per sow (n=3). Endometrial samples were collected from four non-pregnant sows at mid-estrus.
Project description:In honey bees, Vitellogenin (Vg) is hypothesized to be a major factor affecting hormone signaling, food-related behavior, immunity, stress resistance and lifespan. Likewise microRNAs play important roles in posttranscriptional gene regulation and affect many biological processes thereby showing many parallels to Vg functions. The molecular basis of Vg and microRNA interactions is largely unknown. Here, we exploited the well-established RNA interference (RNAi) protocol for Vg knockdown to investigate its effects on microRNA population in honey bee foragerM-bM-^@M-^Ys brain and fat body tissue. To identify microRNAs that are differentially expressed between tissues in control and knockdown foragers, we used M-BM-5ParafloM-BM-. microfluidic oligonucleotide microRNA microarrays. Our results show 76 and 74 miRNAs were expressed in the brain of control and knockdown foragers whereas 66 and 69 miRNAs were expressed in the fat body of control and knockdown foragers respectively. Target prediction identified potential seed matches for differentially expressed subset of microRNAs affected by Vg knockdown. These candidate genes are involved in a broad range of biological processes including insulin signaling, juvenile hormone (JH) and ecdysteroid signaling previously shown to affect foraging behavior. Thus, here we demonstrate a causal link between Vg expression-variation and variation in the abundance of microRNAs in different tissues with possible consequences for regulation of foraging behavior. We knocked down Vitellogenin (Vg) gene expression (using RNAi) in adult workers to identify potential downstream consequences on the expression of microRNA population in the fat body compared to control group (dsRNA-GFP injected bees). Six biological samples of fat body-derived small RNA fraction were prepared for each treatment group (dsRNA-Vg and dsRNA-GFP). Each biological sample contained pooled RNA from 5 unique individuals. Each fat body pool contained a total of 2 M-BM-5g of small RNA fraction, to which each of the 5 individuals contributed equally (400 ng). Pools were named as M-bM-^@M-^\control forager fat bodyM-bM-^@M-^] (GFFb) and M-bM-^@M-^\knockdown forager fat bodyM-bM-^@M-^] (VFFb), followed by a number from 1 to 6.
Project description:In honey bees, Vitellogenin (Vg) is hypothesized to be a major factor affecting hormone signaling, food-related behavior, immunity, stress resistance and lifespan. Likewise microRNAs play important roles in posttranscriptional gene regulation and affect many biological processes thereby showing many parallels to Vg functions. The molecular basis of Vg and microRNA interactions is largely unknown. Here, we exploited the well-established RNA interference (RNAi) protocol for Vg knockdown to investigate its effects on microRNA population in honey bee foragerM-bM-^@M-^Ys brain and fat body tissue. To identify microRNAs that are differentially expressed between tissues in control and knockdown foragers, we used M-BM-5ParafloM-BM-. microfluidic oligonucleotide microRNA microarrays. Our results show 76 and 74 miRNAs were expressed in the brain of control and knockdown foragers whereas 66 and 69 miRNAs were expressed in the fat body of control and knockdown foragers respectively. Target prediction identified potential seed matches for differentially expressed subset of microRNAs affected by Vg knockdown. These candidate genes are involved in a broad range of biological processes including insulin signaling, juvenile hormone (JH) and ecdysteroid signaling previously shown to affect foraging behavior. Thus, here we demonstrate a causal link between Vg expression-variation and variation in the abundance of microRNAs in different tissues with possible consequences for regulation of foraging behavior. We knocked down Vitellogenin (Vg) gene expression (using RNAi) in adult workers to identify potential downstream consequences on the expression of microRNA population in the brain compared to control group (dsRNA-GFP injected bees). Six biological samples of brain-derived small RNA fraction were prepared for each treatment group (dsRNA-Vg and dsRNA-GFP). Each biological sample contained pooled RNA from 5 unique individuals. Each brain pool contained a total of 1 M-BM-5g of small RNA fraction, to which each of the 5 individuals contributed equally (200 ng). Pools were named as M-bM-^@M-^\control forager brainM-bM-^@M-^] (GFBr) and M-bM-^@M-^\knockdown forager brainM-bM-^@M-^] (VFBr), followed by a number from 1 to 6.
Project description:Duck enteritis virus (DEV) is an important herpesvirus pathogen of waterfowl associated with an acute, highly contagious lethal disease. Using a deep sequencing approach on RNA from infected chicken embryo fibroblast (CEF) cultures, we determined the global changes in the microRNA (miRNA) expression profiles during DEV infection. In addition to the changes in the expression of a number of host miRNAs as a result of DEV infection, we identified several novel DEV-encoded miRNAs. Unlike most Mardivirus-encoded miRNAs, the majority of the DEV miRNAs were encoded within the unique long region of the viral genome. The precursors of DEV miR-D18 and miR-D19 overlapped with each other suggesting similarities to miRNA-offset RNAs, although only the DEV-miR-D18-3p was functional in reporter assays. Identification of these novel miRNAs will add to the growing list of virus-encoded miRNAs enabling the exploration of their roles in pathogenesis. Each microRNA is spotted on the array 6 times. We compared expression of duck enteritis virus (DEV)-infected chicken embryo fibroblasts (CEF) with CEF control.
Project description:We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 155 miRNAs including 56 conserved and 99 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode. An array including the 155 aphid microRNAs was designed in order to follow the expression of aphid microRNAs during the modification of reproduction mode of the pea aphid
Project description:The adult vertebrate red spotted newt is a champion of regeneration, demonstrating an amazing ability to regenerate damaged organs and tissues back to an uninjured state without the formation of scar or reduction in function. By developing a novel cardiac resection strategy, our group recently demonstrated that newt hearts could morphologically and functionally regenerate, without scarring, within a period of 2-3 months following injury. MicroRNAs (miRs) have been widely publicized as essential post-transcriptional gene regulators in a variety of biological processes, including regeneration. We have conducted a microarray screen for vertebrate miRs, with several candidate miRs showing significant differential expression at important time-points following injury to the newt heart. The newt microRNA expression between uninjured hearts and regenerating hearts, 7 and 21 days post-injury (dpi), was compared by microarray analysis. Three paired samples were analyzed: Uninjured, 7dpi and 21dpi newt hearts. Three arrays were hybridized comparing two-paired samples each time.