Search

Author(s): The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II Team*; FANTOM Consortium:; Y. Okazaki [1, 2]; M. Furuno [1]; T. Kasukawa [1, 3]; J. [...]

Author(s): J. Kawai [1, 2]; A. Shinagawa [1]; K. Shibata [1, 2]; M. Yoshino [1]; M. Itoh [1, 2]; Y. Ishii [1]; T. Arakawa [1]; A. Hara [1]; Y. Fukunishi [...]

Background: Ornithine decarboxylase (ODC) plays a pivotal role in the synthesis of polyamines, a group of chemical compounds that are essential for cell growth. Recent reports have shown that ODC overexpression may be involved in malignant transformation of immortalized NIH 3T3 cells. We have demonstrated that ODC-overproducing mouse breast cancer cells are more invasive in vitro than control cells. However, little information is available concerning the relationship between ODC overexpression, tumor invasion, and metastasis and the signal transduction pathways involved in ODC-induced transformation and invasion.Purpose: Our purpose was twofold: 1) to determine whether ODC overexpression is directly involved in tumor cell invasion and 2) to determine whether ODC overexpression induces mitogen-activated protein (MAP) kinase activities that are associated with cell growth and transformation.Methods: We transfected C3H clone 8 mouse 10T1/2 fibroblasts with an expression vector that carries a complementary DNA encoding rat ODC. Neomycin-resistant cells that overproduced ODC (4-6.5 times the control levels) were isolated. The transformed phenotype of these cells was determined by assessing colony formation and anchorage-independent growth in soft agar. The invasiveness of the cells was studied by means of an invasion assay that used Matrigel-coated filters in Boyden chambers. The MAP kinase activity of the cells was assayed by an in-gel kinase assay, using myelin basic protein as the substrate.Results: Overexpression of ODC induced not only cell transformation and anchorage-independent growth in soft agar but also invasiveness through a Matrigel-coated filter. The ODC-overproducing transfectants showed enhanced MAP kinase activity that paralleled the magnitude of cell invasiveness.Conclusions: ODC plays a pivotal role not only in cell transformation but also in cancer cell invasion. ODC overexpression enhanced MAP kinase activity.Implications: Our results demonstrate a connection between the polyamine/ODC and the MAP kinase signal transduction pathways and suggest that MAP kinase may play a pivotal role in ODC-induced cell transformation and invasion. [ABSTRACT FROM AUTHOR]

Little is known concerning the effect of CO2 on phytoplankton ecophysiological processes under nutrient and trace element-limited conditions, because most of the CO2 manipulation experiments have been conducted under these element-replete conditions. To investigate the effects of CO2 and iron availability on phytoplankton ecophysiology, we conducted an experiment using a phytoplankton community in the iron-limited, high-nutrient, low-chlorophyll (HNLC) region of the Bering Sea basin in September 2009. Carbonate chemistry was controlled by the bubbling of the several levels of CO2 concentration (180, 380, 600, and 1000 ppm) controlled air, and two iron conditions were established with or without the addition of inorganic iron. We demonstrated that in the iron-limited control conditions, the specific growth rate and the maximum photochemical quantum efficiency (Fv/Fm) of photosystem (PS) II decreased with increasing CO2 levels, suggesting a further decrease in iron bioavailability under the high CO2 conditions. In addition, biogenic silica to particulate nitrogen and biogenic silica to particulate organic carbon ratios increased from 2.65 to 3.75 and 0.39 to 0.50, respectively with an increase in CO2 level in the iron-limited controls. In contrast, in the iron-added treatments, specific growth rate, Fv/Fm values and elemental compositions did not change in response to the CO2 variations, indicating that the addition of iron cancelled out the effect of the modulation of iron bioavailability due to the change in carbonate chemistry. Our results suggest that high CO2 conditions can alter the biogeochemical cycling of nutrients through decreasing iron bioavailability in the iron-limited HNLC regions in the future. [ABSTRACT FROM AUTHOR]

Impacts of the increasing CO2 in seawater (i.e. ocean acidification) on phytoplankton physiology may have various and potentially adverse effects on phytoplankton dynamics and the carbon cycle. We conducted a CO2 manipulation experiment in the Sea of Okhotsk in summer 2006 to investigate the response of the phytoplankton assemblage and dynamics of organic carbon. During the 14-day incubation of nutrientdepleted surface water with a natural phytoplankton assemblage under 150, 280, 480, and 590 μatm pCO2, the relative abundance of fucoxanthin-containing phytoplankton such as diatoms and prymnesiophytes decreased with increasing pCO2. The amount of DOC accumulation also decreased with increasing pCO2, while differences in POC accumulation between the treatments were small and did not show a clear trend with the pCO2. Change in the phytoplankton community composition under different pCO2 conditions will alter the organic carbon dynamics as found in the present experiment. Compared to results in the literature from nutrient-replete conditions indicating a potential enhancement of phytoplankton production with elevated pCO2, the present results indicated a different physiological response of phytoplankton under nutrient-depleted conditions. These results indicate that the continuing increase in atmospheric CO2 can significantly affect the structure of marine ecosystems and carbon cycle in nutrientdepleted subpolar surface waters. [ABSTRACT FROM AUTHOR]

Decrease of Serum Triglyceride in Normal Rat Fed with 2000 ppm Aluminum Diet for 67 Days. II. Feeding Young and Adult Rats a Sucrose Diet with Addition of Aluminum Hydroxide and Aluminum Potassium Sulfate. SUGAWARA, C, SUGAWARA, N., KJYOSAWA, H., AND MIY-AKE, H. (1988) 616–623. To confirm the hypotriglycendemic effect of aluminum (AI), male weanling and adult Wistar rats were fed sucrose diets with the addition of aluminum hydroxide (A1(OH)) or aluminum potassium sulfate (A1K(SO)) for 67 days. As in the foregoing report (C. Sugawara, N. Sugawara, H. Kjyosawa, and H. Miyake, . 607–615), no Al-induced anemia or hypophosphatemia was observed and serum AI did not exceed 20 ng/ml. Serum tnglyceride (TG) was decreased by aluminum. Serum TG was significantly correlated with the serum nonesterified fatty acid (NEFA) concentration in both the Young groups ( = 0.757, = 22, < 0.01) and the Adult groups ( = 0.727, = 19, < 0.01). Neither serum cholesterol nor phospholipids was affected by AI ingestion. Aluminum caused a decrease in hepatic glycogen in all groups, but the decrease was significant only in Adult groups. Glycerol tn[9,10(n)-H]oleate was administered by gastric tube into rats fed for 81 days with experimental diets. In all the Al-treated groups serum H was significantly greater than in control groups at 3 hr after intubation. At 24 hr after intubation, serum H did not differ between Control and Al-treated groups. Total H at 24 hr found in serum, liver, and epididymal adipose tissue was not changed significantly by AI feeding. These effects were observed without measurable increase of AI in the serum. The aorta TG concentration was decreased slightly by AI treatment. Whether an Al-dependent hypotriglycendemic effect occurs in human beings and what other effects, if any, AI has on man should be investigated in the future. [ABSTRACT FROM PUBLISHER]

Allele-specific, monoallelic expression in diploid organisms represents an extreme case of allelic imbalance resulting from incompatibility between cis- and trans-elements. Due to haploinsufficiency, such monoallelic expression can lead to sporadic genetic diseases. In mice, allelic imbalances can be introduced into F1 offspring from inbred strains. Previously, we established F1 hybrid embryonic stem (ES) cell lines derived from four different mouse strains, each belonging to a different subspecies with substantial genetic polymorphisms. In this study, we investigated the neural differentiation capacity of the established ES cell lines. By introducing different culture conditions, which kept the ES cells undifferentiated under various pluripotencies, we succeeded in differentiating the majority of ES cell lines (eight out of eleven) with our default neural differentiation paradigm. Still, three lines exhibited insufficient differentiation despite combining culture conditions promoting undifferentiated as well as differentiated status. In addition, Ube3a imprinting was seen in two lines. Our findings contribute to the methodological understanding of mouse ES cell pluripotency and lead to the practical utility of F1 hybrid ES cells as a model for studying phenotypes resulting from gene locus interactions.

Allele-specific monoallelic gene expression is a unique phenomenon and a great resource for analyzing gene regulation. To study this phenomenon, we established new embryonic stem (ES) cell lines derived from F1 hybrid blastocysts from crosses between four mouse subspecies (Mus musculus domesticus, C57BL/6; M. musculus molossinus, MSM/Ms; M. musculus musculus, PWK; M. musculus castaneus, HMI/Ms) and analyzed the expression levels of undifferentiated pluripotent stem cell markers and karyotypes of each line. To demonstrate the utility of our cell lines, we analyzed the allele-specific expression pattern of the Inpp5d gene as an example. The allelic expression depended on the parental alleles; this dependence could be a consequence of differences in compatibility between cis- and trans-elements of the Inpp5d gene from different subspecies. The use of parental mice from four subspecies greatly enhanced genetic polymorphism. The F1 hybrid ES cells retained this polymorphism not only in the Inpp5d gene, but also at a genome-wide level. As we demonstrated for the Inpp5d gene, the established cell lines can contribute to the analysis of allelic expression imbalance based on the incompatibility between cis- and trans-elements and of phenotypes related to this incompatibility.

MSM/Ms mouse derived from the Japanese wild mouse has unique characteristics compared to the widely used C57BL/6 mouse. To examine the usefulness of the MSM/Ms mouse for the comparative genomic analysis, expression of small RNAs were analyzed by the large-scale sequence analysis for two strains of mouse, C57BL/6 and MSM/Ms. As a trial, expression of box C/D snoRNAs, which are the most abundant small RNAs in the cell, were analyzed. By the comparison of the read number for each fragment, 11 snoRNAs with single nucleotide polymorphisms (SNPs) were detected. One of the snoRNAs, SNORD53, shows the expression only for MSM/Ms and this snoRNA has a mutation in the box sequence in C57BL/6. Thus, it was demonstrated that the proposed experimental system using SNPs can give new insight for the gene expression regulation., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Saito et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

We developed an in vitro system to differentiate embryonic stem cells (ESCs) derived from reciprocally crossed F1 hybrid mice into neurons, and used it to investigate poly(A)+ and total RNA transcription at different stages of cell differentiation. By comparing expression profiles of transcripts assembled from 20 RNA sequencing datasets [2 alleles×(2 cell lines×4 time-points+2 mouse brains)], the relative influence of strain, cell and parent specificities to overall expression could be assessed. Divergent expression profiles of ESCs converged tightly at neural progenitor stage. Patterns of temporal variation of monoallelically expressed transcripts and antisense transcripts were quantified. Comparison of sense and antisense transcript pairs within the poly(A)+ sample, within the total RNA sample, and across poly(A)+ and total RNA samples revealed distinct rates of pairs showing anti-correlated expression variation. Unique patterns of sharing of poly(A)+ and poly(A)- transcription were identified in distinct RNA species. Regulation and functionality of monoallelic expression, antisense transcripts and poly(A)- transcription remain elusive. We demonstrated the effectiveness of our approach to capture these transcriptional activities, and provided new resources to elucidate the mammalian developmental transcriptome., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2019. Published by The Company of Biologists Ltd.)

Understanding gene expression in the brain requires allele-specific transcriptome analysis because of the presence of neuron-specific imprinted genes, which are expressed in a neuron-specific and parent-of-origin-specific manner. Ube3a is a neuron-specific imprinted gene with an expression pattern that changes from biallelic to maternal only (Ube3a imprinting) during differentiation. Because Ube3a imprinting occurs only in neurons, it has the potential to be a marker to assess the quality of neurons produced by in vitro neuronal differentiation of embryonic stem cells (ESCs). For the analysis of Ube3a imprinting, genetic polymorphisms between the two alleles are necessary to identify the parental origin of each. However, ESCs derived from commonly used inbred mouse strains have no genetic polymorphisms. To overcome this problem, we examined 10 markers of neurogenesis to determine whether they were associated with Ube3a imprinting. We measured the relative expression levels of these 10 gene markers and assessed the Ube3a imprinting status of 54 neuron samples differentiated under various in vitro conditions. Then we divided the samples into two groups depending on their Ube3a imprinting status and selected markers statistically associated with Ube3a imprinting. The identified markers included the antisense noncoding transcript of Ube3a and a mature neuron marker Mtap2, consistent with the markers we used empirically in our previous study to assess the quality of differentiated neurons. These findings provide new quality control criteria for differentiated neurons, and could also be applied to human ESCs and induced pluripotent stem cells.