Conservation and divergence of canonical and non-canonical imprinting in murids.

BACKGROUND: Genomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behavior. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified in this murid. To systematically identify imprinted genes and genomic imprints in the rat, we use low input methods for genome-wide analyses of gene expression and DNA methylation to profile embryonic and extraembryonic tissues at allele-specific resolution. RESULTS: We identify 14 and 26 imprinted genes in these tissues, respectively, with 10 of these genes imprinted in both tissues. Comparative analyses with mouse reveal that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes are conserved in the extraembryonic tissue of murids, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extraembryonic imprinting. Meta-analysis of novel imprinted genes reveals multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the appearance of ZFP57 binding motifs, and the insertion of endogenous retroviral promoters. CONCLUSIONS: In summary, we provide an expanded list of imprinted loci in the rat, reveal the extent of conservation of imprinted gene expression, and identify potential mechanisms responsible for the evolution of species-specific imprinting.

Simultaneous harvesting of radiative cooling and solar heating for transverse thermoelectric generation.

For any thermoelectric effects to be achieved, a thermoelectric material must have hot and cold sides. Typically, the hot side can be easily obtained by excess heat. However, the passive cooling method is often limited to convective heat transfer to the surroundings. Since thermoelectric voltage is proportional to the temperature difference between the hot and cold sides, efficient passive cooling to increase the temperature gradient is of critical importance. Here, we report simultaneous harvesting of radiative cooling at the top and solar heating at the bottom to enhance the temperature gradient for a transverse thermoelectric effect which generates thermoelectric voltage perpendicular to the temperature gradient. We demonstrate this concept by using the spin Seebeck effect and confirm that the spin Seebeck device shows the highest thermoelectric voltage when both radiative cooling and solar heating are utilized. Furthermore, the device generates thermoelectric voltage even at night through radiative cooling which enables continuous energy harvesting throughout a day. Planar geometry and scalable fabrication process are advantageous for energy harvesting applications.

Magneto-optical design of anomalous Nernst thermopile.

The introduction of spin caloritronics into thermoelectric conversion has paved a new path for versatile energy harvesting and heat sensing technologies. In particular, thermoelectric generation based on the anomalous Nernst effect (ANE) is an appealing approach as it shows considerable potential to realize efficient, large-area, and flexible use of heat energy. To make ANE applications viable, not only the improvement of thermoelectric performance but also the simplification of device structures is essential. Here, we demonstrate the construction of an anomalous Nernst thermopile with a substantially enhanced thermoelectric output and simple structure comprising a single ferromagnetic material. These improvements are achieved by combining the ANE with the magneto-optical recording technique called all-optical helicity-dependent switching of magnetization. Our thermopile consists only of Co/Pt multilayer wires arranged in a zigzag configuration, which simplifies microfabrication processes. When the out-of-plane magnetization of the neighboring wires is reversed alternately by local illumination with circularly polarized light, the ANE-induced voltage in the thermopile shows an order of magnitude enhancement, confirming the concept of a magneto-optically designed anomalous Nernst thermopile. The sign of the enhanced ANE-induced voltage can be controlled reversibly by changing the light polarization. The engineering concept demonstrated here promotes effective utilization of the characteristics of the ANE and will contribute to realizing its thermoelectric applications.

Seebeck-driven transverse thermoelectric generation.

When a temperature gradient is applied to a closed circuit comprising two different conductors, a charge current is generated via the Seebeck effect1. Here, we utilize the Seebeck-effect-induced charge current to drive 'transverse' thermoelectric generation, which has great potential for energy harvesting and heat sensing applications owing to the orthogonal geometry of the heat-to-charge-current conversion2-9. We found that, in a closed circuit comprising thermoelectric and magnetic materials, artificial hybridization of the Seebeck effect into the anomalous Hall effect10 enables transverse thermoelectric generation with a similar symmetry to the anomalous Nernst effect11-27. Surprisingly, the Seebeck-effect-driven transverse thermopower can be several orders of magnitude larger than the anomalous-Nernst-effect-driven thermopower, which is clearly demonstrated by our experiments using Co2MnGa/Si hybrid materials. The unconventional approach could be a breakthrough in developing applications of transverse thermoelectric generation.

Observation of the Magneto-Thomson Effect.

We report the observation of the higher-order thermoelectric conversion based on a magneto-Thomson effect. By means of thermoelectric imaging techniques, we directly observed the temperature change induced by the Thomson effect in a polycrystalline Bi_{88}Sb_{12} alloy under a magnetic field and found that the magnetically enhanced Thomson coefficient can be comparable to or even larger than the Seebeck coefficient. Our experiments reveal the significant contribution of the higher-order magnetothermoelectric conversion, opening the door to "nonlinear spin caloritronics."

Crystalline-Amorphous Silicon Nanocomposites with Reduced Thermal Conductivity for Bulk Thermoelectrics.

Responding to the need for thermoelectric materials with high efficiency in both conversion and cost, we developed a nanostructured bulk silicon thermoelectric materials by sintering silicon crystal quantum dots of several nanometers in diameters synthesized by plasma-enhanced chemical vapor deposition (PECVD). The material consists of hybrid structures of nanograins of crystalline silicon and amorphous silicon oxide. The percolated nanocrystalline region gives rise to high power factor with the high doping concentration realized by PECVD, and the binding amorphous region reduces thermal conductivity. Consequently, the nondimensional figure of merit reaches 0.39 at 600 °C, equivalent to the best reported value for silicon thermoelectrics. The thermal conductivity of the densely packed material is as low as 5 W m(-1) K(-1) in a wide temperature range from room temperature to 1000 °C, which is beneficial not only for the conversion efficiency but also for material cost by requiring less material to establish certain temperature gradient.

Essential roles of the histone methyltransferase ESET in the epigenetic control of neural progenitor cells during development.

In the developing brain, neural progenitor cells switch differentiation competency by changing gene expression profiles that are governed partly by epigenetic control, such as histone modification, although the precise mechanism is unknown. Here we found that ESET (Setdb1), a histone H3 Lys9 (H3K9) methyltransferase, is highly expressed at early stages of mouse brain development but downregulated over time, and that ablation of ESET leads to decreased H3K9 trimethylation and the misregulation of genes, resulting in severe brain defects and early lethality. In the mutant brain, endogenous retrotransposons were derepressed and non-neural gene expression was activated. Furthermore, early neurogenesis was severely impaired, whereas astrocyte formation was enhanced. We conclude that there is an epigenetic role of ESET in the temporal and tissue-specific gene expression that results in proper control of brain development.

DDM1 (decrease in DNA methylation) genes in rice (Oryza sativa).

Regulation of cytosine methylation in the plant genome is of pivotal in determining the epigenetic states of chromosome regions. Relative tolerance of plant to deficiency in cytosine methylation provides unparalleled opportunities to study the mechanism for regulation of cytosine methylation. The Decrease in DNA Methylation 1 (DDM1) of Arabidopsis thaliana is one of the best characterized plant epigenetic regulators that are necessary for maintenance of cytosine methylation in genomic DNA. Although cytosine methylation could affect various aspects of plant growth and development including those related to agricultural importance, orthologs of DDM1 in plants other than Arabidopsis has not been studied in detail. In this study, we identified two rice genes with similarity to Arabidopsis DDM1 and designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development and their amino acid sequences are 93 % identical to each other. Transgenic rice lines expressing the OsDDM1a cDNA in the antisense orientation exhibited genomic DNA hypomethylation. In those lines, repeated sequences were more severely affected than a single copy sequence as is the case in Arabidopsis ddm1 mutants. Transcripts derived from endogenous transposon-related loci were up-regulated in the antisense OsDDM1 lines, opening a possibility to identify and utilize potentially active transposons for rice functional genomics.

Bursts of retrotransposition reproduced in Arabidopsis.

Retrotransposons, which proliferate by reverse transcription of RNA intermediates, comprise a major portion of plant genomes. Plants often change the genome size and organization during evolution by rapid proliferation and deletion of long terminal repeat (LTR) retrotransposons. Precise transposon sequences throughout the Arabidopsis thaliana genome and the trans-acting mutations affecting epigenetic states make it an ideal model organism with which to study transposon dynamics. Here we report the mobilization of various families of endogenous A. thaliana LTR retrotransposons identified through genetic and genomic approaches with high-resolution genomic tiling arrays and mutants in the chromatin-remodelling gene DDM1 (DECREASE IN DNA METHYLATION 1). Using multiple lines of self-pollinated ddm1 mutant, we detected an increase in copy number, and verified this for various retrotransposons in a gypsy family (ATGP3) and copia families (ATCOPIA13, ATCOPIA21, ATCOPIA93), and also for a DNA transposon of a Mutator family, VANDAL21. A burst of retrotransposition occurred stochastically and independently for each element, suggesting an additional autocatalytic process. Furthermore, comparison of the identified LTR retrotransposons in related Arabidopsis species revealed that a lineage-specific burst of retrotransposition of these elements did indeed occur in natural Arabidopsis populations. The recent burst of retrotransposition in natural population is targeted to centromeric repeats, which is presumably less harmful than insertion into genes. The ddm1-induced retrotransposon proliferations and genome rearrangements mimic the transposon-mediated genome dynamics during evolution and provide experimental systems with which to investigate the controlling molecular factors directly.

An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites.

Differential cytosine methylation of genes and transposons is important for maintaining integrity of plant genomes. In Arabidopsis, transposons are heavily methylated at both CG and non-CG sites, whereas the non-CG methylation is rarely found in active genes. Our previous genetic analysis suggested that a jmjC domain-containing protein IBM1 (increase in BONSAI methylation 1) prevents ectopic deposition of non-CG methylation, and this process is necessary for normal Arabidopsis development. Here, we directly determined the genomic targets of IBM1 through high-resolution genome-wide analysis of DNA methylation. The ibm1 mutation induced extensive hyper-methylation in thousands of genes. Transposons were unaffected. Notably, long transcribed genes were most severely affected. Methylation of genes is limited to CG sites in wild type, but CHG sites were also methylated in the ibm1 mutant. The ibm1-induced hyper-methylation did not depend on previously characterized components of the RNAi-based DNA methylation machinery. Our results suggest novel transcription-coupled mechanisms to direct genic methylation not only at CG but also at CHG sites. IBM1 prevents the CHG methylation in genes, but not in transposons.

Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana.

Differential cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene expression. Through genetic screen of mutants showing ectopic cytosine methylation in a genic region, we identified a jmjC-domain gene, IBM1 (increase in bonsai methylation 1), in Arabidopsis thaliana. In addition to the ectopic cytosine methylation, the ibm1 mutations induced a variety of developmental phenotypes, which depend on methylation of histone H3 at lysine 9. Paradoxically, the developmental phenotypes of the ibm1 were enhanced by the mutation in the chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), which is necessary for keeping methylation and silencing of repeated heterochromatin loci. Our results demonstrate the importance of chromatin remodeling and histone modifications in the differential epigenetic control of repeats and genes.

Ecotype-specific and chromosome-specific expansion of variant centromeric satellites in Arabidopsis thaliana.

Despite the conserved roles and conserved protein machineries of centromeres, their nucleotide sequences can be highly diverse even among related species. The diversity reflects rapid evolution, but the underlying mechanism is largely unknown. One approach to monitor rapid evolution is examination of intra-specific variation. Here we report variant centromeric satellites of Arabidopsis thaliana found through survey of 103 natural accessions (ecotypes). Among them, a cluster of variant centromeric satellites was detected in one ecotype, Cape Verde Islands (Cvi). Recombinant inbred mapping revealed that the variant satellites are distributed in centromeric region of the chromosome 5 (CEN5) of this ecotype. This apparently recent variant accumulation is associated with large deletion of a pericentromeric region and the expansion of satellite region. The variant satellite was bound to HTR12 (centromeric variant histone H3), although expansion of the satellite was not associated with comparable increase in the HTR12 binding. The results suggest that variant satellites with centromere function can rapidly accumulate in one centromere, supporting the model that the satellite repeats in the array are homogenized by occasional unequal crossing-over, which has a potential to generate an expansion of local sequence variants within a centromere cluster.

Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats.

A unique feature of late-flowering fwa epigenetic mutations is that the phenotype is caused by ectopic expression of the homeobox gene FWA. During normal development the FWA gene is expressed specifically in the endosperm in an imprinted manner. Ectopic FWA expression and disruption of imprinting can be induced in mutants of a CG methyltransferase MET1 (methyltransferase 1) or a chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), suggesting that the proper FWA expression depends on cytosine methylation. However, critical methylated residues controlling FWA silencing are not pinpointed. Nor is it understood how the FWA gene is initially methylated and silenced in wild-type plants. Here we mapped sequences critical for FWA silencing by application of RdDM (RNA-directed DNA methylation) to a ddm1-induced stable fwa epiallele. Transcription of double-stranded RNA corresponding to the tandem direct repeats around the FWA transcription start site induced de novo DNA methylation, transcriptional suppression and phenotypic reversion. The induced changes were heritable even without the transgene, which correlates with inheritance of CG methylation in the direct repeats. The newly silenced FWA allele was transcribed in an endosperm-specific and imprinted manner, as is the case for the wild-type FWA gene. The results indicate that methylation of the direct repeats, which presumably originated from a short interspersed nuclear element (SINE), is sufficient to induce proper epigenetic control of the FWA gene.

One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation.

The Arabidopsis FWA gene was initially identified from late-flowering epigenetic mutants that show ectopic FWA expression associated with heritable hypomethylation of repeats around transcription starting sites. Here, we show that wild-type FWA displays imprinted (maternal origin-specific) expression in endosperm. The FWA imprint depends on the maintenance DNA methyltransferase MET1, as is the case in mammals. Unlike mammals, however, the FWA imprint is not established by allele-specific de novo methylation. It is established by maternal gametophyte-specific gene activation, which depends on a DNA glycosylase gene, DEMETER. Because endosperm does not contribute to the next generation, the activated FWA gene need not be silenced again. Double fertilization enables plants to use such "one-way" control of imprinting and DNA methylation in endosperm.

Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis.

Methylation of cytosine residues in eukaryotic genomes is often associated with repeated sequences including transposons and their derivatives. Methylation has been implicated in control of two potential deleterious effects of these repeats: (1) uncontrolled transcription, which often disturbs proper expression of nearby host genes, and (2) changes in genome structure by transposition and ectopic recombination. Arabidopsis thaliana provides a genetically tractable system to examine these possibilities, since viable mutants in DNA methyltransferases are available. Arabidopsis MET1 (METHYLTRANSFERASE1, ortholog of mammalian DNA methyltransferase Dnmt1) is necessary for maintaining genomic cytosine methylation at 5'-CG-3' sites. Arabidopsis additionally methylates non-CG sites using CHROMOMETHYLASE3 (CMT3). We examined the mobility of endogenous CACTA transposons in met1, cmt3, and cmt3-met1 mutants. High-frequency transposition of CACTA elements was detected in cmt3-met1 double mutants. Single mutants in either met1 or cmt3 were much less effective in mobilization, despite significant induction of CACTA transcript accumulation. These results lead us to conclude that CG and non-CG methylation systems redundantly function for immobilization of transposons. Non-CG methylation in plants may have evolved as an additional epigenetic tag dedicated to transposon control. This view is consistent with the recent finding that CMT3 preferentially methylates transposon-related sequences.