ORCID Profile
0000-0002-8625-7872
Current Organisation
University of Tsukuba
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Publisher: Genetics Society of Japan
Date: 2016
DOI: 10.1266/GGS.15-00071
Abstract: Gene regulatory mechanisms are often defined in studies performed in the laboratory but are seldom validated for natural habitat conditions, i.e., in natura. Vernalization, the promotion of flowering by winter cold, is a prominent naturally occurring phenomenon, so far best characterized using artificial warm and cold treatments. The floral inhibitor FLOWERING LOCUS C (FLC) gene of Arabidopsis thaliana has been identified as the central regulator of vernalization. FLC shows an idiosyncratic pattern of histone modification at different stages of cold exposure, believed to regulate transcriptional responses of FLC. Chromatin modifications, including H3K4me3 and H3K27me3, are routinely quantified using chromatin immunoprecipitation (ChIP), standardized for laboratory s les. In this report, we modified a ChIP protocol to make it suitable for analysis of field s les. We first validated candidate normalization control genes at two stages of cold exposure in the laboratory and two seasons in the field, also taking into account nucleosome density. We further describe experimental conditions for performing s ling and s le preservation in the field and demonstrate that these conditions give robust results, comparable with those from laboratory s les. The ChIP protocol incorporating these modifications, "Field ChIP", was used to initiate in natura chromatin analysis of AhgFLC, an FLC orthologue in A. halleri, of which a natural population is already under investigation. Here, we report results on levels of H3K4me3 and H3K27me3 at three representative regions of AhgFLC in controlled cold and field s les, before and during cold exposure. We directly compared the results in the field with those from laboratory s les. These data revealed largely similar trends in histone modification dynamics between laboratory and field s les at AhgFLC, but also identified some possible differences. The Field ChIP method described here will facilitate comprehensive chromatin analysis of AhgFLC in the future to contribute to our understanding of gene regulation in fluctuating natural environments.
Publisher: Wiley
Date: 13-12-2010
Publisher: Genetics Society of Japan
Date: 2016
DOI: 10.1266/GGS.16-00015
Abstract: Iron-sulfur (Fe-S) clusters are ancient cofactors present in all kingdoms of life. Both the Fe-S cluster assembly machineries and target apoproteins are distributed across different subcellular compartments. The essential function of Fe-S clusters in nuclear enzymes is particularly difficult to study. The base excision repair (BER) pathway guards the integrity of DNA enzymes from the DEMETER family of DNA glycosylases in plants are Fe-S cluster-dependent and extend the BER repertowere to excision of 5-methylcytosine (5mC). Recent studies in plants genetically link the majority of proteins from the cytosolic Fe-S cluster biogenesis (CIA) pathway with 5mC BER and DNA repair. This link can now be further explored. First, it opens new possibilities for understanding how Fe-S clusters participate in 5mC BER and related processes. I describe DNA-mediated charge transfer, an Fe-S cluster-based mechanism for locating base lesions with high efficiency, which is used by bacterial DNA glycosylases encoding Fe-S cluster binding domains that are also conserved in the DEMETER family. Second, because detailed analysis of the mutant phenotype of CIA proteins relating to 5mC BER revealed that they formed two groups, we may also gain new insights into both the composition of the Fe-S assembly pathway and the biological contexts of Fe-S proteins.
Publisher: Oxford University Press (OUP)
Date: 04-07-2017
DOI: 10.1093/PCP/PCX092
Abstract: Plants are eukaryotes living mostly immotile in harsh environments. On occasion, it is beneficial for their survival to maintain a transcriptional response to an environmental stress longer than the stress lasts (transcriptional memory) and even to reiterate such a response more quickly or more strongly when the same stress is re-encountered (priming memory). In eukaryotes, transcription takes place in the context of chromatin, the packaging material of DNA. Chromatin regulation is often invoked when it comes to environmental transcriptional and priming memory in plants, but rarely chromatin-based regulation can be accurately assigned to a given aspect of transcription in vivo. The conserved eukaryotic chromatin-modifying system Polycomb/Trithorax can support both long-term stability and flexibility of gene expression in Drosophila. The main principles of Polycomb/Trithorax regulation will be outlined and illustrated with the best-studied case of environmental memory from Arabidopsis. Despite being complex, the Polycomb/Trithorax system relies on experimentally tractable elements in the form of DNA, termed Polycomb/Trithorax Responsive Elements. PREs/TREs are essentially memory DNA elements. Here, relevant information to identify PRE/TRE-like elements in plants is highlighted. Ex les of priming memory in plants are discussed in relation to the first two reported putative memory DNA elements. Arguably, similar cases from plants can be conducive in dissecting the contribution of DNA-based from chromatin-based regulation of transcription, when two types of DNA elements are defined: those representing binding sites for the transcription factors determining the environmental response and those controlling memory by regulating chromatin modification dynamics, ultimately maintaining the corresponding transcriptional state.
Publisher: Oxford University Press (OUP)
Date: 08-2005
DOI: 10.1093/PCP/PCI129
Abstract: Agrobacterium-based transformation was used to introduce a promoter-less glucuronidase uidA gene (beta-glucuronidase GUS) into Lotus japonicus. Transgenic plants were screened for GUS activation at different stages after inoculation with its symbiont, Mesorhizobium loti. Functional GUS fusion frequencies ranged from about 2 to 5% of the total number of transgenic lines. These lines provide excellent histological markers for tissue ontogeny analysis. Some of the activations generated GUS expression patterns that correspond to well-known tissue types, such as lateral root and nodule primordia, root tips and developing nodules (line CHEETAH). Others generated GUS activation associated with predictable but previously unknown (i) tissue types, such as the vascular bundle of the nodule (line VASCO) or (ii) expression domains, such as pericycle, nodule primordia, nodule and flower connective/vascular tissue (line FATA MORGANA) or inner root cortex cells in the vicinity of a curled root hair, nodule primordia and nodule cortex (line TIMPA). Putative members of two gene superfamilies, EH (Esp homolog) and AAA ATPase (ATPase associated with various cellular activities), were located next to the CHEETAH and VASCO insertions, respectively, and a nodulin gene, LjENOD40-2, was located next to the FATA MORGANA insertion. We utilized promoter GUS fusions to investigate the genetic regulation of LjENOD40-2 and FATA MORGANA GUS. The LjENOD40-2 promoter defined a novel expression domain and the FATA MORGANA nodule expression was reiterated by the 2 kb sequence upstream of the T-DNA insertion.
Publisher: Elsevier BV
Date: 04-2007
DOI: 10.1016/J.JPLPH.2006.03.006
Abstract: The autoregulation of nodulation (AON) is a universal mechanism to legumes to control the extent of nodulation via a systemic circuit and if genetically altered, as in the Lotus japonicus har1-1 mutant, leads to hypernodulation and aberrant root development. Increased nodulation of har1-1 is associated with pleiotropic effects both in the absence and presence of the symbiosis. We used two different grafting techniques to investigate the control of the non-symbiotic retarded root growth phenotype of har1-1, and demonstrate that altered root growth in the non-symbiotic condition is controlled by the genotype of both the shoot and the root. Based on these results and on the Gresshoff and Delves [Plant genetic approaches to symbiotic nodulation and nitrogen fixation in legumes. Plant Gene Res 1986 :159-206] AON model, we propose an advanced working model for control of root development by LjHAR1.
Publisher: Public Library of Science (PLoS)
Date: 21-06-2011
Publisher: American Association for the Advancement of Science (AAAS)
Date: 03-01-2003
Abstract: Proliferation of legume nodule primordia is controlled by shoot-root signaling known as autoregulation of nodulation (AON). Mutants defective in AON show supernodulation and increased numbers of lateral roots. Here, we demonstrate that AON in soybean is controlled by the receptor-like protein kinase GmNARK ( Glycine max nodule autoregulation receptor kinase), similar to Arabidopsis CLAVATA1 (CLV1). Whereas CLV1 functions in a protein complex controlling stem cell proliferation by short-distance signaling in shoot apices, GmNARK expression in the leaf has a major role in long-distance communication with nodule and lateral root primordia.
Publisher: Wiley
Date: 05-06-2013
DOI: 10.1111/NPH.12350
Abstract: Iron–sulfur proteins have iron–sulfur clusters as a prosthetic group and are responsible for various cellular processes, including general transcriptional regulation, photosynthesis and respiration. The cytosolic iron–sulfur assembly ( CIA ) pathway of yeast has been shown to be responsible for regulation of iron–sulfur cluster assembly in both the cytosol and the nucleus. However, little is known about the roles of this pathway in multicellular organisms. In a forward genetic screen, we identified an A rabidopsis thaliana mutant with impaired expression of the endosperm‐specific gene F lowering Wageningen ( FWA ). To characterize this mutant, we carried out detailed phenotypic and genetic analyses during reproductive and vegetative development. The mutation affects NAR 1 , which encodes a homolog of a yeast CIA pathway component. Comparison of embryo development in nar1‐3 and other A . thaliana mutants affected in the CIA pathway showed that the embryos aborted at a similar stage, suggesting that this pathway potentially functions in early seed development. Transcriptome analysis of homozygous viable nar1‐4 seedlings showed transcriptional repression of a subset of genes involved in ‘iron ion transport’ and ‘response to nitrate’. nar1‐4 also exhibited resistance to the herbicide paraquat. Our results indicate that A . thaliana NAR 1 has various functions including transcriptional regulation in gametophytes and abiotic stress responses in vegetative tissues.
Publisher: Oxford University Press (OUP)
Date: 09-2008
DOI: 10.1534/GENETICS.108.091736
Abstract: The Arabidopsis mutant Atubp26 initiates autonomous endosperm at a frequency of ∼1% in the absence of fertilization and develops arrested seeds at a frequency of ∼65% when self-pollinated. These phenotypes are similar to those of the FERTILIZATION INDEPENDENT SEED (FIS) class mutants, mea, fis2, fie, and Atmsi1, which also show development of the central cell into endosperm in the absence of fertilization and arrest of the embryo following fertilization. Atubp26 results from a T-DNA insertion in the UBIQUITIN-SPECIFIC PROTEASE gene AtUBP26, which catalyzes deubiquitination of histone H2B and is required for heterochromatin silencing. The paternal copy of AtUBP26 is able to complement the loss of function of the maternal copy in postfertilization seed development. This contrasts to the fis class mutants where the paternal FIS copy does not rescue aborted seeds. As in the fis class mutants, the Polycomb group (PcG) complex target gene PHERES1 (PHE1) is expressed at higher levels in Atubp26 ovules than in wild type there is a lower level of H3K27me3 at the PHE1 locus. The phenotypes suggest that AtUBP26 is required for normal seed development and the repression of PHE1.
Publisher: Proceedings of the National Academy of Sciences
Date: 02-09-2014
Abstract: Eukaryotic nuclear genomes store epigenetic information independent of DNA sequence, for ex le, in the form of 5-methylcytosine (5mC). In organisms as erse as mammals and flowering plants, removal of 5mC profoundly impacts transcription and reproductive development. We found that the highly conserved protein DRE2 in Arabidopsis controls maternal gene expression and seed development by reducing DNA methylation in the maternal, central cell gamete. An antiapoptotic factor, essential from yeast to human, Dre2 is best known as an assembly component for iron and sulfur into cofactors termed Fe-S clusters and has continually emerging biological roles and functions. To our knowledge, we demonstrate the first epigenetic role for Dre2 in any organism.
Publisher: Oxford University Press (OUP)
Date: 08-2001
Publisher: Springer Science and Business Media LLC
Date: 05-2020
DOI: 10.1038/S41467-020-15896-4
Abstract: Natural environments require organisms to possess robust mechanisms allowing responses to seasonal trends. In Arabidopsis halleri , the flowering regulator AhgFLC shows upregulation and downregulation phases along with long-term past temperature, but the underlying machinery remains elusive. Here, we investigate the seasonal dynamics of histone modifications, H3K27me3 and H3K4me3, at AhgFLC in a natural population. Our advanced modelling and transplant experiments reveal that H3K27me3-mediated chromatin regulation at AhgFLC provides two essential properties. One is the ability to respond to the long-term temperature trends via bidirectional interactions between H3K27me3 and H3K4me3 the other is the ratchet-like character of the AhgFLC system, i.e. reversible in the entire perennial life cycle but irreversible during the upregulation phase. Furthermore, we show that the long-term temperature trends are locally indexed at AhgFLC in the form of histone modifications. Our study provides a more comprehensive understanding of H3K27me3 function at AhgFLC in a complex natural environment.
Publisher: Wiley
Date: 31-01-2011
Publisher: Oxford University Press (OUP)
Date: 22-11-2011
DOI: 10.1093/PCP/PCR163
Abstract: A sizeable fraction of eukaryotic genomes is regulated by Polycomb group (PcG) and trithorax group (trxG) proteins, which play key roles in epigenetic repression and activation, respectively. In Drosophila melanogaster, homeotic genes are well-documented PcG targets they are known to contain cis-acting elements termed Polycomb response elements (PREs), which bind PcG proteins and satisfy three defined criteria, and also often contain binding sites for the trithorax (trx) protein. However, the presence of PREs, or an alternative mode for PcG/trxG interaction with the genome, has not been well documented outside Drosophila. In Arabidopsis thaliana, PcG/trxG regulation has been studied extensively for the flowering repressor gene FLOWERING LOCUS C (FLC). Here we evaluate how PRE-like activities that reside within the FLC locus may satisfy the defined Drosophila criteria, by analyzing four FLC transcription states. When the FLC locus is not transcribed, the intrinsic PcG recruitment ability of the coding region can be attributed to two redundant cis-acting elements (Modules IIA and IIB). When FLC is highly expressed, trxG recruitment is to a region overlapping the transcription start site (Module I). Exposure to prolonged cold converts the active FLC state into a repressed state that is maintained after the cold period finishes. These two additional transcriptional states also rely on the same three modules for PcG/trxG regulation. We conclude that each of Modules I, IIA and IIB partially fulfills the PRE function criteria, and that together they represent the functional FLC PRE, which differs structurally from canonical PREs in Drosophila.
Start Date: 2016
End Date: 2018
Funder: Japan Society for the Promotion of Science
View Funded ActivityStart Date: 2015
End Date: 2018
Funder: Japan Society for the Promotion of Science
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Funder: Japan Society for the Promotion of Science
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