The CLAVATA and SHOOT MERISTEMLESS loci competitively regulate meristem activity in Arabidopsis

The CLAVATA (CLV1 and CLV3) and SHOOT MERISTEMLESS (STM) genes specifically regulate shoot meristem development in Arabidopsis. CLV and STH appear to have opposite functions: c1v1 and Clv3 mutants accumulate excess undifferentiated cells in the shoot and floral meristem, while stm mutants fail to form the undifferentiated cells of the shoot meristem during embryonic development. We have identified a weak allele of stm (stm-2) that reveals STM is not only required for the establish- ment of the shoot meristem, but is also required for the continued maintenance of undifferentiated cells in the shoot meristem and for proper proliferation of cells in the floral meristem. We have found evidence of genetic interactions between the CLV and STM loci. clv1 and c1v3 mutations partially suppressed the stm-1 and stm-2 phenotypes, and were capable of suppression in a dominant fashion. clv stm double mutants and plants homozygous for stm but heterozygous for clv, while still lacking an embryonic shoot meristem, exhibited greatly enhanced postembryonic shoot and floral meristem development. Although stm phenotypes are recessive, stm mutations dominantly suppressed clv homozygous and heterozygous phenotypes. These results indicate that the stm phenotype is sensitive to the levels of CLV activity, while the clv phenotype is sensitive to the level of STM activity. We propose that these genes play related but opposing roles in the regulation of cell division and/or cell differentiation in shoot and floral meristems

Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems

Arabidopsis thaliana floral meristems are determinate structures that produce a defined number of organs, after which cell division ceases. A new recessive mutant, carpel factory (caf), converts the floral meristems to an indeterminate state. They produce extra whorls of stamens, and an indefinite number of carpels. Thus, CAF appears to suppress cell division in floral meristems. The function of CAF is partially redundant with the function of the CLAVATA (CLV) and SUPERMAN (SUP) genes, as caf clv and caf sup double mutants show dramatically enhanced floral meristem over-proliferation. caf mutant plants also show other defects, including absence of axillary inflorescence meristems, and abnormally shaped leaves and floral organs. The CAF gene was cloned and found to encode a putative protein of 1909 amino acids containing an N-terminal DExH/DEAD-box type RNA helicase domain attached to a C-terminal RNaseIII-like domain. A very similar protein of unknown function is encoded by a fungal and an animal genome. Helicase proteins are involved in a number of processes, including specific mRNA localization and mRNA splicing. RNase III proteins are involved in the processing of rRNA and some mRNA molecules. Thus CAF may act through some type of RNA processing event(s). CAF gives rise to two major transcripts of 2.5 and 6.2 kb. In situ hybridization experiments show that CAF RNA is expressed throughout all shoot tissues

IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana.

DNA methylation is an epigenetic mark affecting genes and transposons. Screening for mutants that fail to establish DNA methylation yielded two we termed "involved in de novo" (idn) 1 and 2. IDN1 encodes DMS3, an SMC-related protein, and IDN2 encodes a previously unknown double-stranded RNA-binding protein with homology to SGS3. IDN1 and IDN2 control de novo methylation and small interfering RNA (siRNA)-mediated maintenance methylation and are components of the RNA-directed DNA methylation pathway

Exploring the high-pressure materials genome

A thorough in situ characterization of materials at extreme conditions is challenging, and computational tools such as crystal structural search methods in combination with ab initio calculations are widely used to guide experiments by predicting the composition, structure, and properties of high-pressure compounds. However, such techniques are usually computationally expensive and not suitable for large-scale combinatorial exploration. On the other hand, data-driven computational approaches using large materials databases are useful for the analysis of energetics and stability of hundreds of thousands of compounds, but their utility for materials discovery is largely limited to idealized conditions of zero temperature and pressure. Here, we present a novel framework combining the two computational approaches, using a simple linear approximation to the enthalpy of a compound in conjunction with ambient-conditions data currently available in high-throughput databases of calculated materials properties. We demonstrate its utility by explaining the occurrence of phases in nature that are not ground states at ambient conditions and estimating the pressures at which such ambient-metastable phases become thermodynamically accessible, as well as guiding the exploration of ambient-immiscible binary systems via sophisticated structural search methods to discover new stable high-pressure phases.Comment: 14 pages, 6 figure

Loss of the DNA methyltransferase MET1 Induces H3K9 hypermethylation at PcG target genes and redistribution of H3K27 trimethylation to transposons in Arabidopsis thaliana.

Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein-coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. Recently, ectopic genic DNA methylation in the CHG context (where H is any base except G) has been observed in globally DNA hypomethylated mutants such as met1, but neither the nature of the hypermethylated loci nor the biological significance of this epigenetic phenomenon have been investigated. Here, we generated high-resolution, genome-wide maps of both H3K9m2 and H3K27m3 in wild-type and met1 plants, which we integrated with transcriptional data, to explore the relationships between these two marks. We found that ectopic H3K9m2 observed in met1 can be due to defects in IBM1-mediated H3K9m2 demethylation at some sites, but most importantly targets H3K27m3-marked genes, suggesting an interplay between these two silencing marks. Furthermore, H3K9m2/DNA-hypermethylation at these PcG targets in met1 is coupled with a decrease in H3K27m3 marks, whereas CG/H3K9m2 hypomethylated transposons become ectopically H3K27m3 hypermethylated. Our results bear interesting similarities with cancer cells, which show global losses of DNA methylation but ectopic hypermethylation of genes previously marked by H3K27m3

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis.

DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however, its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 preferentially binds histone H3 Lys9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small-RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA

Synchrotron Mössbauer spectroscopic study of ferropericlase at high pressures and temperatures

The electronic spin state of Fe^(2+) in ferropericlase, (Mg_(0.75)Fe_(0.25))O, transitions from a high-spin (spin unpaired) to low-spin (spin paired) state within the Earth’s mid-lower mantle region. To better understand the local electronic environment of high-spin Fe^(2+) ions in ferropericlase near the transition, we obtained synchrotron Mössbauer spectra (SMS) of (Mg_(0.75),Fe_(0.25))O in externally heated and laser-heated diamond anvil cells at relevant high pressures and temperatures. Results show that the quadrupole splitting (QS) of the dominant high-spin Fe^(2+) site decreases with increasing temperature at static high pressure. The QS values at constant pressure are fitted to a temperature-dependent Boltzmann distribution model, which permits estimation of the crystal-field splitting energy (Δ_3) between the d_(xy_ and d_(xz) or d_(zy) orbitals of the t_(2g) states in a distorted octahedral Fe^(2+) site. The derived Δ_3 increases from approximately 36 meV at 1 GPa to 95 meV at 40 GPa, revealing that both high pressure and high temperature have significant effects on the 3d electronic shells of Fe^(2+) in ferropericlase. The SMS spectra collected from the laser-heated diamond cells within the time window of 146 ns also indicate that QS significantly decreases at very high temperatures. A larger splitting of the energy levels at high temperatures and pressures should broaden the spin crossover in ferropericlase because the degeneracy of energy levels is partially lifted. Our results provide information on the hyperfine parameters and crystal-field splitting energy of high-spin Fe^(2+) in ferropericlase at high pressures and temperatures, relevant to the electronic structure of iron in oxides in the deep lower mantle

Infrared Optical Properties of Ferropericlase (Mg1-xFexO): Experiment and Theory

The temperature dependence of the reflectance spectra of magnesium oxide (MgO) and ferropericlase (Mg1-xFexO, for x=0.06 and x=0.27) have been measured over a wide frequency range (~50 to 32000 cm-1) at 295 and 6 K. The complex dielectric function has been determined from a Kramers-Kronig analysis of the reflectance. The spectra of the doped materials resembles pure MgO in the infrared region, but with much broader resonances. We use a shell model to calculate the dielectric function of ferropericlase, including both anharmonic phonon-phonon interactions and disorder scattering. These data are relevant to understanding the heat conductivity of ferropericlase in the earth's lower mantle.Comment: 17 pages, 6 figure