Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation

In plants, the mechanism by which RNA can induce de novo cytosine methylation of homologous DNA is poorly understood. Cytosines in all sequence contexts become modified in response to RNA signals. Recent work has implicated the de novo DNA methyltransferases (DMTases), DRM1 and DRM2, in establishing RNA-directed methylation of the constitutive nopaline synthase promoter, as well as the DMTase MET1 and the putative histone deacetylase HDA6 in maintaining or enhancing CpG methylation induced by RNA. Despite the identification of enzymes that catalyze epigenetic modifications in response to RNA signals, it is unclear how RNA targets DNA for methylation. A screen for mutants defective in RNA-directed DNA methylation identified a novel putative chromatin-remodeling protein, DRD1. This protein belongs to a previously undefined, plant-specific subfamily of SWI2/SNF2-like proteins most similar to the RAD54/ATRX subfamily. In drd1 mutants, RNA-induced non-CpG methylation is almost eliminated at a target promoter, resulting in reactivation, whereas methylation of centromeric and rDNA repeats is unaffected. Thus, unlike the SNF2-like proteins DDM1/Lsh1 and ATRX, which regulate methylation of repetitive sequences, DRD1 is not a global regulator of cytosine methylation. DRD1 is the first SNF2-like protein implicated in an RNA-guided, epigenetic modification of the genome.     

A comparative study into the chemical constitution of cutins and suberins from Picea abies (L.) Karst., Quercus robur L., and Fagus sylvatica L.

The compositions of BF₃/CH₃OH depolymerisates of cutins and suberins from leaf and periderm samples from Picea abies [L.] Karst., Quercus robur L., and Fagus sylvatica L., respectively, were determined by quantitative capillary gas chromatography/mass spectroscopy. Long-chain monobasic, -hydroxymonobasic, dihydroxymonobasic, trihydroxymonobasic and epoxyhydroxymonobasic alkanoic acids constituted the major aliphatic monomers of leaf cutins. The total amounts of cutin monomers ranged from 629 mg · m^–2 (Fagus) to 1350 mg · m^–2 (Quercus). Cutin composition and amounts did not significantly differ between current year and three-year-old needles of Picea. Trans-esterification of periderm samples yielded a much greater variety of aliphatic monomers than obtained from cutins. In addition to the substance classes found with cutins, suberin depolymerisates also contained , -dibasic acids while dihydroxymonobasic acids were lacking. Depolymerisates from periderms taken from different locations on a Picea tree did not differ significantly in their relative composition. The results are discussed in terms of the distinctive characteristics of the aliphatic portions of cutins and suberins, respectively. Discriminant analysis is applied for formulating a quantitative and inarbitrary classification rule for cutins and suberins. The precision, statistical significance and robustness of this classification rule are tested by employing it to a large set of compositional data (70 plant species) from the literature. The relevance of data obtained by depolymerization methods for elucidating the physical structure of cutins and suberins in situ is evaluated.To whom correspondence should be addressedThe authors are indebted to Drs. J. Winkler and H. Krause (Laboratorium für Strukturchemie des Fachbereichs Chemie, Biologie und Geowissenschaften, Technische Universität München, Garching, FRG) for performing capillary gas chromatography-mass spectrometry and their valuable help in the identification of cutin and suberin constituents. The work was supported by grants from the Deutsche Forschungsgemeinschaft and the Bayerisches Staatsministerium für Unterricht, Kultus, Wissenschaft und Kunst.     

A new Xinjiangchelyid turtle (Testudines, Eucryptodira) from the Jurassic Qigu Formation of the southern Junggar Basin, Xinjiang, north-west China

A new eucryptodiran turtle, Xinjiangchelys qiguensis sp. nov. from the Upper Jurassic (Oxfordian — ?Kimmeridgian) Qigu Formation of the southern Junggar Basin (north‐west China) is described. The type material consists of a partial skeleton, including the complete carapace, plastron, nearly all cervical vertebrae, both scapulae, the pelvis and one ulna. It is clearly identifiable as a basal eucryptodire since it lacks the mesoplastron. It is distinguished from other species of Xinjiangchelys by several autapomorphies of the carapace and plastron, such as the first and fifth vertebrals extending on the peripherals, the plastron with three pairs of gulars, and an intergular which does not contact the hyoplastron. In the postcranium, the scapula with a long acromial and a small scapular process, the pelvis with a short ilial shaft and the elongated cervical vertebrae are characteristic. A new phylogenetic analysis of the in‐group phylogeny of the Xinjiangchelyidae is proposed and discussed, resulting in a new classification of the family. Xinjiangchelys (Toxocheloides) narynensis is regarded as a nomen dubium. Shartegemys is referred to Xinjiangchelys, whereas the holotypes of ‘Plesiochelys’chungkingensis and ‘P’. latimarginalis are excluded from the genus Xinjiangchelys but included in the Xinjiangchelyidae.     

Effect of dehulling of rapeseed on feed value and nutrient digestibility of rape products in pigs

In the presented study the influence of dehulling rapeseed on the composition of rapeseed meal (RM) and rapeseed cake (RC) and on its feed value for piglets and growing-finishing pigs was investigated. Before withdrawal of oil, rapeseed (variety Express) was dehulled applying a procedure developed by SKET GmbH Magdeburg and the Section Food-Technology of the University Essen. The steps of the dehulling procedure were described. For RM the oil was removed by the prepress-solvent procedure till a crude fat content of 2.1% in DM. RC was produced by pressing only resulting approximately 13% crude fat in DM. The RM and RC from not dehulled (ND) and dehulled (D) rapeseed were examined analytically. Crude nutrients, sugar and fibre substances, amino acids, some minerals and trace elements, fatty acids, glucosinolates and sinapine, and phytate were determined. By dehulling the seed the crude fibre content was decreased in RM and RC by approximately 40%. The ADF content declined by 35 and 39%, and the NDF content by 28% and 40% in RM and RC, respectively. The decrease in ADL content amounted to 50% and 65% for RM and RC, respectively. On the other hand, the CP content of RM and RC was increased by 7% and 13%, respectively, by dehulling the seed while the amino acid content of rape protein increased only slightly. The contents of glucosinolates and sinapine were also increased by dehulling, while the contents of phytate and phytate P were decreased. In digestibility and balance experiments with piglets and intact hybrid breeds of growing-finishing pigs, the digestibility of organic matter and of crude nutrients and the contents of digestible energy and metabolizable energy were estimated. Furthermore, the precaecal digestibility of crude nutrients and amino acids was determined with fistulated mini-pigs. By dehulling the seeds the digestibility of organic matter from RM and RC was improved in piglets and adult pigs by approximately 10%, and the ME contents increased by 13-15%. The precaecal digestibility of the sum of amino acids was increased by approximately 3 and 6 units in RM and RC, respectively. The precaecal digestibility of lysine in RM and RC reached that of soybean oil meal from not dehulled beans.     

Differential inactivation and methylation of a transgene in plants by two suppressor loci containing homologous sequences

In a previous study on doubly transformed tobacco plants, we observed the unexpected inactivation in trans of T-DNA-I (encoding Kan^rNOS) following the introduction into the same genome of an unlinked copy of T-DNA-II (encoding Hyg^rOCS). This inactivation, which probably resulted from interactions between homologous regions on each T-DNA, was correlated with methylation in the nos _pro, which controlled the expression of both the nptII and nos genes. In this paper, we show that the inactivation and methylation of the nos _pro nptII gene in the presence of a suppressor T-DNA-II locus can be either complete (epistasis) or partial (cellular mosaicism). In plants showing partial suppression, the strength of the Kan^r phenotype, which apparently reflected the proportion of cells expressing the nptII gene, was inversely correlated with the degree of methylation of the nos _pro. The extent of nos _pro methylation decreased progressively in successive generations as suppressor T-DNA-II loci were crossed out. The strength of the Kan^r phenotype was improved and nos _pro methylation was less extensive in first generation Kan^r progeny obtained from outcrossing with untransformed tobacco than from self-fertilization.     

RNA polymerase V-dependent small RNAs in Arabidopsis originate from small,intergenic loci including most SINE repeats

In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (RNAP), RNAP IV and RNAP V. RNAP IV plays a major role in siRNA biogenesis, while RNAP V may recruit DNA methylation machinery to target endogenous loci for silencing. Although small RNA-generating regions that are dependent on both RNAP IV and RNAP V have been identified previously, the genomic loci targeted by RNAP V for siRNA accumulation and silencing have not been described extensively. To characterize the RNAP V-dependent, heterochromatic siRNA-generating regions in the Arabidopsis genome, we deeply sequenced the small RNA populations of wild-type and RNAP V null mutant (nrpe1) plants. Our results showed that RNAP V-dependent siRNA-generating loci are associated predominately with short repetitive sequences in intergenic regions. Suppression of small RNA production from short repetitive sequences was also prominent in RdDM mutants including dms4, drd1, dms3 and rdm1, reflecting the known association of these RdDM effectors with RNAP V. The genomic regions targeted by RNAP V were small, with an estimated average length of 238 bp. Our results suggest that RNAP V affects siRNA production from genomic loci with features dissimilar to known RNAP IV-dependent loci. RNAP V, along with RNAP IV and DRM1/2, may target and silence a set of small, intergenic transposable elements located in dispersed genomic regions for silencing. Silencing at these loci may be actively reinforced by RdDM.