SUMMARYChromatin is a highly organized structure with repetitive nucleosome subunits. Nucleosome distribution patterns, which contain information on epigenetic controls, are dynamically affected by ATP-dependent chromatin remodeling factors (remodelers). However, whether plants have specific nucleosome distribution patterns and how plant remodelers contribute to the pattern formation are not clear. In this study we used the micrococcal nuclease digestion followed by deep sequencing (MNase-seq) assay to show the genome-wide nucleosome pattern in Arabidopsis thaliana. We demonstrated that the nucleosome distribution patterns of Arabidopsis are associated with the gene expression level, and have several specific characteristics that are different from those of animals and yeast. In addition, we found that remodelers in the A. thaliana imitation switch (AtISWI) subfamily are important for the formation of the nucleosome distribution pattern. Double mutations in the AtISWI genes, CHROMATIN REMODELING 11 (CHR11) and CHR17, resulted in the loss of the evenly spaced nucleosome pattern in gene bodies, but did not affect nucleosome density, supporting a previous idea that the primary role of ISWI is to slide nucleosomes in gene bodies for pattern formation.

Polycomb group (PcG) proteins form an epigenetic memory system in plants and animals, but interacting proteins are poorly known in plants. Here, we have identified Arabidopsis UBIQUITIN SPECIFIC PROTEASES (USP; UBP in plant and yeasts) 12 and 13 as partners of the plant-specific PcG protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1). UBP12 binds to chromatin of PcG target genes and is required for histone H3 lysine 27 trimethylation and repression of a subset of PcG target genes. Plants lacking UBP12 and UBP13 developed autonomous endosperm in the absence of fertilization. We have identified UBP12 and UBP13 as new proteins in the plant PcG regulatory network. UBP12 and UBP13 belong to an ancient gene family and represent plant homologues of metazoan USP7. We have found that Drosophila USP7 shares a function in heterochromatic gene repression with UBP12/13 and their homologue UBP26. In summary, we demonstrate that USP7-like proteins are essential for gene silencing in diverse genomic contexts.

Background Stable gene repression is essential for normal growth and development. Polycomb repressive complexes 1 and 2 (PRC1&2) are involved in this process by establishing monoubiquitination of histone 2A (H2Aub1) and subsequent trimethylation of lysine 27 of histone 3 (H3K27me3). Previous work proposed that H2Aub1 removal by the ubiquitin-specific proteases 12 and 13 (UBP12 and UBP13) is part of the repressive PRC1&2 system, but its functional role remains elusive. Results We show that UBP12 and UBP13 work together with PRC1, PRC2, and EMF1 to repress genes involved in stimulus response. We find that PRC1-mediated H2Aub1 is associated with gene responsiveness, and its repressive function requires PRC2 recruitment. We further show that the requirement of PRC1 for PRC2 recruitment depends on the initial expression status of genes. Lastly, we demonstrate that removal of H2Aub1 by UBP12/13 prevents loss of H3K27me3, consistent with our finding that the H3K27me3 demethylase REF6 is positively associated with H2Aub1. Conclusions Our data allow us to propose a model in which deposition of H2Aub1 permits genes to switch between repression and activation by H3K27me3 deposition and removal. Removal of H2Aub1 by UBP12/13 is required to achieve stable PRC2-mediated repression.

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A total of ten ancient colored glass beads were analyzed by confocal Raman microspectroscopy for the non-destructive identification of microcrystals within them. These beads were excavated from different regions of China, including Xinjiang, Henan, Hubei and Guangxi Provinces, and were dated mainly from the 10 th century BC to the 9 th century AD. For the first time, either tin or antimony-based opacifiers/colorants including calcium antimonate (CaSb 2 O 6 , Ca 2 Sb 2 O 7 ), bindheimite (Pb 2 Sb 2 O 7 ), lead tin yellow type II (PbSn 1-x Si x O 3 ) and cassiterite (SnO 2 ) were identified in nine samples. In addition, other crystalline phases such as cuprite (Cu 2 O), a-wollastonite (CaSiO 3 ), diopside (CaMgSi 2 O 6 ), feldspar (KAlSi 3 O 8 ), calcite (CaCO 3 ) and quartz (SiO 2 ) were also detected. Another interesting phenomenon first observed in this study was the coexistence of Sn-and Sb-based opacifiers/colorants in one mosaic bead from Guangxi. The possibility to use Sb-and Sn-based opacifiers/colorants for dating and provenance study of ancient glass found in China is discussed briefly.

Heat-stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, yet it is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. We generated and analyzed RNA and bisulfite-sequencing data of wild-type and h1 mutant seedlings before and after heat stress. Loss of H1 caused activation of pericentromeric Gypsy elements upon heat treatment, despite these elements remaining highly methylated. By contrast, nonpericentromeric Copia elements became activated concomitantly with loss of DNA methylation. The same Copia elements became activated in heat-treated chromomethylase 2 (cmt2) mutants, indicating that H1 represses Copia elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1-deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both H1 and DNA methylation redundantly suppress the plant response to heat stress.

Thirty-seven glass beads excavated from the Han Dynasty tombs in Hepu county, Guangxi, China, were analyzed using a portable X-ray fluorescence (PXRF) spectrometer. Reference sample Corning glass D is used to check precision and accuracy of the equipment for major and minor components. The results of inductively coupled plasma atomic emission spectroscopy and PXRF are compared to evaluate the quality of equipment for trace elements. Combined with the contents of Al 2 O 3 and CaO, a new criterion of subgroup division for potash glass based on the levels of trace elements (Rb and Sr) is proposed. The correlations of Rb and K, Rb and Al, and Sr and Ca are discussed. It is thought that saltpeter was the main flux used to produce potash glasses of different groups. The positive correlation between Rb and Al, and Rb and K indicates that potassium aluminosilicate minerals may be used as raw minerals for potash glasses of group II. The results indicate that the levels of Rb and Sr can be very helpful in subgroup definition and provide useful clues to the raw materials used for glassmaking and provenance study of the potash glass found in Guangxi, China.

The Imitation Switch (ISWI) type adenosine triphosphate (ATP)‐dependent chromatin remodeling factors are conserved proteins in eukaryotes, and some of them are known to form stable remodeling complexes with members from a family of proteins, termed DDT‐domain proteins. Although it is well documented that ISWIs play important roles in different biological processes in many eukaryotic species, the molecular basis for protein interactions in ISWI complexes has not been fully addressed. Here, we report the identification of interaction domains for both ISWI and DDT‐domain proteins. By analyzing CHROMATIN REMODELING11 (CHR11) and RINGLET1 (RLT1), an Arabidopsis thaliana ISWI (AtISWI) and AtDDT‐domain protein, respectively, we show that the SLIDE domain of CHR11 and the DDT domain together with an adjacent sequence of RLT1 are responsible for their binding. The Arabidopsis genome contains at least 12 genes that encode DDT‐domain proteins, which could be grouped into five subfamilies based on the sequence similarity. The SLIDE domain of AtISWI is able to bind members from different AtDDT subfamilies. Moreover, a human ISWI protein SNF2H is capable of binding AtDDT‐domain proteins through its SLIDE domain, suggesting that binding to DDT‐domain proteins is a conserved biochemical function for the SLIDE domain of ISWIs in eukaryotes.