Cytosine methylation at CG sites ( m CG) plays critical roles in development, epigenetic inheritance, and genome stability in mammals and plants. In the dicot model plant Arabidopsis thaliana, methyltransferase 1 (MET1), a principal CG methylase, functions to maintain m CG during DNA replication, with its null mutation resulting in global hypomethylation and pleiotropic developmental defects. Null mutation of a critical CG methylase has not been characterized at a whole-genome level in other higher eukaryotes, leaving the generality of the Arabidopsis findings largely speculative. Rice is a model plant of monocots, to which many of our important crops belong. Here we have characterized a null mutant of OsMet1-2, the major CG methylase in rice. We found that seeds homozygous for OsMet1-2 gene mutation (OsMET1-2 −/− ), which directly segregated from normal heterozygote plants (OsMET1-2 +/− ), were seriously maldeveloped, and all germinated seedlings underwent swift necrotic death. Compared with wild type, genome-wide loss of m CG occurred in the mutant methylome, which was accompanied by a plethora of quantitative molecular phenotypes including dysregulated expression of diverse protein-coding genes, activation and repression of transposable elements, and altered small RNA profiles. Our results have revealed conservation but also distinct functional differences in CG methylases between rice and Arabidopsis.Oryza sativa L. | monocotyledons C ytosine methylation is an evolutionarily conserved epigenetic modification across biological kingdoms (1-3). However, fundamental differences exist for this epigenetic mark between animals and plants in many aspects (1-3). For example, in mammalian somatic cells, methylated cytosines ( m Cs) occur almost exclusively in a CG sequence context, and CG methylation ( m CG) is maintained during DNA replication by a single CG methylase, DNA methyltransferase 1 (DNMT1). Cytosine methylation in plants is more complex, occurs in all sequence contexts (CG, CHG, and CHH; where H is A, T, or C), and is established and maintained by multiple enzymes that have distinct but also overlapping functions (2, 4-6). Nevertheless, m CG stands out as the most pervasive type (2). In the dicot model plant Arabidopsis thaliana, m CG is maintained by a major CG methylase, namely DNA methyltransferase 1 (MET1), the homolog of mammalian DNMT1 (2, 7-11). Null mutation of MET1 (the homozygous met1 mutant) virtually eliminates genome-wide m CG to 1.7% that of wild type (WT), that is, from 24.6% in WT to 0.42% in mutant (12, 13). Homozygous null met1 mutant can be obtained from selfed progenies of heterozygotes (MET1 +/− ) but was often at much lower frequencies than expected by Mendelian segregation (11). Homozygous Arabidopsis met1 plants show pleiotropic developmental abnormalities of variable penetrance, which aggravate in frequency and severity with inbreeding (11). Although conditional knockout DNMT1 mutants were established in human colorectal carcinoma cell lines (14) and loss-of-function DNA methyltran...

Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that of B, however, remains ambiguous and controversial but is suspected to be related to species of Aegilops, section Sitopsis. Here, we report the assembly of chromosome-level genome sequences of all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides, as well as the partial assembly of the Amblyopyrum muticum (synonym Aegilops mutica) genome for phylogenetic analysis. Our results reveal that the donor of the common wheat B subgenome is a distinct, and most probably extinct, diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae. speltoides and Am. muticum belong. In addition, we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex. The five Sitopsis species have various assembled genome sizes (4.11-5.89 Gb) with high proportions of repetitive sequences (85.99%-89.81%); nonetheless, they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex. Differences in genome size were primarily due to independent post-speciation amplification of transposons. We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding. These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex, as well as for wheat improvement.

An inherent challenge in using metal-organic frameworks (MOFs) for catalysis is how to access the catalytic sites generally confined inside the porous structure, in particular for substrates larger than the pores. We present here a promising solution to bypass this roadblock by modulating the facets of a crystalline MOF NENU-3a to enhance the facet exposure of the catalytic sites and the adsorption of substrates. Specifically, by transforming it with encapsulated catalysis-responsible polyoxometalate from octahedron characterized entirely by {111} facets to cube with only {100} facets, much enhanced catalytic activities were observed, especially for sterically demanding substrates that are otherwise hard to diffuse into the pores. Crystallographic analysis and adsorption/desorption experiments collectively established the critical effects of morphological control on the enhanced catalysis. The cubic crystals were then applied for biodiesel production, reaching more than 90% conversion of fatty acids (C12-C22) in comparison to <22% using octahedral crystals.

The non-random spatial packing of chromosomes in the nucleus plays a critical role in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome. We found subtle features including chromatin loops, gene loops, and off-/near-diagonal intensive interaction regions. Gene chromatin loops associated with H3K27me3 could be positively involved in gene expression. In addition to insulated enhancing effects for neighbor gene expression, the identified rice gene loops could bi-directionally (+/-) affect the expression of looped genes themselves. Finally, web-interleaved off-diagonal IHIs/KEEs (Interactive Heterochromatic Islands or KNOT ENGAGED ELEMENTs) could trap transposable elements (TEs) via the enrichment of silencing epigenetic marks. In parallel, the near-diagonal FIREs (Frequently Interacting Regions) could positively affect the expression of involved genes. Our results suggest that the chromatin packing pattern in rice is generally similar to that in Arabidopsis thaliana but with clear differences at specific structural levels. We conclude that genomic composition, epigenetic modification, and transcriptional activity could act in combination to shape global and local chromatin packing in rice. Our results confirm recent observations in rice and A. thaliana but also provide additional insights into the patterns and features of chromatin organization in higher plants.

Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses. In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica, rice, Arabidopsis suecica, banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them. HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.