siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis

Plant microRNAs (miRNAs) and small interfering RNAs (siRNAs) bear a 2′-O-methyl group on the 3′-terminal nucleotide. This methyl group is post-synthetically added by the methyltransferase protein HEN1 and protects small RNAs from enzymatic activities that target the 3′-OH. A mutagenesis screen for suppressors of the partial loss-of-function hen1-2 allele in Arabidopsis identified second-site mutations that restore miRNA methylation. These mutations affect two subunits of the DNA-dependent RNA polymerase IV (Pol IV), which is essential for the biogenesis of 24 nt endogenous siRNAs. A mutation in RNA-dependent RNA polymerase 2, another essential gene for the biogenesis of endogenous 24-nt siRNAs, also rescued the defects in miRNA methylation of hen1-2, revealing a previously unsuspected, negative influence of siRNAs on HEN1-mediated miRNA methylation. In addition, our findings imply the existence of a negative modifier of HEN1 activity in the Columbia genetic background

Small RNA-Directed Epigenetic Natural Variation in Arabidopsis thaliana

Progress in epigenetics has revealed mechanisms that can heritably regulate gene function independent of genetic alterations. Nevertheless, little is known about the role of epigenetics in evolution. This is due in part to scant data on epigenetic variation among natural populations. In plants, small interfering RNA (siRNA) is involved in both the initiation and maintenance of gene silencing by directing DNA methylation and/or histone methylation. Here, we report that, in the model plant Arabidopsis thaliana, a cluster of ∼24 nt siRNAs found at high levels in the ecotype Landsberg erecta (Ler) could direct DNA methylation and heterochromatinization at a hAT element adjacent to the promoter of FLOWERING LOCUS C (FLC), a major repressor of flowering, whereas the same hAT element in ecotype Columbia (Col) with almost identical DNA sequence, generates a set of low abundance siRNAs that do not direct these activities. We have called this hAT element MPF for Methylated region near Promoter of FLC, although de novo methylation triggered by an inverted repeat transgene at this region in Col does not alter its FLC expression. DNA methylation of the Ler allele MPF is dependent on genes in known silencing pathways, and such methylation is transmissible to Col by genetic crosses, although with varying degrees of penetrance. A genome-wide comparison of Ler and Col small RNAs identified at least 68 loci matched by a significant level of ∼24 nt siRNAs present specifically in Ler but not Col, where nearly half of the loci are related to repeat or TE sequences. Methylation analysis revealed that 88% of the examined loci (37 out of 42) were specifically methylated in Ler but not Col, suggesting that small RNA can direct epigenetic differences between two closely related Arabidopsis ecotypes

Multi-image Matching of Airborne SAR Imagery by SANCC

In order to improve accuracy of SAR matching, a multi-image matching method based on sum of adaptive normalized cross-correlation (SANCC) is proposed. It utilizes geometrical and radiometric information of multi-baselinesynthetic aperture radar (SAR)images effectively. Firstly, imaging parameters, platform parameters and approximate digital surface model (DSM) are used to predict matching line. Secondly, similarity and proximity in Gestalt theory are introduced to SANCC, and SANCC measures of potential matching points along the matching line are calculated. Thirdly, multi-image matching results and object coordinates of matching points are obtained by winner-take-all (WTA) optimization strategy. The approach has been demonstrated with airborne SAR images acquired by a Chinese airborne SAR system (CASMSAR system). The experimental results indicate that the proposed algorithm is effective for providing dense and accuracy matching points, reducing the number of mismatches caused by repeated textures, and offering a better solution to match in poor textured areas

A StereoSAR Matching Method Based on Disparity Maps Fusion

A matching algorithm based on disparity maps fusion is proposed. Firstly, on the basis of normalized cross correlation(NCC), various disparity maps are computed using several different matching window sizes. Then, for each disparity of each disparity maps, the confidence level is evaluated by a new confidence measure, which combined left right consistency(LRC) with signal to noise ratio(SNR). Finally, a new proposed disparity maps fusion strategy is used for formation of weighted disparity map in terms of confidence level. This disparity maps fusion strategy considers not only the confidence level of the disparity itself but also its neighbors. The algorithm has been applied to a pair of TanDEM-X spotlight stereo images. The results demonstrate that the accuracy of DEM generated with the proposed algorithm is improved from 11.28 m to 8.41 m and the gross errors are effectively reduced

Extended Yearly LMDI Approaches: A Case Study of Energy Consumption

Although the logarithmic mean Divisia index (LMDI) approach has been widely used in the field of energy and environmental research, it has a shortcoming. Since the LMDI approach only focuses on the base year and reporting year, in situations in which the research period is long, the annual changes during the research period may be difficult to capture. In particular, if there were huge fluctuations in the indicators (such as the energy consumption and carbon emissions) or their drivers during the middle of a research period, a substantial amount of information about the fluctuations will be ignored. Therefore, we propose four extended yearly LMDI approaches, including pure LMDI, weighted LMDI, comprehensive LMDI, and scenario LMDI approaches to better capture fluctuations and compensate for the original LMDI approach’s shortcomings. Additionally, we found that there are mathematical relationships among the four extended LMDI approaches. We further compare these four approaches’ advantages, disadvantages, and applicable situations and analyze a case study on China’s energy consumption based on the four proposed approaches

siRNAs compete with miRNAs for methylation by HEN1 in \u3ci\u3eArabidopsis\u3c/i\u3e (Supplementary Material)

Legends of Supplemental Figure

siRNAs compete with miRNAs for methylation by HEN1 in \u3ci\u3eArabidopsis\u3c/i\u3e

Plant microRNAs (miRNAs) and small interfering RNAs (siRNAs) bear a 2\u27-O-methyl group on the 3\u27-terminal nucleotide. This methyl group is post-synthetically added by the methyltransferase protein HEN1 and protects small RNAs from enzymatic activities that target the 3\u27-OH. A mutagenesis screen for suppressors of the partial loss-offunction hen1-2 allele in Arabidopsis identified second-site mutations that restore miRNA methylation. These mutations affect two subunits of the DNA-dependent RNA polymerase IV (Pol IV), which is essential for the biogenesis of 24 nt endogenous siRNAs. A mutation in RNA-dependent RNA polymerase 2, another essential gene for the biogenesis of endogenous 24-nt siRNAs, also rescued the defects in miRNA methylation of hen1-2, revealing a previously unsuspected, negative influence of siRNAs on HEN1-mediated miRNA methylation. In addition, our findings imply the existence of a negative modifier of HEN1 activity in the Columbia genetic background

Home-based microbial solution to boost crop growth in low-fertility soil

14 páginas.- 6 figuras.- 66 referencias.- Additional Supporting Information may be found online in the Supporting Information section at the end of the article.Soil microbial inoculants are expected to boost crop productivity under climate change and soil degradation. However, the efficiency of native vs commercialized microbial inoculants in soils with different fertility and impacts on resident microbial communities remain unclear.We investigated the differential plant growth responses to native synthetic microbial community (SynCom) and commercial plant growth-promoting rhizobacteria (PGPR). We quantified the microbial colonization and dynamic of niche structure to emphasize the home-field advantages for native microbial inoculants.A native SynCom of 21 bacterial strains, originating from three typical agricultural soils, conferred a special advantage in promoting maize growth under low-fertility conditions. The root : shoot ratio of fresh weight increased by 78-121% with SynCom but only 23-86% with PGPRs. This phenotype correlated with the potential robust colonization of SynCom and positive interactions with the resident community. Niche breadth analysis revealed that SynCom inoculation induced a neutral disturbance to the niche structure. However, even PGPRs failed to colonize the natural soil, they decreased niche breadth and increased niche overlap by 59.2-62.4%, exacerbating competition.These results suggest that the home-field advantage of native microbes may serve as a basis for engineering crop microbiomes to support food production in widely distributed poor soils.The authors are grateful to the editor and anonymous referees.YL is supported by National Key R&D Program of China(2021YFD1900400), Strategic Priority Research Program of the Chinese Academy of Sciences (XDA24020104), Innovation Program of Institute of Soil Science (ISSASIP2201), National Natural Science Foundation of China (41877060), and Youth Innovation Promotion Association of Chinese Academy of Sciences (2016284). D-BM is supported by the Spanish Ministryof Science and Innovation (PID2020-115813RA-I00) and a Project PAIDI 2020 from the Junta de Andalucıa (P20_00879)Peer reviewe

Mechanism exploration and biomarker identification of glycemic deterioration in patients with diseases of the exocrine pancreas

Abstract The damage to the endocrine pancreas among patients with diseases of the exocrine pancreas (DP) leads to reduced glycemic deterioration, ultimately resulting in diabetes of the exocrine pancreas (DEP). The present research aims to investigate the mechanism responsible for glycemic deterioration in DP patients, and to identify useful biomarkers, with the ultimate goal of enhancing clinical practice awareness. Gene expression profiles of patients with DP in this study were acquired from the Gene Expression Omnibus database. The original study defines DP patients to belong in one of three categories: non-diabetic (ND), impaired glucose tolerance (IGT) and DEP, which correspond to normoglycemia, early and late glycemic deterioration, respectively. After ensuring quality control, the discovery cohort included 8 ND, 20 IGT, and 12 DEP, while the validation cohort included 27 ND, 15 IGT, and 20 DEP. Gene set enrichment analysis (GSEA) employed differentially expressed genes (DEGs), while immunocyte infiltration was determined using single sample gene set enrichment analysis (ssGSEA). Additionally, correlation analysis was conducted to establish the link between clinical characteristics and immunocyte infiltration. The least absolute shrinkage and selection operator regression and random forest combined to identify biomarkers indicating glycemic deterioration in DP patients. These biomarkers were further validated through independent cohorts and animal experiments. With glycemic deterioration, biological processes in the pancreatic islets such as nutrient metabolism and complex immune responses are disrupted in DP patients. The expression of ACOT4, B2M, and ACKR2 was upregulated, whereas the expression of CACNA1F was downregulated. Immunocyte infiltration in the islet microenvironment showed a significant positive correlation with the age, body mass index (BMI), HbA1c and glycemia at the 2-h of patients. It was a crucial factor in glycemic deterioration. Additionally, B2M demonstrated a significant positive correlation with immunocyte infiltration and clinical features. Quantitative real-time PCR (qRT-PCR) and western blotting confirmed the upregulation in B2M. Immunofluorescent staining suggested the alteration of B2M was mainly in the alpha cells and beta cells. Overall, the study showed that gradually increased immunocyte infiltration was a significant contributor to glycemic deterioration in patients with DP, and it also highlighted B2M as a biomarker

SDG714, a Histone H3K9 Methyltransferase, Is Involved in Tos17 DNA Methylation and Transposition in Rice

Although the role of H3K9 methylation in rice (Oryza sativa) is unclear, in Arabidopsis thaliana the loss of histone H3K9 methylation by mutation of Kryptonite [also known as SU(VAR)3-9 homolog] reduces genome-wide DNA methylation and increases the transcription of transposable elements. Here, we report that rice SDG714 (for SET Domain Group Protein714) encodes a histone H3K9-specific methyltransferase. The C terminus of SDG714 confers enzymatic activity and substrate specificity, whereas the N terminus localizes it in the nucleus. Loss-of-function mutants of SDG714 (SDG714IR transformants) generated by RNA interference display a mostly glabrous phenotype as a result of the lack of macro trichomes in glumes, leaves, and culms compared with control plants. These mutants also show decreased levels of CpG and CNG cytosine methylation as well as H3K9 methylation at the Tos17 locus, a copia-like retrotransposon widely used for the generation of rice mutants. Most interestingly, loss of function of SDG714 can enhance transcription and cause the transposition of Tos17. Together, these results suggest that histone H3K9 methylation mediated by SDG714 is involved in DNA methylation, the transposition of transposable elements, and genome stability in rice