Cold exposure affects glucose metabolism, lipid droplet deposition and mitophagy in skeletal muscle of newborn goats.

Cold exposure is a common stressor for newborn goats. Skeletal muscle plays an important role in maintaining whole-body homeostasis of glucose and lipid metabolism. However, the molecular mechanisms underlying regulation of skeletal muscle of newborn goats by cold exposure remains unclear. In this study, we found a significant increase (P < 0.01) in serum glucagon levels after 24 h of cold exposure (COLD, 6°C), while glucose and insulin concentrations were significantly decreased (P < 0.01) compared to room temperature (RT, 25°C). Additionally, we found that cold exposure reduced glycogen content (P < 0.01) in skeletal muscle. Pathway enrichment analysis revealed that cold exposure activated skeletal muscle glucose metabolism pathways (including insulin resistance and the insulin signaling pathway) and mitophagy-related pathways. Cold exposure up-regulated the expression of genes involved in fatty acid and triglyceride synthesis, promoting skeletal muscle lipid deposition. Notably, cold exposure induced mitophagy in skeletal muscle.

Active oxygen generation induced by the glucose sensor TaHXK7-1A decreased the drought resistance of transgenic Arabidopsis and wheat (Triticum aestivum L.).

Improving wheat drought resistance is of great significance for grain production and food security. Hexokinases (HXKs) play a role in sugar signal transduction and are involved in abiotic stress responses in wheat. To clarify the relationship between HXKs and drought stress in wheat, we used the rice active oxygen induction gene OsHXK1 as a reference sequence and the homologously cloned wheat TaHXK7-1A gene. TaHXK7-1A was localized in the nucleus and cell membrane. Under drought stress, over-expression of TaHXK7-1A increased the contents of O2·ï¼ and malondialdehyde (MDA) and significantly up-regulated the respiratory burst oxidative homologue (RBOHs) genes in transgenic Arabidopsis. In addition, the over-expression of TaHXK7-1A inhibited the growth of Arabidopsis seedlings and increased ROS accumulation under 6 % exogenous glucose treatment. Gene silencing of TaHXK7-1 decreased the contents of O2·ï¼ and MDA in wheat leaves under drought stress, and the RBOHs was significantly down-regulated, which improved the drought resistance of wheat. The results of yeast one-hybrid, EMSA, and dual-luciferase assays showed that TabHLH148-5A bound to the E-box motif of the TaHXK7-1A promoter and inhibited the expression of TaHXK7-1A. In addition, yeast two-hybrid and luciferase complementation imaging assays showed that TaHXK7-1A interacted with TaGRF3-4A. These results indicate that the glucose sensor TaHXK7-1A was negatively regulated by TabHLH148-5A, interacted with TaGRF3-4A, and negatively regulated wheat drought resistance by regulating RBOHs expression and inducing ROS production, thus providing a theoretical basis for revealing the molecular mechanism of wheat drought resistance.

Transcriptomics reveals a core transcriptional network of K-type cytoplasmic male sterility microspore abortion in wheat (Triticum aestivum L.).

BACKGROUND: Cytoplasmic male sterility (CMS) plays a crucial role in hybrid production. K-type CMS, a cytoplasmic male sterile line of wheat with the cytoplasms of Aegilops kotschyi, is widely used due to its excellent characteristics of agronomic performance, easy maintenance and easy restoration. However, the mechanism of its pollen abortion is not yet clear. RESULTS: In this study, wheat K-type CMS MS(KOTS)-90-110 (MS line) and it's fertile near-isogenic line MR (KOTS)-90-110 (MR line) were investigated. Cytological analysis indicated that the anthers of MS line microspore nucleus failed to divide normally into two sperm nucleus and lacked starch in mature pollen grains, and the key abortive period was the uninucleate stage to dinuclear stage. Then, we compared the transcriptome of MS line and MR line anthers at these two stages. 11,360 and 5182 differentially expressed genes (DEGs) were identified between the MS and MR lines in the early uninucleate and binucleate stages, respectively. Based on GO enrichment and KEGG pathways analysis, it was evident that significant transcriptomic differences were "plant hormone signal transduction", "MAPK signaling pathway" and "spliceosome". We identified 17 and 10 DEGs associated with the IAA and ABA signal transduction pathways, respectively. DEGs related to IAA signal transduction pathway were downregulated in the early uninucleate stage of MS line. The expression level of DEGs related to ABA pathway was significantly upregulated in MS line at the binucleate stage compared to MR line. The determination of plant hormone content and qRT-PCR further confirmed that hormone imbalance in MS lines. Meanwhile, 1 and 2 DEGs involved in ABA and Ethylene metabolism were also identified in the MAPK cascade pathway, respectively; the significant up regulation of spliceosome related genes in MS line may be another important factor leading to pollen abortion. CONCLUSIONS: We proposed a transcriptome-mediated pollen abortion network for K-type CMS in wheat. The main idea is hormone imbalance may be the primary factor, MAPK cascade pathway and alternative splicing (AS) may also play important regulatory roles in this process. These findings provided intriguing insights for the molecular mechanism of microspore abortion in K-type CMS, and also give useful clues to identify the crucial genes of CMS in wheat.

A systematic review and meta-analysis on the correlation between HIV infection and multidrug-resistance tuberculosis.

Background: The emergence of multidrug-resistant tuberculosis (MDR-TB) in HIV-positive people poses a significant challenge to international efforts to eradicate tuberculosis (TB). Many studies found conflicting results when examining the correlation between HIV and MDR-TB. The purpose of the present investigation was to comprehensively review the literature on the association between HIV infection and MDR-TB in order to evaluate the impact of HIV on MDR-TB worldwide. Methods: Utilizing the databases PubMed, Scopus, Google Scholar, and ScienceDirect, studies published between January 2000 and March 2023 that are eligible for meta-analysis were selected. Using the random-effects model, the aggregated odds ratio of the empirical relationship between HIV and MDR-TB was calculated, along with a confidence interval ranging from 0 to 95 %. Examining the asymmetry of the funnel plot and utilizing Egger's and Begg's test, the possibility of publication bias was investigated. The extent of heterogeneity was determined using the I2 statistics. Results: Through a database search, we identified 1214 studies, from which we ultimately selected 15 studies involving 9667 patients. The odds ratio of 2.78 (95 % confidence interval: 1.07-7.20) between HIV/AIDS and MDR-TB indicates a significant positive correlation. Tau 2 = 3.46, chi 2 = 1440.46, df = 14, I2 = 99.0 %, z = 2.10, and p 0.05 indicate that there is substantial heterogeneity among pooled studies. Since I2 is 99 % (>50 %), a random effect model was employed. The percentage of multidrug-resistant HIV-positive patients across all included studies follows a normal distribution, as shown by a Box and whisker plot with a symmetric skewness and a mesokurtic tail and a scatter plot with a significant R2 value below 1 [R2 = 0.2476] showed the positive correlation between multidrug resistance and HIV infection. Conclusion: HIV infection increases MDR-TB risk, and the preceding pooled analysis showed an increased risk trend. Thus, MDR-TB, especially in HIV-positive patients, requires early case detection, quality-assured bacteriology diagnosis, and an effective infection control program.

Low-Temperature-Mediated Promoter Methylation Relates to the Expression of TaPOR2D, Affecting the Level of Chlorophyll Accumulation in Albino Wheat (Triticum aestivum L.).

Chlorophyll is an indispensable photoreceptor in plant photosynthesis. Its anabolic imbalance is detrimental to individual growth and development. As an essential epigenetic modification, DNA methylation can induce phenotypic variations, such as leaf color transformation, by regulating gene expression. Albino line XN1376B is a natural mutation of winter wheat cultivar XN1376; however, the regulatory mechanism of its albinism is still unclear. In this study, we found that low temperatures induced albinism in XN1376B. The number of chloroplasts decreased as the phenomenon of bleaching intensified and the fence tissue and sponge tissue slowly dissolved. We identified six distinct TaPOR (protochlorophyllide oxidoreductase) genes in the wheat genome, and TaPOR2D was deemed to be related to the phenomenon of albinism based on the expression in different color leaves (green leaves, white leaves and returned green leaves) and the analysis of promoters' cis-acting elements. TaPOR2D was localized to chloroplasts. TaPOR2D overexpression (TaPOR2D-OE) enhanced the chlorophyll significantly in Arabidopsis, especially at two weeks; the amount of chlorophyll was 6.46 mg/L higher than in WT. The methylation rate of the TaPOR2D promoter in low-temperature albino leaves is as high as 93%, whereas there was no methylation in green leaves. Correspondingly, three DNA methyltransferase genes (TaMET1, TaDRM and TaCMT) were up-regulated in white leaves. Our study clarified that the expression of TaPOR2D is associated with its promoter methylation at a low temperature; it affects the level of chlorophyll accumulation, which probably causes the abnormal development of plant chloroplasts in albino wheat XN1376B. The results provide a theoretical basis for in-depth analysis of the regulation of development of plant chloroplasts and color variation in wheat XN1376B leaves.

The wheat VQ motif-containing protein TaVQ4-D positively regulates drought tolerance in transgenic plants.

VQ motif-containing proteins play important roles in plant abiotic and biotic stresses. In this study, we cloned the VQ protein gene TaVQ4-D that is induced by drought stress. Arabidopsis and wheat plants overexpressing TaVQ4-D showed increased tolerance to drought stress. In contrast, wheat lines in which TaVQ4-D expression had been silenced showed decreased drought tolerance. Under drought stress conditions, the contents of superoxide dismutase and proline increased and the content of malondialdehyde decreased in transgenic wheat plants overexpressing TaVQ4-D compared with the wild type. At the same time, the expression of reactive oxygen species-scavenging-related genes and stress-related genes was up-regulated. However, plants of TaVQ4-D-silenced wheat lines showed decreased activities of antioxidant enzymes and reduced expression of some stress-related and antioxidant-related genes. In addition, the TaVQ4-D protein physically interacts with two mitogen-activated protein kinases (MPK3 and MPK6) and plays a role in plant drought stress as the phosphorylated substrates of MPK3 and MPK6. In summary, the results of our study suggest that TaVQ4-D can positively regulate drought stress tolerance in wheat.

Traditional Chinese medicine for heart failure with preserved ejection fraction: clinical evidence and potential mechanisms.

Heart failure with preserved ejection fraction accounts for a large proportion of heart failure, and it is closely related to a high hospitalization rate and high mortality rate of cardiovascular disease. Although the methods and means of modern medical treatment of HFpEF are becoming increasingly abundant, they still cannot fully meet the clinical needs of HFpEF patients. Traditional Chinese medicine is an important complementary strategy for the treatment of diseases in modern medicine, and it has been widely used in clinical research on HFpEF in recent years. This article reviews the current situation of HFpEF management, the evolution of guidelines, the clinical evidence and the mechanism of TCM in the treatment of HFpEF. The purpose of this study is to explore the application of TCM for HFpEF, to further improve the clinical symptoms and prognosis of patients and to provide a reference for the diagnosis and treatment of the disease.

Hydrodynamically-driven distribution and remobilization of heavy metals in surface sediments around the coastal area of Shandong Peninsula, China.

Heavy metals (HMs) are considered a major pollutant of the surface sediments of the continental shelf. However, there remains little in-depth research on their fate in the ocean, and particularly on their abundance in sediments and the water column and the underlying drivers. This study examined the concentrations of HMs (Cu, Zn, Cr, Pb, Cd, and As) in surface sediments and suspended particulate matter (SPM) around the coastal area of Shandong Peninsula, China. The division of the sedimentary environment and influencing factors were also analyzed using multivariate statistical analysis Fuzzy c-means (FCM) cluster and Non-Linear Mapping (NLM). The study attempted to understand the distribution and remobilization of HMs in the shallow marginal sea using multi-disciplinary approaches, including satellite remote sensing and numerical simulation. The results showed higher HMs in the surface sediments in Weihai Bay (Zone I) than in the junction of the Chengshantou Cap (Zone III) and north of Wei Bay (Zone II). In addition, the results suggested that Cu, Zn, Cr and Pb originated from natural weathering, with their spatial distributions in the three zones highly regulated by sediment grain size, total nitrogen (TN), and total carbon (TC). In contrast, Cd and As originated from anthropogenic contamination (e.g., industrial discharges and aquaculture) in Zone I. HMs (except As) were influenced by terrigenous total organic carbon (TOC) in Zone III. The results of this study suggest that the difference in sediment re-suspension intensity has an important influence on the distribution of HM concentrations in the north Yellow Sea. This study can act as a reference for understanding the fates and source-sink processes of HMs in offshore sediments. The coupling behaviors and microscopic suspension properties of HMs in surface sediments and SPM require further investigation.

Heterogeneity of fibroblasts is a hallmark of age-associated erectile dysfunction.

BACKGROUND: The prevalence of age-associated erectile dysfunction (ED) increases pronouncedly with age. However, the cellular composition and transcriptomic changes of aging penile corpus cavernosum remain largely unclear. METHODS: Herein, we performed single cell sequencing penile corpus cavernosum from five young with normal erectile response and five old rats with ED. RESULTS: Clustering analysis identified 19 cell types, such as fibroblasts, myofibroblasts and immune cells. We next revealed their transcriptomic alterations and investigated novel subpopulations of major cell types. Among them, fibroblasts possessed the largest cell number and showed apparent heterogeneity. By performing single-cell entropy analysis on fibroblasts, we observed the age-associated decrease of entropy, and aged fibroblasts were found to adopt senescent secretory phenotype, as evidenced by the high expression of genes associated with the senescence-associated secretory phenotype (SASP). Finally, we constructed a comprehensive intercellular communication network and highlighted key mediators of crosstalk between fibroblasts and other cell types. CONCLUSIONS: We plotted a cellular atlas of aging cells within penile corpus cavernosum, especially fibroblasts. Our work will deepen the understanding of the heterogeneity among certain cell types within aged penile corpus cavernosum, which will generate positive effects on the future treatment of age-associated ED.

Genome-Wide Identification and Expression Analysis of TUA and TUB Genes in Wheat (Triticum aestivum L.) during Its Development.

Microtubules play a fundamental role in plant development, morphogenesis, and cytokinesis; they are assembled from heterodimers containing an α-tubulin (TUA) and a ß-tubulin (TUB) protein. However, little research has been conducted on the TUA and TUB gene families in hexaploid wheat (Triticum aestivum L.). In this study, we identified 15 TaTUA and 28 TaTUB genes in wheat. Phylogenetic analysis showed that 15 TaTUA genes were divided into two major subfamilies, and 28 TaTUB genes were divided into five major subfamilies. Mostly, there were similar motif compositions and exon-intron structures among the same subfamilies. Segmental duplication of genes (WGD/segmental) is the main process of TaTUA and TaTUB gene family expansion in wheat. It was found that TaTUA and TaTUB genes presented specific temporal and spatial characteristics based on the expression profiles of 17 tissues during wheat development using publicly available RNA-seq data. It was worth noting, via qRT-PCR, that two TaTUA and five TaTUB genes were highly expressed in fertile anthers compared to male sterility. These were quite different between physiological male sterile lines and S-type cytoplasmic male sterile lines at different stages of pollen development. This study offers fundamental information on the TUA and TUB gene families during wheat development and provides new insights for exploring the molecular mechanism of wheat male sterility.

The Transcription Factors TaTDRL and TaMYB103 Synergistically Activate the Expression of TAA1a in Wheat, Which Positively Regulates the Development of Microspore in Arabidopsis.

Pollen fertility plays an important role in the application of heterosis in wheat (Triticum aestivum L.). However, the key genes and mechanisms underlying pollen abortion in K-type male sterility remain unclear. TAA1a is an essential gene for pollen development in wheat. Here, we explored the mechanism involved in its transcriptional regulation during pollen development, focusing on a 1315-bp promoter region. Several cis-acting elements were identified in the TAA1a promoter, including binding motifs for Arabidopsis thaliana AtAMS and AtMYB103 (CANNTG and CCAACC, respectively). Evolutionary analysis indicated that TaTDRL and TaMYB103 were the T. aestivum homologs of AtAMS and AtMYB103, respectively, and encoded nucleus-localized transcription factors containing 557 and 352 amino acids, respectively. TaTDRL and TaMYB103 were specifically expressed in wheat anthers, and their expression levels were highest in the early uninucleate stage; this expression pattern was consistent with that of TAA1a. Meanwhile, we found that TaTDRL and TaMYB03 directly interacted, as evidenced by yeast two-hybrid and bimolecular fluorescence complementation assays, while yeast one-hybrid and dual-luciferase assays revealed that both TaTDRL and TaMYB103 could bind the TAA1a promoter and synergistically increase its transcriptional activity. Furthermore, TaTDRL-EAR and TaMYB103-EAR transgenic Arabidopsis plants displayed abnormal microspore morphology, reduced pollen viability, and lowered seed setting rates. Additionally, the expression of AtMS2, a TAA1a homolog, was significantly lower in the two repressor lines than in the corresponding overexpression lines or WT plants. In summary, we identified a potential transcriptional regulatory mechanism associated with wheat pollen development.

A superior allele of the wheat gene TaGL3.3-5B, selected in the breeding process, contributes to seed size and weight.

KEY MESSAGE: A superior allele of wheat gene TaGL3.3-5B was identified and could be used in marker-assisted breeding in wheat. Identifying the main genes which mainly regulate the yield-associated traits can significantly increase the wheat production. In this study, gene TaGL3.3 was cloned from common wheat according to the sequence of OsPPKL3. A SNP in the 8th exon of TaGL3.3-5B, T/C in coding sequence (CDS), which resulted in an amino acid change (Val/Ala), was identified between the low 1000-kernel weight (TKW) wheat Chinese Spring and the high TKW wheat Xinong 817 (817). Subsequently, association analysis in the mini-core collection (MCC) and the recombinant inbred lines (RIL) revealed that the allele TaGL3.3-5B-C (from 817) was significantly correlated with higher TKW. The high frequency of TaGL3.3-5B-C in the Chinese modern wheat cultivars indicated that it was selected positively in wheat breeding programs. The overexpression of TaGL3.3-5B-C in Arabidopsis resulted in shorter pods and longer grains than those of wild-type counterparts. Additionally, TaGL3.3 expressed a tissue-specific pattern in wheat as revealed by qRT-PCR. We also found that 817 showed higher expression of TaGL3.3 than that in Chinese Spring (CS) during the seed development. These results demonstrate that TaGL3.3 plays an important role in the formation of seed size and weight. Allele TaGL3.3-5B-C is associated with larger and heavier grains that are beneficial to wheat yield improvement.

Virus-specific editing identification approach reveals the landscape of A-to-I editing and its impacts on SARS-CoV-2 characteristics and evolution.

Upon SARS-CoV-2 infection, viral intermediates specifically activate the IFN response through MDA5-mediated sensing and accordingly induce ADAR1 p150 expression, which might lead to viral A-to-I RNA editing. Here, we developed an RNA virus-specific editing identification pipeline, surveyed 7622 RNA-seq data from diverse types of samples infected with SARS-CoV-2, and constructed an atlas of A-to-I RNA editing sites in SARS-CoV-2. We found that A-to-I editing was dynamically regulated, varied between tissue and cell types, and was correlated with the intensity of innate immune response. On average, 91 editing events were deposited at viral dsRNA intermediates per sample. Moreover, editing hotspots were observed, including recoding sites in the spike gene that affect viral infectivity and antigenicity. Finally, we provided evidence that RNA editing accelerated SARS-CoV-2 evolution in humans during the epidemic. Our study highlights the ability of SARS-CoV-2 to hijack components of the host antiviral machinery to edit its genome and fuel its evolution, and also provides a framework and resource for studying viral RNA editing.

Interplay between Pds5 and Rec8 in regulating chromosome axis length and crossover frequency.

Meiotic chromosomes have a loop/axis architecture, with axis length determining crossover frequency. Meiosis-specific Pds5 depletion mutants have shorter chromosome axes and lower homologous chromosome pairing and recombination frequency. However, it is poorly understood how Pds5 coordinately regulates these processes. In this study, we show that only ~20% of wild-type level of Pds5 is required for homolog pairing and that higher levels of Pds5 dosage-dependently regulate axis length and crossover frequency. Moderate changes in Pds5 protein levels do not explicitly impair the basic recombination process. Further investigations show that Pds5 does not regulate chromosome axes by altering Rec8 abundance. Conversely, Rec8 regulates chromosome axis length by modulating Pds5. These findings highlight the important role of Pds5 in regulating meiosis and its relationship with Rec8 to regulate chromosome axis length and crossover frequency with implications for evolutionary adaptation.

Inhibition effect of ZrF4 on UO2 precipitation in the LiF-BeF2 molten salt.

The dissolution-precipitation behavior of zirconium dioxide (ZrO2) in molten lithium fluoride-beryllium fluoride (LiF-BeF2, (2 : 1 mol, FLiBe)) eutectic salt at 873 K was studied. The results of the dissolution experiment showed that the saturated solubility of ZrO2 in the FLiBe melt was 3.84 × 10-3 mol kg-1 with equilibrium time of 6 h, and its corresponding apparent solubility product (K'sp) was 3.40 × 10-5 mol3 kg-3. The interaction between Zr(iv) and O2- was studied by titrating lithium oxide (Li2O) into the FLiBe melt containing zirconium tetrafluoride (ZrF4), and the concentration of residual Zr(iv) in the melt gradually decreased due to precipitate formation. The precipitate corresponded to ZrO2, as confirmed by the stoichiometric ratio and X-ray diffraction analysis. The K'sp was 3.54 × 10-5 mol3 kg-3, which was highly consistent with that from the dissolution experiment. The obtained K'sp of ZrO2 was in the same order of magnitude as that of uranium dioxide (UO2), indicating that a considerable amount of ZrF4 could inhibit the UO2 formation when oxide contamination occurred in the melt containing ZrF4 and uranium tetrafluoride (UF4). Further oxide titration in the LiF-BeF2-ZrF4 (5 mol%)-UF4 (1.2 mol%) system showed that ZrO2 was formed first with O2- addition less than 1 mol kg-1, and the precipitation of UO2 began only after the O2- addition reached 1 mol kg-1 and the precipitation of ZrO2 decreased the ZrF4 concentration to 0.72 mol kg-1 (3 mol%). Lastly, UO2 and ZrO2 coprecipitated with further O2- addition of more than 1 mol kg-1. The preferential formation of ZrO2 effectively avoided the combination of UF4 and O2-. This study provides a solution for the control of UO2 precipitation in molten salt reactors.

A novel purification method for fluoride or chloride molten salts based on the redox of hydrogen on a nickel electrode.

A novel purification process was proposed for molten salts based on the polarization of a hydrogen electrode on nickel, i.e., H+/H2, Ni electrode. The features of the H+/H2, Ni electrode in typical chloride and fluoride molten salts were investigated. Consistent current electrolysis was performed in a feasible polarization range, and the deoxidation efficiency was higher than that of the traditional chemical or electrochemical purification methods in both chloride and fluoride molten salts. Only H2 was used as a purification source gas, and almost no toxic HF or corrosive HCl emissions were used or occurred in the new process. The application range of the proposed method was also discussed.

Morphological and proteomic analysis of young spikes reveals new insights into the formation of multiple-pistil wheat.

A new multiple-pistil wheat mutant germplasm with more than one pistil in a floret was obtained from natural mutagenesis. This mutant can develop 2-3 grains in a glume after pollination and has a significant grain number advantage compared with normal wheat. However, the basis of the formation of multiple-pistil wheat has thus far not been well established. In this study, we first performed a continuous phenotypic observation of the floral meristem (FM) in multiple-pistil wheat. The results indicated that the secondary pistils are derived from extra stem cells that fail to terminate normally between the carpel primordium and the lodicule primordium. To further probe the potential molecular basis for the formation of secondary pistils, comparative proteomic analyses were conducted. A total of 334 differentially abundant proteins (DAPs) were identified using isobaric tags for relative and absolute quantification (iTRAQ), among which 131 proteins were highly abundant and 203 proteins were less abundant in the young spikes of multiple-pistil wheat. The DAPs, located primarily in the cell, were involved in the translation and the metabolisms of carbohydrate, nucleotide, and amino acid. Differential expression analysis showed that TaHUA2, TaRF2a, TaCHR12 and TaHEN2 may play vital roles in the regulation of wheat flower organ number. In general, the DAPs support the phenotypic analysis results at the molecular level. In combination, these results reveal new insights into the formation of multiple-pistil wheat and provide possible targets for further research on the regulation of floral organ number in wheat.

Sense-antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit.

Antisense transcription of protein-coding genes has been increasingly recognized as an important regulatory mechanism of gene expression. However, less is known about the extent and importance of antisense transcription of noncoding genes. Here, we investigate the breadth and dynamics of antisense transcription of miRNAs, a class of important noncoding RNAs. Because the antisense transcript of a miRNA is likely to form a hairpin suitable as the substrate of ADARs, which convert adenosine to inosine in double-stranded RNAs, we used A-to-I RNA editing as ultrasensitive readout for antisense transcription of the miRNAs. Through examining the unstranded targeted RNA-seq libraries covering all miRNA loci in 25 types of human tissues, we identified 7275 editing events located in 81% of the antisense strand of the miRNA loci, thus uncovering the previously unknown prevalent antisense transcription of the miRNAs. We found that antisense transcripts are tightly regulated, and a substantial fraction of miRNAs and their antisense transcripts are coexpressed. Sense miRNAs have been shown to down-regulate the coexpressed antisense transcripts, whereas the act of antisense transcription, rather than the transcripts themselves, regulates the expression of sense miRNAs. RNA editing tends to decrease the miRNA accessibility of the antisense transcripts, therefore protecting them from being degraded by the sense-mature miRNAs. Altogether, our study reveals the landscape of antisense transcription and editing of miRNAs, as well as a previously unknown reciprocal regulatory circuit of sense-antisense miRNA pairs.

Cyclin-Dependent Kinase Inhibitor Gene TaICK1 acts as a Potential Contributor to Wheat Male Sterility induced by a Chemical Hybridizing Agent.

Heterosis has been widely accepted as an effective strategy to increase yields in plant breeding. Notably, the chemical hybridization agent SQ-1 induces male sterility in wheat, representing a critical potential tool in hybrid seed production. However, the mechanisms underlying the male sterility induced by SQ-1 still remain poorly understood. In this study, a cyclin-dependent kinase inhibitor gene, TaICK1, which encodes a 229 amino acid protein, was identified as a potential contributor to male sterility in common wheat. The expression of TaICK1 was upregulated during the development of anthers in Xinong1376 wheat treated with SQ-1. Meanwhile, the seed setting rate was found to be significantly decreased in TaICK1 transgenic rice. Furthermore, we identified two cyclin proteins, TaCYCD2;1 and TaCYCD6;1, as interactors through yeast two-hybrid screening using TaICK1 as the bait, which were validated using bimolecular fluorescence complementation. Subcellular localization revealed that the proteins encoded by TaICK1, TaCYCD2;1, and TaCYCD6;1 were localized in the cell nucleus. The expression levels of TaCYCD2;1 and TaCYCD6;1 were lower in Xinong1376 treated with SQ-1. A further analysis demonstrated that the expression levels of OsCYCD2;1 and OsCYCD6;1 were lower in transgenic TaICK1 rice lines as well. Taken together, these results suggest that the upregulation of TaICK1, induced by SQ-1, may subsequently suppress the expression of TaCYCD2;1 and TaCYCD6;1 in anthers, resulting in male sterility. This study provides new insights into the understanding of SQ-1-induced wheat male sterility, as well as the developmental mechanisms of anthers.

irCLASH reveals RNA substrates recognized by human ADARs.

Adenosine deaminases acting on RNA (ADARs) convert adenosines to inosines in double-stranded RNA (dsRNA) in animals. Despite their importance, ADAR RNA substrates have not been mapped extensively in vivo. Here we develop irCLASH to map RNA substrates recognized by human ADARs and uncover features that determine their binding affinity and editing efficiency. We also observe a dominance of long-range interactions within ADAR substrates and analyze differences between ADAR1 and ADAR2 editing substrates. Moreover, we unexpectedly discovered that ADAR proteins bind dsRNA substrates tandemly in vivo, each with a 50-bp footprint. Using RNA duplexes recognized by ADARs as readout of pre-messenger RNA structures, we reveal distinct higher-order architectures between pre-messenger RNAs and mRNAs. Our transcriptome-wide atlas of ADAR substrates and the features governing RNA editing observed in our study will assist in the rational design of guide RNAs for ADAR-mediated RNA base editing.