RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data.

Read-through chimeric RNAs are being recognized as a means to expand the functional transcriptome and contribute to cancer tumorigenesis when mis-regulated. However, current software tools often fail to predict them. We have developed RTCpredictor, utilizing a fast ripgrep tool to search for all possible exon-exon combinations of parental gene pairs. We also added exonic variants allowing searches containing common SNPs. To our knowledge, it is the first read-through chimeric RNA specific prediction method that also provides breakpoint coordinates. Compared with 10 other popular tools, RTCpredictor achieved high sensitivity on a simulated and three real datasets. In addition, RTCpredictor has less memory requirements and faster execution time, making it ideal for applying on large datasets.

Exosomes from Intrahepatic Cholestasis of Pregnancy Induce Cell Apoptosis Through the miRNA-6891-5p/YWHAE Pathway.

BACKGROUND: Intrahepatic cholestasis of pregnancy (ICP) is associated with adverse pregnancy outcomes; however, the underlying mechanisms are not fully understood. AIMS: This study aimed to determine the role of exosomal miR-6891-5p in placental trophoblast dysfunction in ICP and identify new biomarkers for ICP diagnosis. METHODS: Serum samples were collected from ICP patients and healthy pregnant women, and serum exosomes were extracted and identified. Fluorescent dye labeling of exosomes and cell-verified cell phagocytosis were performed. In vitro experiments were conducted by adding taurocholic acid to simulate the ICP environment. Cell proliferation and apoptosis levels were detected using flow cytometry and the cell counting kit-8 assay. Mimics were constructed to overexpress miR-6891-5p in cells, and the binding site between miR-6891-5p and YWHAE was verified using luciferase reporter genes. RESULTS: miR-6891-5p expression was significantly decreased in serum exosomes of ICP patients. Co-culturing with exosomes derived from ICP patients' serum (ICP-Exos) decreased HTR-8/SVeno cell proliferation and increased apoptosis levels. miR-6891-5p upregulation in HTR-8/SVeno cells significantly increased cell viability and reduced cell apoptosis levels, as determined by the cell counting kit-8 assay and flow cytometry. A double luciferase assay confirmed that miR-6891-5p affected the expression of the downstream YWHAE protein. CONCLUSIONS: This study indicates that serum exosomes from ICP patients can impact the apoptosis of placental trophoblast HTR-8/SVeno cells through the miR-6891-5P/YWHAE pathway and can serve as specific molecular markers for ICP diagnosis.

Elevated CO2 concentration enhances drought resistance of soybean by regulating cell structure, cuticular wax synthesis, photosynthesis, and oxidative stress response.

The atmospheric [CO2] and the frequency and intensity of extreme weather events such as drought are increased, leading to uncertainty to soybean production. Elevated [CO2] (eCO2) partially mitigates the adverse effects of drought stress on crop growth and photosynthetic performance, but the mitigative mechanism is not well understood. In this study, soybean seedlings under drought stress simulated by PEG-6000 were grown in climate chambers with different [CO2] (400 µmol mol-1 and 700 µmol mol-1). The changes in anatomical structure, wax content, photosynthesis, and antioxidant enzyme were investigated by the analysis of physiology and transcriptome sequencing (RNA-seq). The results showed that eCO2 increased the thickness of mesophyll cells and decreased the thickness of epidermal cells accompanied by reduced stomatal conductance, thus reducing water loss in soybean grown under drought stress. Meanwhile, eCO2 up-regulated genes related to wax anabolism, thus producing more epidermal wax. Under drought stress, eCO2 increased net photosynthetic rate (PN), ribulose-1,5-bisphosphate carboxylase/oxygenase activity, and alerted the gene expressions in photosynthesis. The increased sucrose synthesis and decreased sucrose decomposition contributed to the progressive increase in the soluble saccharide contents under drought stress with or without eCO2. In addition, eCO2 increased the expressions of genes associated with peroxidase (POD) and proline (Pro), thus enhancing POD activity and Pro content and improving the drought resistance in soybean. Taken together, these findings deepen our understanding of the effects of eCO2 on alleviating drought stress in soybean and provide potential target genes for the genetic improvement of drought tolerance in soybean.

The role of ERp29/FOS/EMT pathway in excessive apoptosis of placental trophoblast cells in intrahepatic cholestasis of pregnancy.

BACKGROUND: Abnormal bile acid metabolism leading to changes in placental function during pregnancy. To determine whether endoplasmic reticulum protein 29 (ERp29) can mediate the pregnancy effects of cholestasis by altering the level of trophoblast cell apoptosis. METHODS: ERp29 in serum of 66 intrahepatic cholestasis of pregnancy (ICP) pregnant women and 74 healthy were detected by ELISA. Subcutaneous injection of ethinyl estradiol (E2) was used to induce ICP in pregnant rats. Taurocholic acid (TCA) was used to simulate the ICP environment, and TGF-ß1 was added to induce the epithelial mesenchymal transformation (EMT) process. The scratch, migration, and invasion test were used to detect the EMT process. ERp29 overexpression/knockdown vector were constructed and transfected to verify the role of ERp29 in the EMT process. Downstream gene was obtained through RNA-seq. RESULTS: Compared with the healthy pregnant women, the expression levels of ERp29 in serum of ICP pregnancy women were significantly increased (P < 0.001). ERp29 in the placenta tissue of the ICP pregnant rats increased significantly, and the level of apoptosis increased. The placental tissues of the ICP had high expression of E-cadherin and low expression of N-cadherin, snail1, vimentin. After HTR-8/SVneo cells were induced by TCA, EMT was inhibited, while the ERp29 increased. Cell and animal experiments showed that, knockdown of ERp29 reduced the inhibition of EMT, the ICP progress was alleviated. Overexpression of FOS salvaged the inhibitory effects of ERp29 on cell EMT. DISCUSSION: The high level of ERp29 in placental trophoblast cells reduced FOS mRNA levels, inhibited the EMT process and aggravated the occurrence and development of ICP.

A protein-encoding CCDC7 circular RNA inhibits the progression of prostate cancer by up-regulating FLRT3.

Circular RNAs (circRNAs) are a family of endogenous RNAs that have become a focus of biological research in recent years. Emerging evidence has revealed that circRNAs exert biological functions by acting as transcriptional regulators, microRNA sponges, and binding partners with RNA-binding proteins. However, few studies have identified coding circRNAs, which may lead to a hidden repertoire of proteins. In this study, we unexpectedly discovered a protein-encoding circular RNA circCCDC7(15,16,17,18,19) while we were searching for prostate cancer related chimeric RNAs. circCCDC7(15,16,17,18,19) is derived from exon 19 back spliced to exon 15 of the CCDC7 gene. It is significantly downregulated in patients with high Gleason score. Prostate cancer patients with decreased circCCDC7(15,16,17,18,19) expression have a worse prognosis, while linear CCDC7 had no such association. Overexpressed circCCDC7(15,16,17,18,19) inhibited prostate cancer cell migration, invasion, and viability, supporting classification of circCCDC7(15,16,17,18,19) as a bona fide tumor suppressor gene. We provide evidence that its tumor suppressive activity is driven by the protein it encodes, and that circCCDC7(15,16,17,18,19) encodes a secretory protein. Consistently, conditioned media from circCCDC7(15,16,17,18,19) overexpressing cells has the same tumor suppressive activity. We further demonstrate that the tumor suppressive activity of circCCDC7(15,16,17,18,19) is at least partially mediated by FLRT3, whose expression also negatively correlates with Gleason score and clinical prognosis. In conclusion, circCCDC7(15,16,17,18,19) functions as a tumor suppressor in prostate cancer cells through the circCCDC7-180aa secretory protein it encodes, and is a promising therapeutic peptide for prostate cancer.

Effect of Glycolipids Application Combined with Nitrogen Fertilizer Reduction on Maize Nitrogen Use Efficiency and Yield.

Microbial-driven N turnover is important in regulating N fertilizer use efficiency through the secretion of metabolites like glycolipids. Currently, our understanding of the potential of glycolipids to partially reduce N fertilizer use and the effects of glycolipids on crop yield and N use efficiency is still limited. Here, a three-year in situ field experiment was conducted with seven treatments: no fertilization (CK); chemical N, phosphorus and potassium (NPK); NPK plus glycolipids (N+PKT); and PK plus glycolipids with 10% (0.9 N+PKT), 20% (0.8 N+PKT), 30% (0.7 N+PKT), and 100% (PKT) N reduction. Compared with NPK, glycolipids with 0-20% N reduction did not significantly reduce maize yields, and also increased N uptake by 6.26-11.07%, but no significant changes in grain or straw N uptake. The N resorption efficiency under 0.9 N+PKT was significantly greater than that under NPK, while the apparent utilization rates of N fertilizer and partial factor productivity of N under 0.9 N+PKT were significantly greater than those under NPK. Although 0.9 N+PKT led to additional labor and input costs, compared with NPK, it had a greater net economic benefit. Our study demonstrates the potential for using glycolipids in agroecosystem management and provides theoretical support for optimizing fertilization strategies.

Association of maternal mineral status with the risk of preterm birth: a retrospective cohort study.

Background: There has been a gradual increase in the proportion of preterm birth in China during the past several decades. Maternal malnutrition is a significant determinant for preterm birth. Nevertheless, comprehensive studies investigating serum mineral levels during pregnancy associated with preterm birth remain scarce. This study aims to assess the associations between maternal serum mineral levels and the risk of preterm birth. Methods: This retrospective cohort study of 18,048 pregnant women used data from a tertiary hospital in China from January 2016 to December 2022. Demographic data and serum mineral concentrations in the second and third trimesters of mothers were collected from the hospital information system. Analysis was performed using restricted cubic splines and logistic regression models. Results: The proportion of preterm birth in this study was 6.01%. Phosphorus [P for overall = 0.005; P for nonlinear = 0.490; OR (95%CI) = 1.11 (1.04, 1.18)] and chlorine [P for overall = 0.002; P for nonlinear = 0.058; OR (95%CI) = 1.11 (1.03, 1.19)] showed a significant positive correlation with preterm birth in a linear fashion. Furthermore, serum levels of potassium (P for nonlinear <0.001), sodium (P for nonlinear = 0.004), and magnesium (P for nonlinear <0.001) exhibited non-linear relationships with the risk of preterm birth. Conclusion: Serum levels of some minerals during pregnancy were associated with the risk of preterm birth among pregnant women. In addition to commonly recognized micronutrients such as folic acid, iron, and vitamin D, healthcare providers should also pay attention to the levels of these minerals during pregnancy.

UBA1-CDK16 : A Sex-Specific Chimeric RNA and Its Role in Immune Sexual Dimorphism.

RNA processing mechanisms, such as alternative splicing and RNA editing, have been recognized as critical means to expand the transcriptome. Chimeric RNAs formed by intergenic splicing provide another potential layer of RNA diversification. By analyzing a large set of RNA-Seq data and validating results in over 1,200 blood samples, we identified UBA1-CDK16 , a female-specific chimeric transcript. Intriguingly, both parental genes, are expressed in males and females. Mechanistically, UBA1-CDK16 is produced by cis-splicing between the two adjacent X-linked genes, originating from the inactive X chromosome. A female-specific chromatin loop, formed between the junction sites, facilitates the alternative splicing of its readthrough precursor. This unique chimeric transcript exhibits evolutionary conservation, evolving to be female-specific from non-human primates to humans. Furthermore, our investigation reveals that UBA1-CDK16 is enriched in the myeloid lineage and plays a regulatory role in myeloid differentiation. Notably, female COVID-19 patients who tested negative for this chimeric transcript displayed higher counts of neutrophils, highlighting its potential role in disease pathogenesis. These findings support the notion that chimeric RNAs represent a new repertoire of transcripts that can be regulated independently from the parental genes, and a new class of RNA variance with potential implications in sexual dimorphism and immune responses.