Somatosensory neurons express specific sets of lincRNAs, and lincRNA CLAP promotes itch sensation in mice.

Somatosensory neurons are highly heterogeneous with distinct types of neural cells responding to specific stimuli. However, the distribution and roles of cell-type-specific long intergenic noncoding RNAs (lincRNAs) in somatosensory neurons remain largely unexplored. Here, by utilizing droplet-based single-cell RNA-seq (scRNA-seq) and full-length Smart-seq2, we show that lincRNAs, but not coding mRNAs, are enriched in specific types of mouse somatosensory neurons. Profiling of lincRNAs from single neurons located in dorsal root ganglia (DRG) identifies 200 lincRNAs localized in specific types or subtypes of somatosensory neurons. Among them, the conserved cell-type-specific lincRNA CLAP associates with pruritus and is abundantly expressed in somatostatin (SST)-positive neurons. CLAP knockdown reduces histamine-induced Ca2+ influx in cultured SST-positive neurons and in vivo reduces histamine-induced scratching in mice. In vivo knockdown of CLAP also decreases the expression of neuron-type-specific and itch-related genes in somatosensory neurons, and this partially depends on the RNA binding protein MSI2. Our data reveal a cell-type-specific landscape of lincRNAs and a function for CLAP in somatosensory neurons in sensory transmission.

A meta-analysis of the prognostic impact of tissue golgi protein 73 (tGP73) in hepatocellular carcinoma.

INTRODUCTION: To date, an increasing number of studies have revealed that GP73 may have prognostic value in liver cancer. However, most of the studies evaluated serum GP73, and the results regarding the prognostic value of tGP73 in liver cancer are still controversial. Therefore, in this meta-analysis, we aimed to determine whether tGP73 has any prognostic value in patients with HCC. MATERIALS AND METHODS: Relevant publications were searched for in PubMed, EMBASE, OVID, the Cochrane Library, and the Web of Science databases up to March 2023. The hazard ratio (HR) or odds ratio (OR) with corresponding 95% confidence intervals (95% CIs) of eligible studies were assessed by fixed-effects or random-effects models. In addition, subgroup analyses were conducted to investigate the possible causes of heterogeneity, and publication bias analysis was also performed to assess the reliability of the meta-analysis results. RESULTS: A total of 10 studies were included. These studies included 1569 HCC patients, and a meta-analysis was performed. The results of our meta-analysis showed that higher GP73 expression levels were significantly associated with poorer OS (HR = 1.87, 95% CI: 1.41-2.48, P < 0.0001, I2 = 58%). However, there was no significant correlation between high GP73 expression and disease-free survival (DFS) (HR: 1.43, 95% CI: 0.93-2.33, P = 0.100). In addition, abnormal GP73 expression was also related to higher tumour tissue differentiation grade (OR = 3.03, 95% CI = 2.01-4.57, P < 0.0001, I2 = 89%), later tumour stage (OR = 5.89, 95% CI = 2.31-14.99, P < 0.0001, I2 = 0%), vascular invasion (OR = 1.72, 95% CI = 1.12-2.64, P = 0.010, I2 = 0%), multiple tumours (OR = 2.44, 95% CI = 1.37-3.68, P = 0.001, I2 = 44%) and early postoperative tumour recurrence (OR = 1.92, 95% CI = 1.10-3.28, P = 0.020, I2 = 62%). CONCLUSIONS: The meta-analysis showed that the overexpression of GP73 may be related to a poor prognosis of HCC, and it may also have a predictive effect on the invasion and metastasis of HCC.

Equilibrium, kinetics and thermodynamics of Cu(II) biosorption on Chinese chestnut shell pretreated with steam explosion.

The shells of Chinese chestnuts (Castanea mollissima) are an agricultural residue. This work aimed to evaluate this feasibility of using steam explosion to modify this residue for Cu(II) biosorption from aqueous solutions. Equilibrium, kinetic and thermodynamic parameters were evaluated. The steam-explosion pretreatment increased the surface area of the chestnut shell and exposed more hydroxyl and carboxyl groups, which are binding sites for Cu(II). It changed the sorption from a spontaneous process driven by enthalpy to a nonspontaneous one driven by entropy. It increased the Cu(II) sorption capacity at higher temperatures while it decreased the capacity at lower ones. Compared with untreated chestnut shell, the steam-exploded shell is preferable for Cu(II) sorption at higher temperatures.

Synthesis and thermoelectric properties of Rashba semiconductor BiTeBr with intensive texture.

Bismuth tellurohalides with Rashba-type spin splitting exhibit unique Fermi surface topology and are developed as promising thermoelectric materials. However, BiTeBr, which belongs to this class of materials, is rarely investigated in terms of the thermoelectric transport properties. In the study, polycrystalline bulk BiTeBr with intensive texture was synthesized via spark plasma sintering (SPS). Additionally, its thermoelectric properties above room temperature were investigated along both the in-plane and out-plane directions, and they exhibit strong anisotropy. Low sound velocity along two directions is found and contributes to its low lattice thermal conductivity. Polycrystalline BiTeBr exhibits relatively good thermoelectric performance along the in-plane direction, with a maximum dimensionless figure of merit (ZT) of 0.35 at 560 K. Further enhancements of ZT are expected by utilizing systematic optimization strategies.

Coordinated post-translational responses of aquaporins to abiotic and nutritional stimuli in Arabidopsis roots.

In plants, aquaporins play a crucial role in regulating root water transport in response to environmental and physiological cues. Controls achieved at the post-translational level are thought to be of critical importance for regulating aquaporin function. To investigate the general molecular mechanisms involved, we performed, using the model species Arabidopsis, a comprehensive proteomic analysis of root aquaporins in a large set of physiological contexts. We identified nine physiological treatments that modulate root hydraulics in time frames of minutes (NO and H2O2 treatments), hours (mannitol and NaCl treatments, exposure to darkness and reversal with sucrose, phosphate supply to phosphate-starved roots), or days (phosphate or nitrogen starvation). All treatments induced inhibition of root water transport except for sucrose supply to dark-grown plants and phosphate resupply to phosphate-starved plants, which had opposing effects. Using a robust label-free quantitative proteomic methodology, we identified 12 of 13 plasma membrane intrinsic protein (PIP) aquaporin isoforms, 4 of the 10 tonoplast intrinsic protein isoforms, and a diversity of post-translational modifications including phosphorylation, methylation, deamidation, and acetylation. A total of 55 aquaporin peptides displayed significant changes after treatments and enabled the identification of specific and as yet unknown patterns of response to stimuli. The data show that the regulation of PIP and tonoplast intrinsic protein abundance was involved in response to a few treatments (i.e. NaCl, NO, and nitrate starvation), whereas changes in the phosphorylation status of PIP aquaporins were positively correlated to changes in root hydraulic conductivity in the whole set of treatments. The identification of in vivo deamidated forms of aquaporins and their stimulus-induced changes in abundance may reflect a new mechanism of aquaporin regulation. The overall work provides deep insights into the in vivo post-translational events triggered by environmental constraints and their possible role in regulating plant water status.

Clinical Characteristics and Treatment of Trigeminal Neuralgia Following Herpes Zoster.

OBJECTIVE: The aim of this study was to illustrate the clinical characteristics and treatment of trigeminal neuralgia following herpes zoster. METHODS: From August 1, 2011 to August 1, 2013, 23 consecutive patients with trigeminal neuralgia following herpes zoster underwent microvascular decompression (MVD) at our cranial nerve disease center. All patients underwent preoperative MRI evaluation, intraoperative observation, and clinical effect evaluation. Clinical data were collected and analyzed in our center. RESULTS: V2 division was the most commonly affected branch. Unlike pretrigeminal neuralgia (PTN), trigger zone was only found in a small part of patients (21.7%). Unlike PTN, the adhesions and compressions between trigeminal nerve and offending vessels were usually not serious; trigeminal nerve usually is atrophic; superior cerebellar artery was the most common offending vessels (65.2%). Of 23 patients, 19 experienced pain relief (82.6%), 1 patient suffered from hearing loss, and another one suffered from cerebrospinal fluid leak; no severe complications were found. During follow-up period, no recurrence was found (3 lost). CONCLUSIONS: For patients who suffered from trigeminal neuralgia following herpes zoster, trigger zone was only found in a small part of patients. The trigeminal nerve usually is atrophic; microvascular decompression was equally applied to these patients if vessel compression was confirmed.

Clinical characteristics and surgical techniques of trigeminal neuralgia caused simply by venous compression.

OBJECTIVE: The objective of this study was to introduce the operation essentials for treatment of patients with vein compression so as to obtain a satisfactory decompression without sacrificing veins. METHODS: We chose 15 patients with trigeminal neuralgia caused by venous from June 15, 2010, through June 15, 2011, and performed microvascular decompression for each patient. By collecting clinical data, such as preoperative magnetic resonance imaging scans, key operative procedures, surgical outcomes, and complications, we explored the operation techniques for these patients and finally summarized our experiences and ideas. RESULTS: For all the 15 patients, 9 cases had excellent remission, 3 cases had delayed excellent remission, 1 case had good remission, and 2 cases had failed result; the total remission rate was 86.7%; 3 cases had facial numbness. CONCLUSIONS: For patients with vein compression, we combine the following 4 procedures together: (1) fully releasing the arachnoid around trigeminal nerve, (2) exploration and decompression of the whole trigeminal root from Meckel cave to pons, (3) cauterization of companioned petrosal vein tributaries by bipolar coagulation, and (4) placing Teflon between trigeminal nerve and offending petrosal vein, thus could acquire a satisfactory effect (remission rate, 86.7%).

Surgical skills of adhesions and transposition of trigeminal nerve for primary trigeminal neuralgia.

OBJECTIVE: The aims of this study were to investigate disposal of adhesions and transposition of the trigeminal nerve during microvascular decompression and evaluate its surgical effect. METHODS: By collecting the clinical data of typical trigeminal neuralgia patients we treated from January 2013 to May 2013, we chose 120 patients with adhesions and transposition of trigeminal nerve, analyzed their preoperative imaging features and surgical procedures, and evaluated postoperative effect after 3-month follow-up. RESULTS: Among these 120 patients, 113 cases showed positive effect in magnetic resonance imaging (three-dimensional time-of-flight); the positive rate was 94.2%. During the operation, firstly we proceed to separate the nerve and artery, secondly we released the vascular compression, finally we removed the superior cerebellar artery to the nerve's head end. Postoperative effect evaluation stated that 101 patients showed immediate remission and 13 patients showed delayed remission (3 min after operation) and the surgery was ineffective for 6 patients; the remission rate was 95%. There were no severe complications. CONCLUSIONS: Magnetic resonance imaging (three-dimensional time-of-flight) before operation could clearly display the neurovascular relationship of trigeminal neuralgia patients. It offers great help for preoperative evaluation. Separation between arachnoid, nerve, and artery; vascular decompression; and removal of the superior cerebellar artery to the head end could resolve adhesions and transposition of trigeminal nerve during microvascular decompression, which showed significant effects.

ITGB2 fosters the cancerous characteristics of ovarian cancer cells through its role in mitochondrial glycolysis transformation.

Related studies have shown that ITGB2 mediates mitochondrial glycolytic transformation in cancer-associated fibroblasts and participates in tumor occurrence, metastasis and invasion of cancer cells. Based on these studies, we tried to construct a mitochondrial glycolysis regulatory network and explored its effect on mitochondrial homeostasis and ovarian cancer cells' cancerous characteristics. Our research revealed a distinct increase in the expression of ITGB2 and associated signaling pathway elements (PI3K-AKT-mTOR) in cases of ovarian cancer. ITGB2 might control mTOR expression via the PI3K-AKT pathway, thus promote mitochondrial glycolysis transformation and cell energy supply in ovarian cancer. This pathway could also inhibit mitophagy, maintain mitochondrial stability, and enhance the cancerous characteristics in case of ovarian cancer cells by mediating mitochondrial glycolytic transformation. Thus, we concluded that ITGB2-associated signaling route (PI3K-AKT-mTOR) may contribute to the progression of cancerous traits in ovarian cancer via mediating mitochondrial glycolytic transformation.

Arenitalea lutea gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from intertidal sand.

A yellow, rod-shaped, Gram-negative, facultatively aerobic, gliding bacterium, designed strain P7-3-5(T), was isolated from intertidal sand of the Yellow Sea, China. Analysis of 16S rRNA gene sequences revealed that strain P7-3-5(T) formed a distinct lineage within the family Flavobacteriaceae, sharing 94.2-96.9 % sequence similarity with type strains of species of the most closely related genera, including Hyunsoonleella, Jejuia, Marinivirga and Algibacter. The strain grew at 4-40 °C and with 0.5-5.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed gelatin and DNA. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and anteiso-C15 : 0 and the major respiratory quinone was MK-6. Polar lipids included phosphatidylethanolamine (PE), three unidentified aminolipids (AL1-3) and four unidentified lipids (L1-4). The genomic DNA G+C content of strain P7-3-5(T) was 32.1 mol%. Data from this polyphasic study suggest that strain P7-3-5(T) represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Arenitalea lutea gen. nov., sp. nov. is proposed. The type strain of Arenitalea lutea is P7-3-5(T) ( = CGMCC 1.12213(T) = KACC 16457(T)).

Neptunomonas qingdaonensis sp. nov., isolated from intertidal sand.

A Gram-negative, motile, aerobic, oxidase- and catalase-positive rod, designated P10-2-4(T), was isolated from an intertidal sand sample collected from a coastal area of Qingdao (Yellow Sea), China. The isolate reduced nitrate to nitrite and grew at 4-33 °C and with 0.5-12 % (w/v) NaCl. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C18 : 1ω7c and C16 : 0. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The major respiratory quinone was Q-8. The genomic DNA G+C content was 45.1 %. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain P10-2-4(T) belonged to the genus Neptunomonas. The isolate shared the highest 16S rRNA gene sequence similarity (98.1 %) with Neptunomonas japonica JAMM 0745(T) and 96.9, 96.5 and 95.9 % sequence similarities with N. antarctica S3-22(T), N. concharum LHW37(T) and N. naphthovorans NAG-2N-126(T), respectively, strains of the other three recognized species in the genus. DNA-DNA relatedness between strain P10-2-4(T) and N. japonica JCM 14595(T) was 35.6 %. Furthermore, strain P10-2-4(T) could be distinguished from the representatives of the genus Neptunomonas by a combination of phenotypic characteristics, such as temperature and NaCl concentration for growth, nitrate reduction, DNase activity and assimilation of substrates. The data from this study suggests that strain P10-2-4(T) represents a novel species in the genus Neptunomonas, for which the name Neptunomonas qingdaonensis sp. nov. is proposed. The type strain is P10-2-4(T) ( = CGMCC 1.10971(T)  = KCTC 23686(T)).

Pseudorhodobacter antarcticus sp. nov., isolated from Antarctic intertidal sandy sediment, and emended description of the genus Pseudorhodobacter Uchino et al. 2002 emend. Jung et al. 2012.

A Gram-negative, aerobic, non-motile, pink-pigmented and rod-shaped strain, designated ZS3-33(T), was isolated from Antarctic intertidal sandy sediment. The strain grew optimally at 15 °C and with 1.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 20. It could not produce bacteriochlorophyll a. The predominant cellular fatty acid was C18 : 1ω7c and the predominant respiratory quinone was Q-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine, two unidentified aminophospholipids and an unidentified aminolipid. Analyses of 16S rRNA gene sequences revealed that strain ZS3-33(T) belonged to the genus Pseudorhodobacter, showing 97.4 % similarity to the type strain of Pseudorhodobacter ferrugineus and 95.3 % similarity to the type strain of Pseudorhodobacter aquimaris. Levels of gyrB gene sequence similarity between strain ZS3-33(T) and the type strains of P. ferrugineus and P. aquimaris were 87.6 and 81.7 %, respectively. DNA-DNA relatedness between strain ZS3-33(T) and P. ferrugineus DSM 5888(T) was 56.6 %. The genomic DNA G+C content of strain ZS3-33(T) was 57.1 mol%. Based on data from this polyphasic study, strain ZS3-33(T) represents a novel species of the genus Pseudorhodobacter, for which the name Pseudorhodobacter antarcticus sp. nov. is proposed. The type strain is ZS3-33(T) ( = CGMCC 1.10836(T) = KCTC 23700(T)). An emended description of the genus Pseudorhodobacter Uchino et al. 2002 emend. Jung et al. 2012 is also proposed.

Albimonas pacifica sp. nov., isolated from seawater of the Pacific, and emended description of the genus Albimonas.

A Gram-stain-negative, aerobic, catalase- and oxidase-positive, non-flagellated, rod-shaped bacterium, designated strain P-50-3(T), was isolated from seawater of the Pacific. The strain grew at 10-40 °C (optimum at 30 °C) and with 0-12 % (w/v, optimum 2 %) NaCl. It reduced nitrate to nitrite but did not hydrolyse gelatin, starch or Tween 80. Analysis of 16S rRNA gene sequences showed that strain P-50-3(T) clustered tightly with the genus Albimonas and shared the highest 16S rRNA gene sequence similarity (94.3 %) with the type strain of Albimonas donghaensis. The major respiratory quinone was Q-10 and the major cellular fatty acids were C18 : 1ω7c, C18 : 0, 11-methyl C18 : 1ω7c and C16 : 0. Polar lipids included phosphatidylglycerol (PG), phosphatidylcholine (PC), two unidentified aminolipids and an unidentified lipid. The genomic DNA G+C content of strain P-50-3(T) was 69.0 mol%. On the basis of the data obtained in this polyphasic study, strain P-50-3(T) represents a novel species within the genus Albimonas, for which the name Albimonas pacifica sp. nov. is proposed. The type strain of Albimonas pacifica is P-50-3(T) ( = KACC 16527(T) = CGMCC 1.11030(T)). An emended description of the genus Albimonas Lim et al. 2008 is also proposed.

Marinicauda pacifica gen. nov., sp. nov., a prosthecate alphaproteobacterium of the family Hyphomonadaceae isolated from deep seawater.

A marine prosthecate bacterium, designated strain P-1 km-3(T), was isolated from deep seawater from the Pacific. Cells of strain P-1 km-3(T) were Gram-stain-negative, aerobic, catalase- and oxidase-positive, dimorphic rods with a single polar prostheca or flagellum. The strain hydrolysed gelatin and grew at 6-40 °C (optimum, 30 °C) and with 0.5-12% (w/v) NaCl (optimum, 2%). Phylogenetic analysis of the 16S rRNA gene sequences revealed that strain P-1 km-3(T) belonged to the family Hyphomonadaceae in the class Alphaproteobacteria and represented a separate lineage, located between the genera Oceanicaulis and Woodsholea. Sequence similarities of strain P-1 km-3(T) with type strains of species of the genera Oceanicaulis and Woodsholea were 93.2-93.9%. The predominant cellular fatty acids in strain P-1 km-3(T) were C18:1ω7c, C18:0, 11-methyl C18:1ω7c, C17:0 and C19:0 cyclo ω8c. The major respiratory quinone of strain P-1 km-3(T) was Q-10. The polar lipids of strain P-1 km-3(T) comprised glucuronopyranosyldiglyceride (GUDG), monoglycosyldiglyceride (MGDG), sulfo-quinovosyl diacylglycerol (SQDG), phosphatidylglycerol (PG), an unidentified phospholipid (PL) and an unidentified lipid (L). The genomic DNA G+C content of strain P-1 km-3(T) was 66.0 mol%. On the basis of the polyphasic data presented in this study, strain P-1 km-3(T) is proposed to represent a novel species in a new genus, Marinicauda pacifica gen. nov., sp. nov., within the family Hyphomonadaceae. The type strain of the type species is P-1 km-3(T) (=KACC 16526(T)=CGMCC 1.11031(T)).

[Optical emission spectroscopy of MPCVD plasma].

The plasma of CH4/H2 was diagnosed with optical emission spectroscopy on a high-pressure microwave plasma apparatus at 2.45 GHz. The existing radicals in the plasma and the influence of the methane concentration on radical concentration and distribution were researched. The results indicate that the radicals of CH, Halpha, Hbeta, Hgamma, C2 and little impurity atom Mo exist in the plasma. The intensity of emission spectrum of the radicals increases with the increase in the methane concentration, especially the intensity of C2 has a notable increase. The ratio of the intensity of the CH to Halpha is unchanging with the increase in methane concentration, while that of C2 to Halpha has a marked increase. The uniformity of the space distribution of the radicals becomes worse with the increase in methane concentration.

Marinobacter antarcticus sp. nov., a halotolerant bacterium isolated from Antarctic intertidal sandy sediment.

A Gram-staining-negative, aerobic, motile, oxidase- and catalase-positive, rod-shaped strain, designated ZS2-30(T), was isolated from Antarctic intertidal sandy sediment. The strain grew at 4-35 °C (optimum, 25 °C) and in 0-25% (w/v) NaCl (optimum, 3.0-4.0%). It could reduce nitrate to nitrite and hydrolyse Tween 80. The predominant cellular fatty acids of strain ZS2-30(T) were summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c), C(16:0), C(18:1)ω9c, C(16:1)ω9c, C(12:0) 3-OH and C(12:0). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified aminophospholipid. The genomic DNA G+C content of strain ZS2-30(T) was 55.8 mol%. Analyses of 16S rRNA gene sequences revealed that strain ZS2-30(T) was affiliated with the genus Marinobacter. It showed highest 16S rRNA gene sequence similarities to the type strains of three species of the genus Marinobacter, namely Marinobacter maritimus (98.3%), Marinobacter psychrophilus (98.1%) and Marinobacter goseongensis (97.1%), but the DNA-DNA relatedness values between strain ZS2-30(T) and the above three species were all lower than 45%. Moreover, strain ZS2-30(T) could be distinguished from closely related species of the genus Marinobacter by various phenotypic properties. Based on this taxonomic study using a polyphasic approach, strain ZS2-30(T) is considered to represent a novel species in the genus Marinobacter, for which the name Marinobacter antarcticus sp. nov. is proposed. The type strain of Marinobacter antarcticus is ZS2-30(T) ( = CGMCC 1.10835(T) = KCTC 23684(T)).

Overexpression miR-520a-3p inhibits acute myeloid leukemia progression via targeting MUC1.

BACKGROUND: Acute myeloid leukemia (AML) is one of the familiar malignant tumors in the hematological system. miR-520a-3p is reported to be involved in several cancers' progression. However, miR-520a-3p role in AML remains unclear. In this study, we aimed to clarify the role and potential mechanism of miR-520a-3p in AML. METHODS: Cell viability, proliferation, cycle and apoptosis were detected by MTT assay, colony formation assay, flow cytometry, respectively. The levels of PNCA, Bcl-2, Cleaved caspase 3, Cleaved caspase 9 and ß-catenin protein were detected by Western blot. Dual-luciferase reported assay was performed to detect the regulation between miR-520a-3p and MUC1. To verify the effect of miR-520a-3p on tumor proliferation in vivo, a non-homogenous transplant model of tumors was established. RESULTS: miR-520a-3p expression was down-regulated, and MUC1 expression was up-regulated in AML patients. miR-520a-3p overexpression suppressed THP-1 cell proliferation, induced cell cycle G0/G1 inhibition and promoted apoptosis. miR-520a-3p targeted MUC1 and negatively regulated its expression. MUC1 knockdown inhibited THP-1 cell proliferation and promoted apoptosis. miR-520a-3p overexpression inhibited AML tumors growth. CONCLUSION: Overexpression miR-520a-3p inhibited AML cell proliferation, and promoted apoptosis via inhibiting MUC1 expression and repressing Wnt/ß-catenin pathway activation.

Knockout of circRNAs by base editing back-splice sites of circularized exons.

Many circular RNAs (circRNAs) are produced from back-splicing of exons of precursor mRNAs and are generally co-expressed with cognate linear RNAs. Methods for circRNA-specific knockout are lacking, largely due to sequence overlaps between forms. Here, we use base editors (BEs) for circRNA depletion. By targeting splice sites involved in both back-splicing and canonical splicing, BEs can repress circular and linear RNAs. Targeting sites predominantly for circRNA biogenesis, BEs could efficiently repress the production of circular but not linear RNAs. As hundreds of exons are predominantly back-spliced to produce circRNAs, this provides an efficient method to deplete circRNAs for functional study.

m6A-modified lincRNA Dubr is required for neuronal development by stabilizing YTHDF1/3 and facilitating mRNA translation.

Long intergenic noncoding RNAs (lincRNAs) are crucial regulators in numerous biological processes. However, the functions and mechanisms of m6A-modified lincRNAs in neuronal development remain unclear. Here, we report an m6A-modified lincRNA, Dppa2 upstream binding RNA (Dubr), abundantly expressed at the early developmental stage of dorsal root ganglion (DRG) and cerebral cortex. Silencing Dubr impairs axon elongation of DRG neurons and axon projection and migration of cortical neurons, whereas lacking m6A modification of Dubr fully loses its functions. Mechanically, Dubr interacts with m6A-binding proteins, the YTHDF1/3 complex, through its m6A motifs to protect YTHDF1/3 from degradation via the proteasome pathway. Furthermore, Tau and Calmodulin are regulated by YTHDF1/3 and m6A-modified Dubr. Overexpression of YTHDF1/3 not only rescues the reduced Tau and Calmodulin but also restores axon elongation of DRG neurons by Dubr knockdown. This study uncovers a critical role of m6A-modified lincRNA in neuronal development by regulating the degradation of RNA-binding protein.

SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells.

Single-cell RNA-seq (scRNA-seq) profiles gene expression with high resolution. Here, we develop a stepwise computational method-called SCAPTURE to identify, evaluate, and quantify cleavage and polyadenylation sites (PASs) from 3' tag-based scRNA-seq. SCAPTURE detects PASs de novo in single cells with high sensitivity and accuracy, enabling detection of previously unannotated PASs. Quantified alternative PAS transcripts refine cell identity analysis beyond gene expression, enriching information extracted from scRNA-seq data. Using SCAPTURE, we show changes of PAS usage in PBMCs from infected versus healthy individuals at single-cell resolution.