Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling.

Cell fate transitions involve rapid gene expression changes and global chromatin remodeling, yet the underlying regulatory pathways remain incompletely understood. Here, we identified the RNA-processing factor Nudt21 as a novel regulator of cell fate change using transcription-factor-induced reprogramming as a screening assay. Suppression of Nudt21 enhanced the generation of induced pluripotent stem cells, facilitated transdifferentiation into trophoblast stem cells, and impaired differentiation of myeloid precursors and embryonic stem cells, suggesting a broader role for Nudt21 in cell fate change. We show that Nudt21 directs differential polyadenylation of over 1,500 transcripts in cells acquiring pluripotency, although only a fraction changed protein levels. Remarkably, these proteins were strongly enriched for chromatin regulators, and their suppression neutralized the effect of Nudt21 during reprogramming. Collectively, our data uncover Nudt21 as a novel post-transcriptional regulator of cell fate and establish a direct, previously unappreciated link between alternative polyadenylation and chromatin signaling.

Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation.

Endogenous retroviruses (ERVs) are remnants of ancient parasitic infections and comprise sizable portions of most genomes. Although epigenetic mechanisms silence most ERVs by generating a repressive environment that prevents their expression (heterochromatin), little is known about mechanisms silencing ERVs residing in open regions of the genome (euchromatin). This is particularly important during embryonic development, where induction and repression of distinct classes of ERVs occur in short temporal windows. Here, we demonstrate that transcription-associated RNA degradation by the nuclear RNA exosome and Integrator is a regulatory mechanism that controls the productive transcription of most genes and many ERVs involved in preimplantation development. Disrupting nuclear RNA catabolism promotes dedifferentiation to a totipotent-like state characterized by defects in RNAPII elongation and decreased expression of long genes (gene-length asymmetry). Our results indicate that RNA catabolism is a core regulatory module of gene networks that safeguards RNAPII activity, ERV expression, cell identity, and developmental potency.

Human pre-mRNA 3' end processing: reconstituting is believing.

It is every biochemist's dream to reconstitute a biological process in vitro using defined components, because doing so not only reduces a biological phenomenon to one or a series of biochemical reactions, but also defines the minimal list of essential components. In this issue of Genes & Development, Boreikaite and colleagues (pp. 210-224) and Schmidt and colleagues (pp. 195-209) report their independent reconstitution of human pre-mRNA 3' end processing.

Structural Insights into the Human Pre-mRNA 3'-End Processing Machinery.

The mammalian pre-mRNA 3'-end-processing machinery consists of cleavage and polyadenylation specificity factor (CPSF), cleavage stimulation factor (CstF), and other proteins, but the overall architecture of this machinery remains unclear. CPSF contains two functionally distinct modules: a cleavage factor (mCF) and a polyadenylation specificity factor (mPSF). Here, we have produced recombinant human CPSF and CstF and examined these factors by electron microscopy (EM). We find that mPSF is the organizational core of the machinery, while the conformations of mCF and CstF and the position of mCF relative to mPSF are highly variable. We have identified by cryo-EM a segment in CPSF100 that tethers mCF to mPSF, and we have named it the PSF interaction motif (PIM). Mutations in the PIM can abolish CPSF formation, indicating that it is a crucial contact in CPSF. We have also obtained reconstructions of mCF and CstF77 by cryo-EM, assembled around the mPSF core.

Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.

Alternative mRNA processing is a critical mechanism for proteome expansion and gene regulation in higher eukaryotes. The SR family proteins play important roles in splicing regulation. Intriguingly, mammalian genomes encode many poorly characterized SR-like proteins, including subunits of the mRNA 3'-processing factor CFIm, CFIm68 and CFIm59. Here we demonstrate that CFIm functions as an enhancer-dependent activator of mRNA 3' processing. CFIm regulates global alternative polyadenylation (APA) by specifically binding and activating enhancer-containing poly(A) sites (PASs). Importantly, the CFIm activator functions are mediated by the arginine-serine repeat (RS) domains of CFIm68/59, which bind specifically to an RS-like region in the CPSF subunit Fip1, and this interaction is inhibited by CFIm68/59 hyper-phosphorylation. The remarkable functional similarities between CFIm and SR proteins suggest that interactions between RS-like domains in regulatory and core factors may provide a common activation mechanism for mRNA 3' processing, splicing, and potentially other steps in RNA metabolism.

Dynamic Fluorescence Sensing of Bromide Ions by Photochromic Bi(III)-Coordination Polymers Based on a Ligand Integrated by Naphthalene Diimides and Pyridinium in Solution and Films.

Bismuth(III)-based complexes have garnered increasing attention in fluorescence sensing due to their environmentally friendly and sustainable characteristics. A Bismuth(III) coordination polymer (CP),1-Cl based on a naphthalene diimides(NDI)-pyridinium is synthesized by an in situ reaction method. Notable for its sensitivity to visible light, 1-Cl shows excellent photochromic properties, and the integration of NDI and pyridinium in one ligand makes photogenerated radicals more stable. Structural analysis and theoretical calculations are employed to investigate the potential pathway of photoinduced electron transfer (ET) during the photochromic process. Notably, in aqueous solutions, 1-Cl displays an extraordinary fluorescence enhancement response to bromide ion (Br-), resulting in a distinct transition from yellow to orange in color. The potential mechanism of fluorescence sensing has been revealed through single-crystal X-ray diffraction analysis. This insight highlights a continuous substitution process where the Cl- ions are successively replaced by Br- ions. Consequently, a single-crystal-to-single-crystal transformation (SCSC) occurs, yielding the intermediate species, 1-Cl-Br, which ultimately transforms into the final product, 1-Br. Finally, the photochromic film is successfully prepared and applied to practical applications such as ink-free printing, information anti-counterfeiting, and the visual detection of Br- ions. This work combines photochromism with fluorescence sensing, broadening the research field and practical application of photochromic materials.

Thermoelectric Generator Through Dual-Direction Thermal Regulation by Thermal Diodes for Waste Heat Harvesting.

Thermal energy harvesting provides an opportunity for multi-node systems to achieve self-power autonomy. Thermoelectric generators (TEGs), either by thermocouple arrangement with higher-aspect-ratios or thermoelectric films overlay, are limited by the small temperature difference and its short-duration (less than dozens of minutes), hindering the harvesting efficiency. Here, by introducing thermal diodes with dual-direction thermal regulation ability to optimize the heat flux path, the proposed TEGs exhibit enhanced power-supply capability with unprecedented long-duration (more than hours). In contrast with conventional TEGs with fixed-leg dimensions enabled single output, these compact-TEGs can supply up to fourteen output-channels for selection, the produced power ranges from 1.11 to 921.99 µW, open circuit voltage ranges from 8.07 to 51.32 mV, when the natural temperature difference is 53.84 °C. Compared to the most recent TEGs, the proposed TEGs in this study indicate higher power (more than hundreds times) and much longer output duration (2.4-120 times) in a compact manner.

Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation.

Eukaryotic gene expression is extensively regulated by cellular stress and pathogen infections. We have previously shown that herpes simplex virus 1 (HSV-1) and several cellular stresses cause widespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII) in host genes and that the viral immediate early factor ICP27 plays an important role in HSV-1-induced DoTT. Here, we show that HSV-1 infection also leads to widespread changes in alternative polyadenylation (APA) of host mRNAs. In the majority of cases, polyadenylation shifts to upstream poly(A) sites (PAS), including many intronic PAS. Mechanistically, ICP27 contributes to HSV-1-mediated APA regulation. HSV-1- and ICP27-induced activation of intronic PAS is sequence-dependent and does not involve general inhibition of U1 snRNP. HSV1-induced intronic polyadenylation is accompanied by early termination of RNAPII. HSV-1-induced mRNAs polyadenylated at intronic PAS (IPA) are exported into the cytoplasm while APA isoforms with extended 3' UTRs are sequestered in the nuclei, both preventing the expression of the full-length gene products. Finally we provide evidence that HSV-induced IPA isoforms are translated. Together with other recent studies, our results suggest that viral infection and cellular stresses induce a multi-faceted host response that includes DoTT and changes in APA profiles.

Three-Dimensional Viologen-Based Lanthanide-Organic Frameworks: Photochromism and Fluorescence Detection of Quinolone Antibiotics.

Quinolone antibiotic residues, norfloxacin (NORF) and ciprofloxacin (CIP), have attracted more attention due to their frequent detection in surface water and food field, which seriously threaten the health of animals and humans. Rapid and efficient detection of NORF and CIP is critical for environmental testing and ecosystems. Herein, two novel isostructural viologen-functionalized Ln(III) complexes [Ln2L0.5(IPA)3]n (Ln = Eu, 1; Tb, 2; L = N,N'-bis (2-carboxyethyl)-4,4'-bipyridridylium dichloride, H2IPA = isophthalic acid) with a three-dimensional structure have been synthesized solvothermally. Complexes 1 and 2 exhibited reversible photochromism under UV light. In addition, complex 1 exhibits excellent pH tolerance and can be seen as an efficient fluorescent probe for the detection of NORF and CIP with detection limits of 7.90 × 10-7 and 9.48 × 10-7 M, respectively. Furthermore, the good photoresponsive and outstanding fluorescent properties of 1 were further exploited in dual-function paper involving erasable inkless printing and detection of NORF and CIP. Our work reports a new strategy for recognizing NORF and CIP based on the luminescent color change of the viologen-based Ln-MOFs, providing a new direction for the development of multifunctional materials.

Conformation- and Coordination Mode-Dependent Stimuli-Responsive Salicylaldehyde Hydrazone Zn(II) Complexes.

Luminescent Zn(II) complexes that respond to external stimuli are of wide interest due to their potential applications. Schiff base with O,N,O-hydrazone shows excellent luminescence properties with multi-coordination sites for different coordination modes. In this work, three salicylaldehyde hydrazone Zn(II) complexes (1, 2a, 2b) were synthesized and their stimuli-responsive behaviors in different states were explored. Only complex 1 exhibits reversible and self-recoverable photochromic and photoluminescence properties in solution. This may be due to the configuration eversion and the excited-state intramolecular proton transfer (ESIPT) process. In the solid state, 2a has obvious mechanochromic luminescence property, which is caused by the destruction of intermolecular interactions and the transformation from crystalline state to amorphous state. 2a and 2b have delayed fluorescence properties due to effective halogen bond interactions in structures. 2a could undergo crystal-phase transformation into its polymorphous 2b by force/vapor stimulation. Interestingly, 2b shows photochromic property, which can be attributed to the electron transfer and generation of radicals induced by UV irradiation. Due to different conformations and coordination modes, the three Zn(II) complexes show different stimuli-responsive properties. This work presents the multi-stimuli-responsive behaviors of salicylaldehyde hydrazone Zn(II) complexes in different states and discusses the response mechanism in detail, which may provide new insights into the design of multi-stimuli-responsive materials.

Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing.

RNA molecules can fold into complex structures and interact with trans-acting factors to control their biology. Recent methods have been focused on developing novel tools to measure RNA structure transcriptome-wide, but their utility to study and predict RNA-protein interactions or RNA processing has been limited thus far. Here, we extend these studies with the first transcriptome-wide mapping method for cataloging RNA solvent accessibility, icLASER. By combining solvent accessibility (icLASER) with RNA flexibility (icSHAPE) data, we efficiently predict RNA-protein interactions transcriptome-wide and catalog RNA polyadenylation sites by RNA structure alone. These studies showcase the power of designing novel chemical approaches to studying RNA biology. Further, our study exemplifies merging complementary methods to measure RNA structure inside cells and its utility for predicting transcriptome-wide interactions that are critical for control of and regulation by RNA structure. We envision such approaches can be applied to studying different cell types or cells under varying conditions, using RNA structure and footprinting to characterize cellular interactions and processing involving RNA.

The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site.

The key RNA sequence elements and protein factors necessary for 3' processing of polyadenylated mRNA precursors are well known. Recent studies, however, have significantly reshaped current models for the protein-RNA interactions involved in poly(A) site recognition, painting a picture more complex than previously envisioned and also providing new insights into regulation of this important step in gene expression. Here we review the recent advances in this area and provide a perspective for future studies.

Transcriptomic Analyses of Brains of RBM8A Conditional Knockout Mice at Different Developmental Stages Reveal Conserved Signaling Pathways Contributing to Neurodevelopmental Diseases.

RNA-binding motif 8A (RBM8A) is a core component of the exon junction complex (EJC) that binds pre-mRNAs and regulates their splicing, transport, translation, and nonsense-mediated decay (NMD). Dysfunction in the core proteins has been linked to several detriments in brain development and neuropsychiatric diseases. To understand the functional role of Rbm8a in brain development, we have generated brain-specific Rbm8a knockout mice and used next-generation RNA-sequencing to identify differentially expressed genes (DEGs) in mice with heterozygous, conditional knockout (cKO) of Rbm8a in the brain at postnatal day 17 (P17) and at embryonic day 12. Additionally, we analyzed enriched gene clusters and signaling pathways within the DEGs. At the P17 time point, between the control and cKO mice, about 251 significant DEGs were identified. At E12, only 25 DEGs were identified in the hindbrain samples. Bioinformatics analyses have revealed many signaling pathways related to the central nervous system (CNS). When E12 and P17 results were compared, three DEGs, Spp1, Gpnmb, and Top2a, appeared to peak at different developmental time points in the Rbm8a cKO mice. Enrichment analyses suggested altered activity in pathways affecting cellular proliferation, differentiation, and survival. The results support the hypothesis that loss of Rbm8a causes decreased cellular proliferation, increased apoptosis, and early differentiation of neuronal subtypes, which may lead ultimately to an altered neuronal subtype composition in the brain.

Reference values of impulse oscillometry (IOS) for healthy Chinese children aged 4-17 years.

OBJECTIVE: To establish the predicted value of pulmonary function determined by impulse oscillometry (IOS) in children (4-17 years old) in China. METHODS: A total of 6270 healthy children aged 4-17 years in China were included. The Master Screen IOS pulmonary function device (Jaeger Co, Germany) was used to detect the respiratory impedance (Zrs), resonant frequency (Fres), respiratory system resistance (Rrs) and respiratory system reactance (Xrs) at various oscillation frequencies, and the indices above were analysed. Stepwise multivariate regression was used to establish the regression equation of related parameters of IOS in different sexes, ages, height, and weight. RESULTS: The differences in the main IOS parameters between different age stages were statistically significant regardless of sex (P < 0.05). The stepwise multivariate regression analysis showed that IOS parameters were related to height, age, and weight, and most IOS parameters were most closely related to height (the absolute value of the regression coefficient was the largest). With increasing age and height, the values of Z5, R5, R20, R5-R20, and Fres decreased, while the value of X5 increased. Through height, age, and weight, we obtained the normal predicted values equation of children's IOS parameters. Compared with the other reference equations, our reference equation is more suitable for Chinese children. CONCLUSIONS: The study revealed the reference values of IOS parameters in healthy Chinese children. In the evaluation of results for lung function measurements, this predicted value equation is more consistent with the characteristics of Chinese children than other reference equations. CLINICAL TRIAL: ChiCTR: 1800019029.

Multistimuli-Responsive Materials Based on Zn(II)-Viologen Coordination Polymers and Their Applications in Inkless Print and Anticounterfeiting.

Recently, stimuli-responsive materials have attracted great attention, while most of them respond to single or two stimuli. Thus, it is essential to design multifunctional stimuli-responsive materials and develop their applications. The strategy that constructing high-dimensional coordination polymers facilitates the application scope of a viologen-based photochromic system is put forward and confirmed for the first time. Herein, a novel multistimuli-responsive viologen-based Zn-MOF with a two-dimensional framework has been successfully designed and synthesized. Complex 1 exhibits chromic behavior under a variety of external stimuli such as 365 nm UV, X-rays, heat, electricity, and ethylamine. More interestingly, the crystal state of complex 1 displays dual fluorescence and room-temperature phosphorescence (RTP) emission and emits a yellow afterglow when turning off the UV lamp. In addition, Eu(III)-functionalized hybrids, Eu3+@Zn-MOF, were prepared by coordinated postsynthetic modification based on viologen complexes for the first time. The sample of Eu3+@Zn-MOF inherits the photochromic characteristics of the viologen complexes and gives the distinctive fluorescence of the europium ions. Based on the multicolor switching of 1 and Eu3+@Zn-MOF, their possible practical utilization was successfully developed in the fields of inkless, erasable print media, electrochromic information tag printing, information encryption, and anticounterfeiting.

Solvent-Modulated Self-Assembly of Naphthalenediimide-Based Cd(II) Complexes and the Controllable Photochromism via Conformational Isomerization.

Rational regulation of the properties of photochromic materials is a challenging and meaningful work. In the present work, NDI-based complexes, namely, [Cd0.5(NDI)(HBDC)]·H2O (1) and a series of conformational isomers of {[Cd(NDI)0.5(BDC)]·MeCN}n (2), were synthesized by varying the solvent conditions (H2BDC = terephthalic acid, NDI = N,N'-bis(3-pyridylcarbonylhydrazine)-1,4,5,8-naphthalene diimide). Complex 1 exhibits a 0D mononuclear structure without photochromic behavior due to the bad conjugation of the naphthalene diimide moiety. The conformational isomers of complex 2 manifest a 3D network, showing ultra-fast photo-induced intermolecular electron transfer photochromic behavior under X-ray, UV, and visible light. However, they show different photochromic rates and coloring contrast upon photoirradiation, which originates from their difference in the distances of lone pair(COO)···π(NDI). This was realized via controlling the solvent ratio in the reaction system. In addition, compared to UV/X-ray light, 2 exhibits greater sensitivity to visible light and is an organic-inorganic hybrid material with photomodulated luminescence. Based on the excellent performance, complex 2 can be applied to filter paper, showing potential applications as an inkless printing medium and selective perception of ammonia and amine vapors in the solid state via different visual color changes.

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3' processing.

AAUAAA is the most highly conserved motif in eukaryotic mRNA polyadenylation sites and, in mammals, is specifically recognized by the multisubunit CPSF (cleavage and polyadenylation specificity factor) complex. Despite its critical functions in mRNA 3' end formation, the molecular basis for CPSF-AAUAAA interaction remains poorly defined. The CPSF subunit CPSF160 has been implicated in AAUAAA recognition, but direct evidence has been lacking. Using in vitro and in vivo assays, we unexpectedly found that CPSF subunits CPSF30 and Wdr33 directly contact AAUAAA. Importantly, the CPSF30-RNA interaction is essential for mRNA 3' processing and is primarily mediated by its zinc fingers 2 and 3, which are specifically targeted by the influenza protein NS1A to suppress host mRNA 3' processing. Our data suggest that AAUAAA recognition in mammalian mRNA 3' processing is more complex than previously thought and involves multiple protein-RNA interactions.

Hybrid endoscopic submucosal dissection: An alternative resection modality for large laterally spreading tumors in the cecum?

BACKGROUND: Endoscopic resection for large, laterally spreading tumors (LSTs) in the cecum is challenging. Here we report on the clinical outcomes of hybrid endoscopic submucosal dissection (ESD) in large cecal LSTs. METHODS: We retrospectively reviewed data from patients with cecal LSTs ≥ 2 cm who underwent ESD or hybrid ESD procedures between January of 2008 and June of 2019. We compared the baseline characteristics and clinical outcomes, including procedure time, the en bloc and complete resection rates, and adverse events. RESULTS: A total of 62 patients were enrolled in the study. There were 27 patients in the ESD group and 35 patients in the hybrid ESD group, respectively. Hybrid ESD was more used for lesions with submucosal fibrosis. No other significant differences were found in patient characteristics between the two groups. The hybrid ESD group had a significantly shorter procedure time compared with the ESD group (27.60 ± 17.21 vs. 52.63 ± 44.202 min, P = 0.001). The en bloc resection rate (77.1% vs. 81.5%, P = 0.677) and complete resection rate (71.4% vs. 81.5%, P = 0.359) of hybrid ESD were relatively lower than that of the ESD group in despite of no significant difference was found. The perforation and post-procedure bleeding rate (2.9% vs. 3.7%, P = 0.684) were similar between the two groups. One patient perforated during the ESD procedure, which was surgically treated. One patient in the hybrid ESD group experienced post-procedure bleeding, which was successfully treated with endoscopic hemostasis. Post-procedural fever and abdominal pain occurred in six patients in the ESD group and five patients in the hybrid ESD group. One patient in the ESD group experienced recurrence, which was endoscopically resected. CONCLUSION: The results of this study indicate that hybrid ESD may be an alternative resection strategy for large cecal LSTs with submucosal fibrosis.

Experience with Esophageal Granular Cell Tumors: Clinical and Endoscopic Analysis of 22 Cases.

BACKGROUND: Esophageal granular cell tumors (GCTs) are rare tumors. Differences in reports on the clinical features of GCTs in the esophagus and some controversies about the diagnostic strategy for esophageal GCTs exist. OBJECTIVES: We aimed to investigate the clinical features and diagnosis of esophageal GCTs. Additionally, we sought to determine the prevalence of gastroesophageal reflux disease and reflux esophagitis in patients with esophageal GCTs. METHODS: We retrospectively studied the clinical features, endoscopic features, and management of 22 patients with esophageal GCTs. RESULTS: Esophageal GCTs were more common in men than in women with a ratio of 1.2:1 and were predominantly found in the distal esophagus. Ten patients with esophageal GCTs had regurgitation and/or heartburn symptoms, and eight patients were confirmed to have reflux esophagitis by endoscopy. All esophageal GCTs were protuberant lesions covered by normal esophageal epithelium. The endoscopic morphology of esophageal GCTs was diverse. On endoscopic ultrasonography, these tumors appeared as homogeneous or inhomogeneous hypoechoic lesions with clear borders originating from the submucosal or mucosal layer. Eleven patients underwent endoscopic forceps biopsy at the first endoscopy, and only six patients were correctly diagnosed by pathology. Nevertheless, the 18 lesions treated with endoscopic resection were all correctly diagnosed without complications, and no patients developed recurrence during the follow-up period. CONCLUSIONS: The occurrence of esophageal GCTs may be related to esophageal inflammation. As a method for obtaining an accurate pathological diagnosis and for treatment, endoscopic resection should be offered as the primary option for patients with esophageal GCTs.