Decoding the specificity of m6A RNA methylation and its implication in cancer therapy.

N6-methyladenosine (m6A) is the most abundant endogenous modification in eukaryotic RNAs. It plays important roles in various biological processes and diseases, including cancers. More and more studies have revealed that the deposition of m6A is specifically regulated in a context-dependent manner. Here, we review the diverse mechanisms that determine the topology of m6A along RNAs and the cell-type-specific m6A methylomes. The exon junction complex (EJC) as well as histone modifications play important roles in determining the topological distribution of m6A along nascent RNAs, while the transcription factors and RNA-binding proteins, which usually bind specific DNAs and RNAs in a cell-type-specific manner, largely account for the cell-type-specific m6A methylomes. Due to the lack of specificity of m6A writers and readers, there are still challenges to target the core m6A machinery for cancer therapies. Therefore, understanding the mechanisms underlying the specificity of m6A modifications in cancers would be important for future cancer therapies through m6A intervention.

Three-axis angle measurement method based on an optical wedge.

A three-axis angle measurement method is proposed using an optical wedge as a reflector. In this paper, the mathematical model of three-axis angle solving corresponding to the method is derived, and it is verified and corrected by establishing an optical simulation model, and, finally, the feasibility and measurement accuracy of the method are verified by using a principle prototype. The experimental results show that the RMS values of the measurement errors of pitch angle α, yaw angle ß, and roll angle γ are 6.27 ' ' , 4.35 ' ' , and 17.68 ' ' , respectively, within the measurement range of ±2∘, and the measurement accuracy is insensitive to the measurement distance.

Toxicokinetics of MDMA and Its Metabolite MDA in Rats.

OBJECTIVES: To investigate the toxicokinetic differences of 3,4-methylenedioxy-N-methylamphetamine (MDMA) and its metabolite 4,5-methylene dioxy amphetamine (MDA) in rats after single and continuous administration of MDMA, providing reference data for the forensic identification of MDMA. METHODS: A total of 24 rats in the single administration group were randomly divided into 5, 10 and 20 mg/kg experimental groups and the control group, with 6 rats in each group. The experimental group was given intraperitoneal injection of MDMA, and the control group was given intraperitoneal injection of the same volume of normal saline as the experimental group. The amount of 0.5 mL blood was collected from the medial canthus 5 min, 30 min, 1 h, 1.5 h, 2 h, 4 h, 6 h, 8 h, 10 h, 12 h after administration. In the continuous administration group, 24 rats were randomly divided into the experimental group (18 rats) and the control group (6 rats). The experimental group was given MDMA 7 d by continuous intraperitoneal injection in increments of 5, 7, 9, 11, 13, 15, 17 mg/kg per day, respectively, while the control group was given the same volume of normal saline as the experimental group by intraperitoneal injection. On the eighth day, the experimental rats were randomly divided into 5, 10 and 20 mg/kg dose groups, with 6 rats in each group. MDMA was injected intraperitoneally, and the control group was injected intraperitoneally with the same volume of normal saline as the experimental group. On the eighth day, 0.5 mL of blood was taken from the medial canthus 5 min, 30 min, 1 h, 1.5 h, 2 h, 4 h, 6 h, 8 h, 10 h, 12 h after administration. Liquid chromatography-triple quadrupole tandem mass spectrometry was used to detect MDMA and MDA levels, and statistical software was employed for data analysis. RESULTS: In the single-administration group, peak concentrations of MDMA and MDA were reached at 5 min and 1 h after administration, respectively, with the largest detection time limit of 12 h. In the continuous administration group, peak concentrations were reached at 30 min and 1.5 h after administration, respectively, with the largest detection time limit of 10 h. Nonlinear fitting equations for the concentration ratio of MDMA and MDA in plasma and administration time in the single-administration group and continuous administration group were as follows: T=10.362C-1.183, R2=0.974 6; T=7.397 3C-0.694, R2=0.961 5 (T: injection time; C: concentration ratio of MDMA to MDA in plasma). CONCLUSIONS: The toxicokinetic data of MDMA and its metabolite MDA in rats, obtained through single and continuous administration, including peak concentration, peak time, detection time limit, and the relationship between concentration ratio and administration time, provide a theoretical and data foundation for relevant forensic identification.

Ablation of Plasma Prekallikrein Decreases Low-Density Lipoprotein Cholesterol by Stabilizing Low-Density Lipoprotein Receptor and Protects Against Atherosclerosis.

BACKGROUND: High blood cholesterol accelerates the progression of atherosclerosis, which is an asymptomatic process lasting for decades. Rupture of atherosclerotic plaques induces thrombosis, which results in myocardial infarction or stroke. Lowering cholesterol levels is beneficial for preventing atherosclerotic cardiovascular disease. METHODS: Low-density lipoprotein (LDL) receptor (LDLR) was used as bait to identify its binding proteins in the plasma, and the coagulation factor prekallikrein (PK; encoded by the KLKB1 gene) was revealed. The correlation between serum PK protein content and lipid levels in young Chinese Han people was then analyzed. To investigate the effects of PK ablation on LDLR and lipid levels in vivo, we genetically deleted Klkb1 in hamsters and heterozygous Ldlr knockout mice and knocked down Klkb1 using adeno-associated virus-mediated shRNA in rats. The additive effect of PK and proprotein convertase subtilisin/kexin 9 inhibition also was evaluated. In addition, we applied the anti-PK neutralizing antibody that blocked the PK and LDLR interaction in mice. Mice lacking both PK and apolipoprotein e (Klkb1-/-Apoe-/-) were generated to assess the role of PK in atherosclerosis. RESULTS: PK directly bound LDLR and induced its lysosomal degradation. The serum PK concentrations positively correlated with LDL cholesterol levels in 198 young Chinese Han adults. Genetic depletion of Klkb1 increased hepatic LDLR and decreased circulating cholesterol in multiple rodent models. Inhibition of proprotein convertase subtilisin/kexin 9 with evolocumab further decreased plasma LDL cholesterol levels in Klkb1-deficient hamsters. The anti-PK neutralizing antibody could similarly lower plasma lipids through upregulating hepatic LDLR. Ablation of Klkb1 slowed the progression of atherosclerosis in mice on Apoe-deficient background. CONCLUSIONS: PK regulates circulating cholesterol levels through binding to LDLR and inducing its lysosomal degradation. Ablation of PK stabilizes LDLR, decreases LDL cholesterol, and prevents atherosclerotic plaque development. This study suggests that PK is a promising therapeutic target to treat atherosclerotic cardiovascular disease.

Combined inhibition of surface CD51 and γ-secretase-mediated CD51 cleavage improves therapeutic efficacy in experimental metastatic hepatocellular carcinoma.

BACKGROUND & AIMS: Integrin αv (ITGAV, CD51) is regarded as a key component in multiple stages of tumor progression. However, the clinical failure of cilengitide, a specific inhibitor targeting surface CD51, suggests the importance of yet-unknown mechanisms by which CD51 promotes tumor progression. METHODS: In this study, we used several hepatocellular carcinoma (HCC) cell lines and murine hepatoma cell lines. To investigate the role of CD51 on HCC progression, we used a 3D invasion assay and in vivo bioluminescence imaging. We used periostin-knockout transgenic mice to uncover the role of the tumor microenvironment on CD51 cleavage. Moreover, we used several clinically relevant HCC models, including patient-derived organoids and patient-derived xenografts, to evaluate the therapeutic efficacy of cilengitide in combination with the γ-secretase inhibitor LY3039478. RESULTS: We found that CD51 could undergo transmembrane cleavage by γ-secretase to produce a functional intracellular domain (CD51-ICD). The cleaved CD51-ICD facilitated HCC invasion and metastasis by promoting the transcription of oxidative phosphorylation-related genes. Furthermore, we identified cancer-associated fibroblast-derived periostin as the major driver of CD51 cleavage. Lastly, we showed that cilengitide-based therapy led to a dramatic therapeutic effect when supplemented with LY3039478 in both patient-derived organoid and xenograft models. CONCLUSIONS: In summary, we revealed previously unrecognized mechanisms by which CD51 is involved in HCC progression and uncovered the underlying cause of cilengitide treatment failure, as well as providing evidence supporting the translational prospects of combined CD51-targeted therapy in the clinic. IMPACT AND IMPLICATIONS: Integrin αv (CD51) is a widely recognized pro-tumoral molecule that plays a crucial role in various stages of tumor progression, making it a promising therapeutic target. However, despite early promising results, cilengitide, a specific antagonist of CD51, failed in a phase III clinical trial. This prompted further investigation into the underlying mechanisms of CD51's effects. This study reveals that the γ-secretase complex directly cleaves CD51 to produce an intracellular domain (CD51-ICD), which functions as a pro-tumoral transcriptional regulator and can bypass the inhibitory effects of cilengitide by entering the nucleus. Furthermore, the localization of CD51 in the nucleus is significantly associated with the prognosis of patients with HCC. These findings provide a theoretical basis for re-evaluating cilengitide in clinical settings and highlight the importance of identifying a more precise patient subpopulation for future clinical trials targeting CD51.

Programmable optical switching integrated chip for 4-bit binary true/inverse/complement code conversions based on fluorinated photopolymers.

In this work, programmable optical switching integrated chips for 4-bit binary true/inverse/complement optical code conversions (OCCs) are proposed based on fluorinated photopolymers. Fluorinated bis-phenol-A novolac resin (FAR) with low absorption loss and fluorinated polyacrylate (FPA) with high thermal stability are self-synthesized as core and cladding layer, respectively. The basic architecture of operating unit for the photonic chip designed is composed of directional coupler Mach-Zehnder interferometer (DC-MZI) thermo-optic (TO) switching, X-junction, and Y-bunching waveguide structures. The waveguide module by cascading 16 operating units could realize OCCs function through optical transmission matrix. The response time of the 4-bit binary OCCs is measured as about 300 µs. The insertion loss and extinction ratio of the actual chip are obtained as about 10.5 dB and 15.2 dB, respectively. The electric driving power consumption for OCCs is less than 6 mW. The true/inverse/complement OCCs are achieved by the programmable modulation circuit. The proposed technique is suitable for achieving optical digital computing system with high-speed signal processing and low power consumption.

Triple-layered optical interconnecting integrated waveguide chip based on epoxy cross-linking fluorinated polymer photonic platform.

In this study, a triple-layered optical interconnecting integrated waveguide chip was designed and fabricated using an epoxy cross-linking polymer photonic platform. Fluorinated photopolymers FSU-8 and AF-Z-PC EP were self-synthesized as waveguide cores and cladding materials, respectively. The triple-layered optical interconnecting waveguide device comprised 4 × 4 arrayed waveguide grating (AWG) -based wavelength-selective switching (WSS) arrays, 4 × 4 multi-mode interference (MMI) -cascaded channel-selective switching (CSS) arrays, and 3 × 3 direct-coupling (DC) interlayered switching arrays. The overall optical polymer waveguide module was fabricated by direct UV writing. For the multilayered WSS arrays, the wavelength-shifting sensitivity was ∼0.48 nm/°C. For the multilayered CSS arrays, the average switching time was ∼280 µs, and the maximum power consumption was <30 mW. For interlayered switching arrays, the extinction ratio approximated 15.2 dB. The transmission loss for the triple-layered optical waveguide chip was measured as 10.0-12.1 dB. The flexible multilayered photonic integrated circuits (PIC) can be used in high-density integrated optical interconnecting systems with a large-volume optical information transmission capacity.

N(6)-methyladenosine-binding protein YTHDF1 suppresses EBV replication and promotes EBV RNA decay.

N6 -methyladenosine (m6 A) modification of mRNA mediates diverse cellular and viral functions. Infection with Epstein-Barr virus (EBV) is causally associated with nasopharyngeal carcinoma (NPC), 10% of gastric carcinoma, and various B-cell lymphomas, in which the viral latent and lytic phases both play vital roles. Here, we show that EBV transcripts exhibit differential m6 A modification in human NPC biopsies, patient-derived xenograft tissues, and cells at different EBV infection stages. m6 A-modified EBV transcripts are recognized and destabilized by the YTHDF1 protein, which leads to the m6 A-dependent suppression of EBV infection and replication. Mechanistically, YTHDF1 hastens viral RNA decapping and mediates RNA decay by recruiting RNA degradation complexes, including ZAP, DDX17, and DCP2, thereby post-transcriptionally downregulating the expression of EBV genes. Taken together, our results reveal the critical roles of m6 A modifications and their reader YTHDF1 in EBV replication. These findings contribute novel targets for the treatment of EBV-associated cancers.

Targeted manipulation of m6A RNA modification through CRISPR-Cas-based strategies.

N6-methyladenosine (m6A) is a reversible and prevalent internal modification in RNAs and can be dynamically modulated by methyltransferase and demethylase. Targeted manipulation of m6A RNA modification is critical in studying the functions of specific m6A sites as well as developing molecular therapies through targeting m6A. The CRISPR-Cas systems including CRISPR-Cas9 and CRISPR-Cas13 have been widely used to edit and modify specific nucleotides on DNA and RNA through fusing effective proteins such as enzymes with Cas9/13. Through taking advantage of the m6A methyltransferase and demethylase, a series of CRISPR-Cas-based methods have also been developed to manipulate the m6A methylation at specific RNA sites. This review summarizes the latest CRISPR-Cas13 and Cas9 toolkits for m6A site-specific manipulation, including fundamental components, on-target efficiency, editing window, PAM/PFS requirement, and subcellularly localized targeting as well as potential limitations. We thus aim to provide an overview to assist researchers to choose an optimal tool to manipulate m6A for different purposes and also point out possible optimization strategies.

An accurate interatomic potential for the TiAlNb ternary alloy developed by deep neural network learning method.

The complex phase diagram and bonding nature of the TiAl system make it difficult to accurately describe its various properties and phases by traditional atomistic force fields. Here, we develop a machine learning interatomic potential with a deep neural network method for the TiAlNb ternary alloy based on a dataset built by first-principles calculations. The training set includes bulk elementary metals and intermetallic structures with slab and amorphous configurations. This potential is validated by comparing bulk properties-including lattice constant and elastic constants, surface energies, vacancy formation energies, and stacking fault energies-with their respective density functional theory values. Moreover, our potential could accurately predict the average formation energy and stacking fault energy of γ-TiAl doped with Nb. The tensile properties of γ-TiAl are simulated by our potential and verified by experiments. These results support the applicability of our potential under more practical conditions.

Integrative network analysis identifies cell-specific trans regulators of m6A.

N6-methyladenosine (m6A) is a reversible and dynamic RNA modification in eukaryotes. However, how cells establish cell-specific m6A methylomes is still poorly understood. Here, we developed a computational framework to systematically identify cell-specific trans regulators of m6A through integrating gene expressions, binding targets and binding motifs of large number of RNA binding proteins (RBPs) with a co-methylation network constructed using large-scale m6A methylomes across diverse cell states. We applied the framework and successfully identified 32 high-confidence m6A regulators that modulated the variable m6A sites away from stop codons in a cell-specific manner. To validate them, we knocked down three regulators respectively and found two of them (TRA2A and CAPRIN1) selectively promoted the methylations of the m6A sites co-localized with their binding targets on RNAs through physical interactions with the m6A writers. Knockdown of TRA2A increased the stabilities of the RNAs with TRA2A bound near the m6A sites and decreased the viability of cells. The successful identification of m6A regulators demonstrates a powerful and widely applicable strategy to elucidate the cell-specific m6A regulators. Additionally, our discovery of pervasive trans-acting regulating of m6A provides novel insights into the mechanisms by which spatial and temporal dynamics of m6A methylomes are established.

Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers.

Hippo-YAP signaling pathway functions in early lineage differentiation of pluripotent stem cells, but the detailed mechanisms remain elusive. We found that knockout (KO) of Mst1 and Mst2, two key components of the Hippo signaling in mouse embryonic stem cells (ESCs), resulted in a disruption of differentiation into mesendoderm lineage. To further uncover the underlying regulatory mechanisms, we performed a series of ChIP-seq experiments with antibodies against YAP, ESC master transcription factors and some characterized histone modification markers as well as RNA-seq assays using wild type and Mst KO samples at ES and day 4 embryoid body stage respectively. We demonstrate that YAP is preferentially co-localized with super-enhancer (SE) markers such as Nanog, Sox2, Oct4 and H3K27ac in ESCs. The hyper-activation of nuclear YAP in Mst KO ESCs facilitates the binding of Nanog, Sox2 and Oct4 as well as H3K27ac modification at the loci where YAP binds. Moreover, Mst depletion results in novel SE formation and enhanced liquid-liquid phase-separated Med1 condensates on lineage associated genes, leading to the upregulation of these genes and the distortion of ESC differentiation. Our study reveals a novel mechanism on how Hippo-YAP signaling pathway dictates ESC lineage differentiation.

Genome Resource of a Hypervirulent Strain C9-3 of Xanthomonas oryzae pv. oryzae Causing Bacterial Blight of Rice.

Xanthomonas oryzae pv. oryzae is the causal agent of bacterial blight, one of the most devastating diseases of rice. Here, a hypervirulent strain, C9-3, defeating Xa1, Xa10, xa13, and Xa23 resistance genes, was used to extract genomic DNA for single molecule real-time (SMRT) sequencing. After assembly, the genome consists of a single-circular chromosome with the size of 4,924,298 bp with G+C content of 63.7% and contains 4,715 genes. Annotation and analysis of the TALE genes using a suite of applications named AnnoTALE suggested that 17 transcription activator-like effectors, including 15 typical TALEs and 2 iTALEs/truncTALEs, were encoded in the genome. The approach and genome resource will contribute to the discovery of new virulence effectors and understanding on rice-X. oryzae pv. oryzae interactions.

The bonding variation of γ-TiAl during deformation.

To improve the ductility of γ-TiAl, the complicated interaction of Ti-Al chemical bonds, Al-Al covalent bonds, and Ti metallic bonds in the process of deformation should be evaluated. The electronic structure variation of γ-TiAl during deformation is investigated using first-principles calculation with the local energy schemes. The relative influence of these bonds on atomic stability is for the first time qualitatively evaluated by the combination of local energy schemes and Electron Localization Function (ELF) analysis. The discrepant influence pattern of some alloy elements on ductility is discussed based on the bonding analysis.

Synergizing Phase and Cavity in CoMoOx Sy Yolk-Shell Anodes to Co-Enhance Capacity and Rate Capability in Sodium Storage.

Sodium-ion batteries (SIBs) have been recognized as the promising alternatives to lithium-ion batteries for large-scale applications owing to their abundant sodium resource. Currently, one significant challenge for SIBs is to explore feasible anodes with high specific capacity and reversible pulverization-free Na+ insertion/extraction. Herein, a facile co-engineering on polymorph phases and cavity structures is developed based on CoMo-glycerate by scalable solvothermal sulfidation. The optimized strategy enables the construction of CoMoOx Sy with synergized partially sulfidized amorphous phase and yolk-shell confined cavity. When developed as anodes for SIBs, such CoMoOx Sy electrodes deliver a high reversible capacity of 479.4 mA h g-1 at 200 mA g-1 after 100 cycles and a high rate capacity of 435.2 mA h g-1 even at 2000 mA g-1 , demonstrating superior capacity and rate capability. These are attributed to the unique dual merits of the anodes, that is, the elastic bountiful reaction pathways favored by the sulfidation-induced amorphous phase and the sodiation/desodiation accommodatable space benefits from the yolk-shell cavity. Such yolk-shell nano-battery materials are merited with co-tunable phases and structures, facile scalable fabrication, and excellent capacity and rate capability in sodium storage. This provides an opportunity to develop advanced practical electrochemical sodium storage in the future.

IDOL G51S Variant Is Associated With High Blood Cholesterol and Increases Low-Density Lipoprotein Receptor Degradation.

OBJECTIVE: A high level of LDL-C (low-density lipoprotein cholesterol) is a major risk factor for cardiovascular disease. The E3 ubiquitin ligase named IDOL (inducible degrader of the LDLR [LDL receptor]; also known as MYLIP [myosin regulatory light chain interacting protein]) mediates degradation of LDLR through ubiquitinating its C-terminal tail. But the expression profile of IDOL differs greatly in the livers of mice and humans. Whether IDOL is able to regulate LDL-C levels in humans remains to be determined. Approach and Results: By using whole-exome sequencing, we identified a nonsynonymous variant rs149696224 in the IDOL gene that causes a G51S (Gly-to-Ser substitution at the amino acid site 51) from a Chinese Uygur family. Large cohort analysis revealed IDOL G51S carriers (+/G51S) displayed significantly higher LDL-C levels. Mechanistically, the G51S mutation stabilized IDOL protein by inhibiting its dimerization and preventing self-ubiquitination and subsequent proteasomal degradation. IDOL(G51S) exhibited a stronger ability to promote ubiquitination and degradation of LDLR. Adeno-associated virus-mediated expression of IDOL(G51S) in mouse liver decreased hepatic LDLR and increased serum levels of LDL-C, total cholesterol, and triglyceride. CONCLUSIONS: Our study demonstrates that IDOL(G51S) is a gain-of-function variant responsible for high LDL-C in both humans and mice. These results suggest that IDOL is a key player regulating cholesterol level in humans.

hsa_circ_0000520 influences herceptin resistance in gastric cancer cells through PI3K-Akt signaling pathway.

BACKGROUND: To investigate whether hsa_circ_0000520 affects Herceptin resistance in gastric cancer by regulating the PI3K-AKT signaling. METHODS: The expression of hsa_circ_0000520 was detected by qRT-PCR in gastric cancer tissues and cell lines. A Herceptin-resistant gastric cancer cell was established. PcDNA and pcDNA-hsa_circ_0000520 were transfected into NCI-N87R cells and treated with Herceptin at a concentration of 10 µg/mL for 24 hours. MTT tested cell proliferation, and apoptosis was measured by flow cytometry. IGF-1 treatment was used to activate PI3K-Akt signaling. The expression levels of related proteins were detected. RESULTS: The expression of hsa_circ_0000520 was reduced in gastric cancer tissues and cell lines, and hsa_circ_0000520 in NCI-N87R cells was significantly lower than that of NCI-N87 cells. Compared with the CON group, the cell viability of the Herceptin group was significantly reduced, the apoptosis rate was significantly increased, the level of Bax protein was significantly increased, and the levels of Bcl-2, p-PI3K, and p-Akt protein were significantly reduced. Compared with the Herceptin + pcDNA group, the cell viability of the Herceptin + hsa_circ_0000520 group was significantly reduced, the apoptosis rate was significantly increased, the level of Bax protein was significantly increased, and the levels of p-PI3K and p-Akt proteins were significantly reduced. After IGF-1 treatment, the cell viability was significantly increased, the apoptosis rate was significantly reduced, the level of Bax protein was significantly reduced, and the level of Bcl-2 protein was significantly increased. CONCLUSION: Hsa_circ_0000520 overexpression may reverse the Herceptin resistance of gastric cancer cells by inhibiting the PI3K-Akt signaling pathway.

Comparative analysis of radiofrequency ablation and resection for colorectal liver metastases in caudate lobe: a retrospective study.

Objective: To assess the therapeutic efficiency of radiofrequency ablation (RFA) for colorectal liver metastases (CRLM) in the caudate lobe compared with that of surgical resection.Methods: After approved by institutional review board, we retrospectively reviewed 20 patients with caudate CRLM treated by RFA or resection between 2006 and 2017. Comparative analysis was performed based on the different therapies, including patient characteristics, therapeutic outcomes, recurrences, and survivals.Results: During the median follow-up of 7 years (range, 2 -11 years), no differences in complications and recurrences were found between RFA and surgery groups (p > .05). The median overall survival (OS) of patients after RFA and resection were 41 months (95% confidence interval (CI) 23.5-70.5) and 54 months (95% CI 31.1-77.7), respectively (p = .627, hazard radio (HR) 0.7, 95% CI 0.2-2.6). However, OS of resection group was better than that of RFA group for large caudate CRLMs (>3 cm) (p = .042, HR 4.4, 95% CI 0.6-32.6).Conclusions: RFA is a feasible, safe, and effective treatment for CRLM in the caudate. Surgical resection revealed superior outcomes in the treatment of caudate CRLMs, particularly in cases with a hepatic tumor size >3 cm.

m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome.

N(6)-Methyladenosine (m(6)A) is a widespread, reversible chemical modification of RNA molecules, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m(6)A modified ('m(6)A levels') or the relationship of m(6)A modification(s) to alternative RNA isoforms. To deconvolute the m(6)A epitranscriptome, we developed m(6)A-level and isoform-characterization sequencing (m(6)A-LAIC-seq). We found that cells exhibit a broad range of nonstoichiometric m(6)A levels with cell-type specificity. At the level of isoform characterization, we discovered widespread differences in the use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3' untranslated regions, while nonmethylated transcript isoforms tend to use distal APA sites. m(6)A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m(6)A modifications.

Suboptimal RNA-RNA interaction limits U1 snRNP inhibition of canonical mRNA 3' processing.

It is increasingly appreciated that U1 snRNP transcriptomically suppresses the usage of intronic polyadenylation site (PAS) of mRNAs, an outstanding question is why frequently used PASs are not suppressed. Here we found that U1 snRNP could be transiently associated with sequences upstream of actionable PASs in human cells, and RNA-RNA interaction might contribute to the association. By focusing on individual PAS, we showed that the stable assembly of U1 snRNP near PAS might be generally required for U1 inhibition of mRNA 3' processing. Therefore, actionable PASs that often lack optimal U1 snRNP docking site nearby is free from U1 inhibitory effect. Consistently, natural 5' splicing site (5'-SS) is moderately enriched ~250 nt upstream of intronic PASs whose usage is sensitive to functional knockdown of U1 snRNA. Collectively, our results provided an insight into how U1 snRNP selectively inhibits the usage of PASs in a cellular context, and supported a prevailing model that U1 snRNP scans pre-mRNA through RNA-RNA interaction to find a stable interaction site to exercise its function in pre-mRNA processing, including repressing the usage of cryptic PASs.