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1.
Mol Cell ; 77(5): 999-1013.e6, 2020 03 05.
Artigo em Inglês | MEDLINE | ID: mdl-32017896

RESUMO

U6 snRNA, as an essential component of the catalytic core of the pre-mRNA processing spliceosome, is heavily modified post-transcriptionally, with 2'-O-methylation being most common. The role of these modifications in pre-mRNA splicing as well as their physiological function in mammals have remained largely unclear. Here we report that the La-related protein LARP7 functions as a critical cofactor for 2'-O-methylation of U6 in mouse male germ cells. Mechanistically, LARP7 promotes U6 loading onto box C/D snoRNP, facilitating U6 2'-O-methylation by box C/D snoRNP. Importantly, ablation of LARP7 in the male germline causes defective U6 2'-O-methylation, massive alterations in pre-mRNA splicing, and spermatogenic failure in mice, which can be rescued by ectopic expression of wild-type LARP7 but not an U6-loading-deficient mutant LARP7. Our data uncover a novel role of LARP7 in regulating U6 2'-O-methylation and demonstrate the functional requirement of such modification for splicing fidelity and spermatogenesis in mice.


Assuntos
Precursores de RNA/metabolismo , Splicing de RNA , RNA Mensageiro/metabolismo , RNA Nuclear Pequeno/metabolismo , Proteínas de Ligação a RNA/metabolismo , Espermatogênese , Espermatozoides/metabolismo , Spliceossomos/metabolismo , Animais , Fertilidade , Regulação da Expressão Gênica no Desenvolvimento , Células HEK293 , Humanos , Masculino , Metilação , Camundongos Endogâmicos C57BL , Camundongos Knockout , Precursores de RNA/genética , RNA Mensageiro/genética , RNA Nuclear Pequeno/genética , Proteínas de Ligação a RNA/genética , Ribonucleoproteínas Nucleolares Pequenas/genética , Ribonucleoproteínas Nucleolares Pequenas/metabolismo , Transdução de Sinais , Espermatogênese/genética , Spliceossomos/genética
2.
Nucleic Acids Res ; 52(D1): D273-D284, 2024 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-37956310

RESUMO

Although over 170 chemical modifications have been identified, their prevalence, mechanism and function remain largely unknown. To enable integrated analysis of diverse RNA modification profiles, we have developed RMBase v3.0 (http://bioinformaticsscience.cn/rmbase/), a comprehensive platform consisting of eight modules. These modules facilitate the exploration of transcriptome-wide landscape, biogenesis, interactome and functions of RNA modifications. By mining thousands of epitranscriptome datasets with novel pipelines, the 'RNA Modifications' module reveals the map of 73 RNA modifications of 62 species. the 'Genes' module allows to retrieve RNA modification profiles and clusters by gene and transcript. The 'Mechanisms' module explores 23 382 enzyme-catalyzed or snoRNA-guided modified sites to elucidate their biogenesis mechanisms. The 'Co-localization' module systematically formulates potential correlations between 14 histone modifications and 6 RNA modifications in various cell-lines. The 'RMP' module investigates the differential expression profiles of 146 RNA-modifying proteins (RMPs) in 18 types of cancers. The 'Interactome' integrates the interactional relationships between 73 RNA modifications with RBP binding events, miRNA targets and SNPs. The 'Motif' illuminates the enriched motifs for 11 types of RNA modifications identified from epitranscriptome datasets. The 'Tools' introduces a novel web-based 'modGeneTool' for annotating modifications. Overall, RMBase v3.0 provides various resources and tools for studying RNA modifications.


Assuntos
MicroRNAs , Conformação de Ácido Nucleico , MicroRNAs/metabolismo , Processamento Pós-Transcricional do RNA , Análise de Sequência de RNA , Transcriptoma/genética , Bases de Dados Genéticas
3.
Genome Res ; 32(6): 1026-1041, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35609991

RESUMO

Polypeptides encoded by long noncoding RNAs (lncRNAs) are a novel class of functional molecules. However, whether these hidden polypeptides participate in the TP53 pathway and play a significant biological role is still unclear. Here, we discover that TP53-regulated lncRNAs can encode peptides, two of which are functional in various human cell lines. Using ribosome profiling and RNA-seq approaches in HepG2 cells, we systematically identified more than 300 novel TP53-regulated lncRNAs and further confirmed that 15 of these TP53-regulated lncRNAs encode peptides. Furthermore, several peptides were validated by mass spectrometry. Ten of the novel translational lncRNAs are directly inducible by TP53 in response to DNA damage. We show that the TP53-inducible peptides TP53LC02 and TP53LC04, but not their lncRNAs, can suppress cell proliferation. TP53LC04 peptide also has a function associated with cell proliferation by regulating the cell cycle in response to DNA damage. This study shows that TP53-regulated lncRNAs can encode new functional peptides, leading to the expansion of the TP53 tumor-suppressor network and providing novel potential targets for cancer therapy.


Assuntos
RNA Longo não Codificante , Proliferação de Células/genética , Humanos , Peptídeos/metabolismo , Peptídeos/farmacologia , RNA Longo não Codificante/metabolismo , Ribossomos/metabolismo , Proteína Supressora de Tumor p53/genética
4.
FASEB J ; 38(10): e23644, 2024 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-38738472

RESUMO

Tumors typically lack canonical danger signals required to activate adaptive immunity and also frequently employ substantial immunomodulatory mechanisms that downregulate adaptive responses and contribute to escape from immune surveillance. Given the variety of mechanisms involved in shielding tumors from immune recognition, it is not surprising that single-agent immunomodulatory approaches have been largely unsuccessful in generating durable antitumor responses. Here we report a unique combination of immunomodulatory and cytostatic agents that recondition the tumor microenvironment and eliminate complex and/or poor-prognosis tumor types including the non-immunogenic 4T-1 model of TNBC, the aggressive MOC-2 model of HNSCC, and the high-risk MYCN-amplified model of neuroblastoma. A course of therapy optimized for TNBC cured a majority of tumors in both ectopic and orthotopic settings and eliminated metastatic spread in all animals tested at the highest doses. Immune responses were transferable between therapeutic donor and naïve recipient through adoptive transfer, and a sizeable abscopal effect on distant, untreated lesions could be demonstrated experimentally. Similar results were observed in HNSCC and neuroblastoma models, with characteristic remodeling of the tumor microenvironment documented in all model systems. scRNA-seq analysis implicated upregulation of innate immune responses and antigen presentation in tumor cells and the myeloid cell compartment as critical early events. This analysis also highlighted the potential importance of the autonomic nervous system in the governance of inflammatory processes. The data indicate that the targeting of multiple pathways and mechanisms of action can result in substantial synergistic antitumor effects and suggest follow-up in the neoadjuvant setting may be warranted.


Assuntos
Microambiente Tumoral , Animais , Camundongos , Microambiente Tumoral/imunologia , Linhagem Celular Tumoral , Neuroblastoma/imunologia , Neuroblastoma/terapia , Neuroblastoma/patologia , Feminino , Humanos , Imunomodulação , Camundongos Endogâmicos C57BL
5.
Nature ; 567(7748): 414-419, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30867593

RESUMO

DNA and histone modifications have notable effects on gene expression1. Being the most prevalent internal modification in mRNA, the N6-methyladenosine (m6A) mRNA modification is as an important post-transcriptional mechanism of gene regulation2-4 and has crucial roles in various normal and pathological processes5-12. However, it is unclear how m6A is specifically and dynamically deposited in the transcriptome. Here we report that histone H3 trimethylation at Lys36 (H3K36me3), a marker for transcription elongation, guides m6A deposition globally. We show that m6A modifications are enriched in the vicinity of H3K36me3 peaks, and are reduced globally when cellular H3K36me3 is depleted. Mechanistically, H3K36me3 is recognized and bound directly by METTL14, a crucial component of the m6A methyltransferase complex (MTC), which in turn facilitates the binding of the m6A MTC to adjacent RNA polymerase II, thereby delivering the m6A MTC to actively transcribed nascent RNAs to deposit m6A co-transcriptionally. In mouse embryonic stem cells, phenocopying METTL14 knockdown, H3K36me3 depletion also markedly reduces m6A abundance transcriptome-wide and in pluripotency transcripts, resulting in increased cell stemness. Collectively, our studies reveal the important roles of H3K36me3 and METTL14 in determining specific and dynamic deposition of m6A in mRNA, and uncover another layer of gene expression regulation that involves crosstalk between histone modification and RNA methylation.


Assuntos
Adenosina/análogos & derivados , Histonas/química , Histonas/metabolismo , Lisina/metabolismo , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Transcrição Gênica , Adenosina/metabolismo , Animais , Diferenciação Celular , Linhagem Celular , Células-Tronco Embrionárias/metabolismo , Humanos , Lisina/química , Metilação , Metiltransferases/deficiência , Metiltransferases/genética , Metiltransferases/metabolismo , Camundongos , RNA Polimerase II/metabolismo , Elongação da Transcrição Genética , Transcriptoma/genética
6.
Nucleic Acids Res ; 51(D1): D315-D327, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36408909

RESUMO

tRNA molecules contain dense, abundant modifications that affect tRNA structure, stability, mRNA decoding and tsRNA formation. tRNA modifications and related enzymes are responsive to environmental cues and are associated with a range of physiological and pathological processes. However, there is a lack of resources that can be used to mine and analyse these dynamically changing tRNA modifications. In this study, we established tModBase (https://www.tmodbase.com/) for deciphering the landscape of tRNA modification profiles from epitranscriptome data. We analysed 103 datasets generated with second- and third-generation sequencing technologies and illustrated the misincorporation and termination signals of tRNA modification sites in ten species. We thus systematically demonstrate the modification profiles across different tissues/cell lines and summarize the characteristics of tRNA-associated human diseases. By integrating transcriptome data from 32 cancers, we developed novel tools for analysing the relationships between tRNA modifications and RNA modification enzymes, the expression of 1442 tRNA-derived small RNAs (tsRNAs), and 654 DNA variations. Our database will provide new insights into the features of tRNA modifications and the biological pathways in which they participate.


Assuntos
Bases de Dados Genéticas , Processamento Pós-Transcricional do RNA , RNA de Transferência , Humanos , Neoplasias/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA de Transferência/química , RNA de Transferência/metabolismo
7.
Nucleic Acids Res ; 51(D1): D46-D56, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36399495

RESUMO

Non-coding RNAs (ncRNAs) are emerging as key regulators of various biological processes. Although thousands of ncRNAs have been discovered, the transcriptional mechanisms and networks of the majority of ncRNAs have not been fully investigated. In this study, we updated ChIPBase to version 3.0 (https://rnasysu.com/chipbase3/) to provide the most comprehensive transcriptional regulation atlas of ncRNAs and protein-coding genes (PCGs). ChIPBase has identified ∼151 187 000 regulatory relationships between ∼171 600 genes and ∼3000 regulators by analyzing ∼55 000 ChIP-seq datasets, which represent a 30-fold expansion. Moreover, we de novo identified ∼29 000 motif matrices of transcription factors. In addition, we constructed a novel 'Enhancer' module to predict ∼1 837 200 regulation regions functioning as poised, active or super enhancers under ∼1300 conditions. Importantly, we constructed exhaustive coexpression maps between regulators and their target genes by integrating expression profiles of ∼65 000 normal and ∼15 000 tumor samples. We built a 'Disease' module to obtain an atlas of the disease-associated variations in the regulation regions of genes. We also constructed an 'EpiInter' module to explore potential interactions between epitranscriptome and epigenome. Finally, we designed 'Network' module to provide extensive and gene-centred regulatory networks. ChIPBase will serve as a useful resource to facilitate integrative explorations and expand our understanding of transcriptional regulation.


Assuntos
Regulação da Expressão Gênica , RNA não Traduzido , RNA não Traduzido/genética , RNA não Traduzido/metabolismo , Fatores de Transcrição/metabolismo , Redes Reguladoras de Genes
8.
PLoS Genet ; 18(7): e1010298, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35857772

RESUMO

During meiosis, DNA double-strand breaks (DSBs) occur throughout the genome, a subset of which are repaired to form reciprocal crossovers between chromosomes. Crossovers are essential to ensure balanced chromosome segregation and to create new combinations of genetic variation. Meiotic DSBs are formed by a topoisomerase-VI-like complex, containing catalytic (e.g. SPO11) proteins and auxiliary (e.g. PRD3) proteins. Meiotic DSBs are formed in chromatin loops tethered to a linear chromosome axis, but the interrelationship between DSB-promoting factors and the axis is not fully understood. Here, we study the localisation of SPO11-1 and PRD3 during meiosis, and investigate their respective functions in relation to the chromosome axis. Using immunocytogenetics, we observed that the localisation of SPO11-1 overlaps relatively weakly with the chromosome axis and RAD51, a marker of meiotic DSBs, and that SPO11-1 recruitment to chromatin is genetically independent of the axis. In contrast, PRD3 localisation correlates more strongly with RAD51 and the chromosome axis. This indicates that PRD3 likely forms a functional link between SPO11-1 and the chromosome axis to promote meiotic DSB formation. We also uncovered a new function of SPO11-1 in the nucleation of the synaptonemal complex protein ZYP1. We demonstrate that chromosome co-alignment associated with ZYP1 deposition can occur in the absence of DSBs, and is dependent on SPO11-1, but not PRD3. Lastly, we show that the progression of meiosis is influenced by the presence of aberrant chromosomal connections, but not by the absence of DSBs or synapsis. Altogether, our study provides mechanistic insights into the control of meiotic DSB formation and reveals diverse functional interactions between SPO11-1, PRD3 and the chromosome axis.


Assuntos
Arabidopsis , Arabidopsis/genética , Arabidopsis/metabolismo , Cromatina/genética , Pareamento Cromossômico/genética , Cromossomos/metabolismo , Quebras de DNA de Cadeia Dupla , Endodesoxirribonucleases/genética , Endodesoxirribonucleases/metabolismo , Meiose/genética
9.
Small ; : e2403211, 2024 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-38958082

RESUMO

Prussian blue analogs (PBAs) have been widely recognized as superior cathode materials for sodium-ion batteries (SIBs) owing to numerous merits. However, originating from the rapid crystal growth, PBAs still suffer from considerable vacancy defects and interstitial water, making the preparation of long-cycle-life PBAs the greatest challenge for its practical application. Herein, a novel equilibrium chelation strategy is first proposed to synthesize a high crystallinity (94.7%) PBAs, which is realized by modulating the chelating potency of strong chelating agents via "acid effect" to achieve a moderate chelating effect, forcefully breaking through the bottleneck of poor cyclic stability for PBAs cathodes. Impressively, the as-prepared highly crystalline PBAs represent an unprecedented level of electrochemical performance including ultra-long lifespan (10000 cycles with 86.32% capacity maintenance at 6 A g-1), excellent rate capability (82.0 mAh g-1 at 6 A g-1). Meanwhile, by pairing with commercial hard carbon, the as-prepared PBAs-based SIBs exhibit high energy density (350 Wh kg-1) and excellent capacity retention (82.4% after 1500 cycles), highlighting its promising potential for large-scale energy storage applications.

10.
Nat Methods ; 18(10): 1213-1222, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34594034

RESUMO

Recent years have witnessed rapid progress in the field of epitranscriptomics. Functional interpretation of the epitranscriptome relies on sequencing technologies that determine the location and stoichiometry of various RNA modifications. However, contradictory results have been reported among studies, bringing the biological impacts of certain RNA modifications into doubt. Here, we develop a synthetic RNA library resembling the endogenous transcriptome but without any RNA modification. By incorporating this modification-free RNA library into established mapping techniques as a negative control, we reveal abundant false positives resulting from sequence bias or RNA structure. After calibration, precise and quantitative mapping expands the understanding of two representative modification types, N6-methyladenosine (m6A) and 5-methylcytosine (m5C). We propose that this approach provides a systematic solution for the calibration of various RNA-modification mappings and holds great promise in epitranscriptomic studies.


Assuntos
Epigênese Genética , Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , RNA/genética , Transcriptoma , Calibragem , Regulação da Expressão Gênica , Células HeLa , Humanos
11.
Acc Chem Res ; 56(22): 3198-3210, 2023 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-37931323

RESUMO

ConspectusPost-transcriptional modifications are ubiquitous in both protein-coding and noncoding RNAs (ncRNAs), playing crucial functional roles in diverse biological processes across all kingdoms of life. These RNA modifications can be achieved through two distinct mechanisms: RNA-independent and RNA-guided (also known as RNA-dependent). In the RNA-independent mechanism, modifications are directly introduced onto RNA molecules by enzymes without the involvement of other RNA molecules, while the cellular RNA-guided RNA modification system exists in the form of RNA-protein complexes, wherein one guide RNA collaborates with a set of proteins, including the modifying enzyme. The primary function of guide RNAs lies in their ability to bind to complementary regions within the target RNAs, orchestrating the installation of specific modifications. Both mechanisms offer unique advantages and are critical to the diverse and dynamic landscape of RNA modifications. RNA-independent modifications provide rapid and direct modification of RNA molecules, while RNA-guided mechanisms offer precise and programmable means to introduce modifications at specific RNA sites. Recently, emerging evidence has shed light on RNA-guided RNA modifications as a captivating area of research, providing precise and programmable control over RNA sequences and functions.In this Account, we focus on RNA modifications synthesized in an RNA-guided manner, including 2'-O-methylated nucleotides (Nm), pseudouridine (Ψ), N4-acetylcytidine (ac4C), and inosine (I). This Account sheds light on the intricate processes of biogenesis and elucidates the regulatory roles of these modifications in RNA metabolism. These roles include pivotal functions such as RNA stability, translation, and splicing, where each modification contributes to the diverse and finely tuned regulatory landscape of RNA biology. In addition to elucidating the biogenesis and functions of these modifications, we also provide an overview of high-throughput methods and their underlying biochemical principles used for the transcriptome-wide investigation of these modifications and their fundamental interactions in RNA-guided systems. This includes exploring RNA-protein interactions and RNA-RNA interactions, which play crucial roles in the dynamic regulatory networks of RNA-guided modifications. The ever-advancing methodologies have greatly enhanced our understanding of the dynamic and widespread nature of RNA-guided RNA modifications and their regulatory functions. Furthermore, the applications of RNA-guided RNA modifications are discussed, illuminating their potential in diverse fields. From basic research to gene therapy, the programmable nature of RNA-guided modifications presents exciting opportunities for manipulating gene expression and developing innovative therapeutic strategies.


Assuntos
RNA Guia de Sistemas CRISPR-Cas , RNA , RNA/química , Processamento Pós-Transcricional do RNA
12.
Langmuir ; 40(15): 7843-7859, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38557084

RESUMO

Two-dimensional materials have shown immense promise for gas-sensing applications due to their remarkable surface-to-volume ratios and tunable chemical properties. However, despite their potential, the utilization of ReSe2 as a gas-sensing material for nitrogen-containing molecules, including NO2, NO, and NH3, has remained unexplored. The choice of doping atoms in ReSe2 plays a pivotal role in enhancing the gas adsorption and gas-sensing capabilities. Herein, the adsorption properties of nitrogen-containing gas molecules on metal and non-metal single-atom (Au, Pt, Ni, P, and S)-doped ReSe2 monolayers have been evaluated systematically via ab initio calculations based on density functional theory. The findings strongly suggest that intrinsic ReSe2 has better selectivity toward NO2 than toward NO and NH3. Moreover, our results provide compelling evidence that all of the dopants, with the exception of S, significantly enhance both the adsorption strength and charge transfer between ReSe2 and the investigated molecules. Notably, P-decorated ReSe2 showed the highest adsorption energy for NO2 and NO (-1.93 and -1.52 eV, respectively) with charge transfer above 0.5e, while Ni-decorated ReSe2 exhibited the highest adsorption energy for NH3 (-0.76 eV). In addition, on the basis of transition theory, we found that only Au-ReSe2 and Ni-ReSe2 can serve as reusable chemiresisitve gas sensors for reliable detection of NO and NH3, respectively. Hence, our findings indicate that gas-sensing applications can be significantly improved by utilizing a single-atom-doped ReSe2 monolayer.

13.
Ann Clin Microbiol Antimicrob ; 23(1): 55, 2024 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-38886754

RESUMO

PURPOSE AND METHOD: Necrotizing tracheobronchitis is a rare clinical entity presented as a necrotic inflammation involving the mainstem trachea and distal bronchi. We reported a case of severe necrotizing tracheobronchitis caused by influenza B and methicillin-resistant Staphylococcus aureus (MRSA) co-infection in an immunocompetent patient. CASE PRESENTATION: We described a 36-year-old man with initial symptoms of cough, rigors, muscle soreness and fever. His status rapidly deteriorated two days later and he was intubated. Bronchoscopy demonstrated severe necrotizing tracheobronchitis, and CT imaging demonstrated multiple patchy and cavitation formation in both lungs. Next-generation sequencing (NGS) and bronchoalveolar lavage fluid (BALF) culture supported the co-infection of influenza B and MRSA. We also found T lymphocyte and NK lymphocyte functions were extremely suppressed during illness exacerbation. The patient was treated with antivirals and antibiotics including vancomycin. Subsequent bronchoscopy and CT scans revealed significant improvement of the airway and pulmonary lesions, and the lymphocyte functions were restored. Finally, this patient was discharged successfully. CONCLUSION: Necrotizing tracheobronchitis should be suspected in patients with rapid deterioration after influenza B infection. The timely diagnosis of co-infection and accurate antibiotics are important to effective treatment.


Assuntos
Bronquite , Coinfecção , Influenza Humana , Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Humanos , Masculino , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Coinfecção/microbiologia , Influenza Humana/complicações , Adulto , Infecções Estafilocócicas/tratamento farmacológico , Infecções Estafilocócicas/microbiologia , Infecções Estafilocócicas/diagnóstico , Infecções Estafilocócicas/complicações , Bronquite/microbiologia , Bronquite/tratamento farmacológico , Bronquite/complicações , Bronquite/diagnóstico , Bronquite/virologia , Antibacterianos/uso terapêutico , Traqueíte/microbiologia , Traqueíte/tratamento farmacológico , Traqueíte/complicações , Traqueíte/virologia , Vírus da Influenza B/isolamento & purificação , Broncoscopia , Necrose , Tomografia Computadorizada por Raios X , Líquido da Lavagem Broncoalveolar/microbiologia , Antivirais/uso terapêutico
14.
Nucleic Acids Res ; 50(D1): D279-D286, 2022 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-34747466

RESUMO

RNA polymerase III (Pol III) transcribes hundreds of non-coding RNA genes (ncRNAs), which involve in a variety of cellular processes. However, the expression, functions, regulatory networks and evolution of these Pol III-transcribed ncRNAs are still largely unknown. In this study, we developed a novel resource, Pol3Base (http://rna.sysu.edu.cn/pol3base/), to decode the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs. The current release of Pol3Base includes thousands of regulatory relationships between ∼79 000 ncRNAs and transcription factors by mining 56 ChIP-seq datasets. By integrating CLIP-seq datasets, we deciphered the interactions of these ncRNAs with >240 RNA binding proteins. Moreover, Pol3Base contains ∼9700 RNA modifications located within thousands of Pol III-transcribed ncRNAs. Importantly, we characterized expression profiles of ncRNAs in >70 tissues and 28 different tumor types. In addition, by comparing these ncRNAs from human and mouse, we revealed about 4000 evolutionary conserved ncRNAs. We also identified ∼11 403 tRNA-derived small RNAs (tsRNAs) in 32 different tumor types. Finally, by analyzing somatic mutation data, we investigated the mutation map of these ncRNAs to help uncover their potential roles in diverse diseases. This resource will help expand our understanding of potential functions and regulatory networks of Pol III-transcribed ncRNAs.


Assuntos
Bases de Dados Genéticas , Neoplasias/genética , RNA Polimerase III/genética , RNA não Traduzido/genética , Proteínas de Ligação a RNA/genética , Software , Fatores de Transcrição/genética , Animais , Mineração de Dados , Conjuntos de Dados como Assunto , Evolução Molecular , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Humanos , Internet , Camundongos , Mutação , Neoplasias/classificação , Neoplasias/metabolismo , Neoplasias/patologia , RNA Polimerase III/metabolismo , RNA de Transferência/classificação , RNA de Transferência/genética , RNA de Transferência/metabolismo , RNA não Traduzido/classificação , RNA não Traduzido/metabolismo , Proteínas de Ligação a RNA/classificação , Proteínas de Ligação a RNA/metabolismo , Fatores de Transcrição/classificação , Fatores de Transcrição/metabolismo , Transcrição Gênica
15.
Nucleic Acids Res ; 50(D1): D421-D431, 2022 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-34755848

RESUMO

tRNA-derived small RNA (tsRNA), a novel type of regulatory small noncoding RNA, plays an important role in physiological and pathological processes. However, the understanding of the functional mechanism of tsRNAs in cells and their role in the occurrence and development of diseases is limited. Here, we integrated multiomics data such as transcriptome, epitranscriptome, and targetome data, and developed novel computer tools to establish tsRFun, a comprehensive platform to facilitate tsRNA research (http://rna.sysu.edu.cn/tsRFun/ or http://biomed.nscc-gz.cn/DB/tsRFun/). tsRFun evaluated tsRNA expression profiles and the prognostic value of tsRNAs across 32 types of cancers, identified tsRNA target molecules utilizing high-throughput CLASH/CLEAR or CLIP sequencing data, and constructed the interaction networks among tsRNAs, microRNAs, and mRNAs. In addition to its data presentation capabilities, tsRFun offers multiple real-time online tools for tsRNA identification, target prediction, and functional enrichment analysis. In summary, tsRFun provides a valuable data resource and multiple analysis tools for tsRNA investigation.


Assuntos
Bases de Dados de Ácidos Nucleicos , MicroRNAs/genética , Neoplasias/genética , RNA Mensageiro/genética , Pequeno RNA não Traduzido/genética , RNA de Transferência/genética , Software , Sequenciamento de Cromatina por Imunoprecipitação , Regulação Neoplásica da Expressão Gênica , Genoma Humano , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Internet , MicroRNAs/classificação , MicroRNAs/metabolismo , Neoplasias/diagnóstico , Neoplasias/metabolismo , Neoplasias/mortalidade , Conformação de Ácido Nucleico , Prognóstico , RNA Mensageiro/classificação , RNA Mensageiro/metabolismo , Pequeno RNA não Traduzido/classificação , Pequeno RNA não Traduzido/metabolismo , RNA de Transferência/classificação , RNA de Transferência/metabolismo , Análise de Sobrevida , Transcriptoma
16.
Biochem Genet ; 2024 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-38683465

RESUMO

Ovarian cancer develops insidiously and is frequently diagnosed at advanced stages. Screening for ovarian cancer is an effective strategy for reducing mortality. This study aimed to investigate the molecular mechanisms underlying the development of ovarian cancer and identify novel tumor biomarkers for the diagnosis and prognosis of ovarian cancer. Three databases containing gene expression profiles specific to serous ovarian cancer (GSE18520, GSE12470, and GSE26712) were acquired. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were analyzed for the differentially expressed gene (DEGs). The protein-protein interaction (PPI) network was constructed using the STRING database. The pivotal genes in the PPI network were screened using the Cytoscape software. Survival curve analysis was performed using a Kaplan-Meier Plotter. The cancer genome atlas and Gene Expression Omnibus databases were used to find the relationship between Hub gene and serous ovarian cancer. PCR and immunohistochemistry were used to detect the expression of Hub gene in serous ovarian cancer tissues and cells. Downstream pathways of the candidate tumor marker genes were predicted using Gene Set Enrichment Analysis. In this study, 252 DEGs were screened for pathway enrichment. 20 Hub genes were identified. Survival analysis suggested that Aurka, Bub1b, Cenpf, Cks1b, Kif20a, Mad2l1, Racgap1, and Ube2c were associated with the survival of patients with serous ovarian cancer. MAD2L1 and BUB1B levels were significantly different in serous ovarian cancer at different stages. Finally, Mad2l1 was found to play a role in the cell cycle, oocyte meiosis, and ubiquitin-mediated proteolysis. Meanwhile, Bub1b may play a role in the cell cycle, ubiquitin-mediated proteolysis, and spliceosome processes. Mad2l1 and Bub1b could be used as markers to predict ovarian carcinogenesis and prognosis, providing candidate targets for the diagnosis and treatment of serous ovarian cancer.

17.
Sensors (Basel) ; 24(13)2024 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-39001103

RESUMO

Flexible ammonia (NH3) gas sensors have gained increasing attention for their potential in medical diagnostics and health monitoring, as they serve as a biomarker for kidney disease. Utilizing the pre-designable and porous properties of covalent organic frameworks (COFs) is an innovative way to address the demand for high-performance NH3 sensing. However, COF particles frequently encounter aggregation, low conductivity, and mechanical rigidity, reducing the effectiveness of portable NH3 detection. To overcome these challenges, we propose a practical approach using polyvinyl alcohol-carrageenan (κPVA) as a template for in the situ growth of two-dimensional COF film and particles to produce a flexible hydrogel gas sensor (COF/κPVA). The synergistic effect of COF and κPVA enhances the gas sensing, water retention, and mechanical properties. The COF/κPVA hydrogel shows a 54.4% response to 1 ppm NH3 with a root mean square error of less than 5% and full recovery compared to the low response and no recovery of bare κPVA. Owing to the dual effects of the COF film and the particles anchoring the water molecules, the COF/κPVA hydrogel remained stable after 70 h in atmospheric conditions, in contrast, the bare κPVA hydrogel was completely dehydrated. Our work might pave the way for highly sensitive hydrogel gas sensors, which have intriguing applications in flexible electronic devices for gas sensing.

18.
Nano Lett ; 23(20): 9227-9234, 2023 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-37791735

RESUMO

Crafting vacancies offers an efficient route to upgrade the selectivity and productivity of nanomaterials for CO2 electroreduction. However, defective nanoelectrocatalysts bear catalytically active vacancies mostly on their surface, with the rest of the interior atoms adiaphorous for CO2-to-product conversion. Herein, taking nanosilver as a prototype, we arouse the catalytic ability of internal atoms by creating homogeneous vacancies realized via electrochemical reconstruction of silver halides. The homogeneous vacancies-rich nanosilver, compared to the surface vacancies-dominated counterpart, features a more positive d-band center to trigger an intensified hybridization of the Ag_d orbital with the C_P orbital of the *COOH intermediate, leading to an accelerated CO2-to-CO transformation. These structural and electronic merits allow a large-area (9 cm-2) electrode to generate nearly pure CO with a CO/H2 Faradaic efficiency ratio of 6932 at an applied current of 7.5 A. These findings highlight the potential of designing new-type defects in realizing the industrialization of electrocatalytic CO2 reduction.

19.
J Environ Manage ; 365: 121490, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38917537

RESUMO

Exploring the spatiotemporal variations of vegetation net primary productivity (NPP) and analyzing the relationships between NPP and its influencing factors are vital for ecological protection in the Beijing-Tianjin-Hebei (BTH) region. In this study, we employed the CASA model in conjunction with spatiotemporal analysis techniques to estimate and analyze the spatiotemporal variations of NPP in BTH and different ecological function sub-regions over the past two decades. Subsequently, we established three scenarios (actual, climate-driven and land cover-driven) to assess the influencing factors and quantify their relative contributions. The results indicated that the overall NPP in BTH exhibited a discernible upward trend from 2000 to 2020, with a growth rate of 3.83 gC·m-2a-1. Furthermore, all six sub-regions exhibited an increase. The Bashang Plateau Ecological Protection Zone (BP) exhibited the highest growth rate (5.03 gC·m-2a-1), while the Low Plains Ecological Restoration Zone (LP) exhibited the lowest (2.07 gC·m-2a-1). Geographically, the stability of NPP exhibited a spatial pattern of gradual increase from west to east. Climate and land cover changes collectively increased NPP by 0.04 TgC·a-1 and 0.07 TgC·a-1, respectively, in the BTH region. Climate factors were found to have the greatest influence on NPP variations, contributing 40.49% across the BTH region. This influence exhibited a decreasing trend from northwest to southeast, with precipitation identified as the most influential climatic factor compared to temperature and solar radiation. Land cover change has profound effects on ecosystems, which is an important factor on NPP. From 2000 to 2020, 15.45% area of the BTH region underwent land cover type change, resulting in a total increase in NPP of 1.33 TgC. The conversion of grass into forest brought about the 0.89 TgC increase in NPP, which is the largest of all change types. In the area where land cover had undergone change, the land cover factor has been found to be the dominant factor influencing variations in NPP, with an average contribution of 49.37%. In contrast, in the south-central area where there has been no change in land cover, the residual factor has been identified as the most influential factor influencing variations in NPP. Our study highlights the important role of land cover change in influencing NPP variations in BTH. It also offers a novel approach to elucidating the influences of diverse factors on NPP, which is crucial for the scientific assessment of vegetation productivity and carbon sequestration capacity.


Assuntos
Clima , Pequim , Ecossistema , Conservação dos Recursos Naturais , China
20.
Angew Chem Int Ed Engl ; : e202409094, 2024 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-38806443

RESUMO

Supramolecular artificial light-harvesting system with highly efficient host-guest energy transfer pathway provides an ideal platform for optimizing the photochemistry process. The consecutive photo-induced electron transfer (conPET) process overcomes the energy limitation of visible-light photocatalysis, but is often compromised by mismatching between the absorption of ground state dye and its radical, weakening the efficiency of photoredox reaction. By encapsulating a conPET photocatalyst rhodamine 6G into metal-organic cage, the supramolecular approach was undertaken to tackle the intrinsic difficulty of matching the light absorption of photoexcitation between rhodamine 6G and its radical. The highly efficient Förster resonance energy transfer from the photoexcited cage to rhodamine 6G forced by host-guest encapsulation facilitates the conPET process for the single-wavelength light-driven activation of aryl halides by stabilizing and accelerating the production and accumulation of the rhodamine 6G radical intermediate. The tunable and flexible nature of the supramolecular host-guest complex renders the cage-based encapsulation strategy promising for the development of ideal photocatalysts toward the better utilization of solar energy.

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