Long non-coding RNAs(lncRNAs),which represent a new frontier in molecular biology,play important roles in regulating gene expression at epigenetic,transcriptional and post-transcriptional levels.More and more lncRNAs ...Long non-coding RNAs(lncRNAs),which represent a new frontier in molecular biology,play important roles in regulating gene expression at epigenetic,transcriptional and post-transcriptional levels.More and more lncRNAs have been found to play important roles in normal cell physiological activities,and participate in the development of varieties of tumors and other diseases.Previously,we have only been able to determine the function of lncRNAs through multiple mechanisms,including genetic imprinting,chromatin remodeling,splicing regulation,mRNA decay,and translational regulation.Application of technological advances to research into the function of lncRNAs is extremely important.The major tools for exploring lncRNAs include microarrays,RNA sequencing(RNA-seq),Northern blotting,real-time quantitative reverse transcription-polymerase chain reaction(qRT-PCR),fluorescence in situ hybridization(FISH),RNA interference(RNAi),RNA-binding protein immunoprecipitation(RIP),chromatin isolation by RNA purification(ChIRP),crosslinking-immunopurification(CLIP),and bioinformatic prediction.In this review,we highlight the functions of lncRNAs,and advanced methods to research lncRNA-protein interactions.展开更多
Background:Resistance to ferroptosis,a regulated cell death caused by irondependent excessive accumulation of lipid peroxides,has recently been linked to lung adenocarcinoma(LUAD).Intracellular antioxidant systems are...Background:Resistance to ferroptosis,a regulated cell death caused by irondependent excessive accumulation of lipid peroxides,has recently been linked to lung adenocarcinoma(LUAD).Intracellular antioxidant systems are required for protection against ferroptosis.The purpose of the present studywas to investigate whether and how extracellular system desensitizes LUAD cells to ferroptosis.Methods:Established human lung fibroblasts MRC-5,WI38,and human LUAD H1650,PC9,H1975,H358,A549,and H1299 cell lines,tumor and matched normal adjacent tissues of LUAD,and plasma from healthy individuals and LUAD patients were used in this study.Immunohistochemistry and immunoblotting were used to analyze protein expression,and quantitative reverse transcription-PCR was used to analyze mRNA expression.Cell viability,cell death,and the lipid reactive oxygen species generationwere measured to evaluate the responses to ferroptosis.Exosomes were observed using transmission electron microscope.The localization of arachidonic acid(AA)was detected using click chemistry labeling followed by confocal microscopy.Interactions between RNAs and proteins were detected using RNA pull-down,RNA immunoprecipitation and photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation methods.Proteomic analysis was used to investigate RNA-regulated proteins,and metabolomic analysis was performed to analyze metabolites.Cellderived xenograft,patient-derived xenograft,cell-implanted intrapulmonary LUAD mouse models and plasma/tissue specimens from LUAD patients were used to validate the molecular mechanism.Results:Plasma exosome from LUAD patients specifically reduced lipid peroxidation and desensitized LUAD cells to ferroptosis.A potential explanation is that exosomal circRNA_101093(cir93)maintained an elevation in intracellular cir93 in LUAD to modulate AA,a poly-unsaturated fatty acid critical for ferroptosisassociated increased peroxidation in the plasma membrane.Mechanistically,cir93 interacted with and increased fatty acid-binding protei展开更多
Elucidating protein translational regulation is crucial for understanding cellular function and drug development.A key molecule in protein translation is ribosome,which is a super-molecular complex extensively studied...Elucidating protein translational regulation is crucial for understanding cellular function and drug development.A key molecule in protein translation is ribosome,which is a super-molecular complex extensively studied for more than a half century.The structure and dynamics of ribosome complexes were resolved recently thanks to the development of X-ray crystallography,Cryo-EM,and single molecule biophysics.Current studies of the ribosome have shown multiple functional states,each with a unique conformation.In this study,we analyzed the RNA-protein distances of ribosome(2.5 MDa)complexes and compared these changes among different ribosome complexes.We found that the RNA-protein distance is significantly correlated with the ribosomal functional state.Thus,the analysis of RNA-protein binding distances at important functional sites can distinguish ribosomal functional states and help understand ribosome functions.In particular,the mechanism of translational attenuation by nascent peptides and antibiotics was revealed by the conformational changes of local functional sites.展开更多
Cells use various RNA (Ribonucleic Acid) regulatory mechanisms in order to temporally and coordinately influence the rate of protein synthesis. A deeper understanding of the dynamics of RNA regulation can ultimately...Cells use various RNA (Ribonucleic Acid) regulatory mechanisms in order to temporally and coordinately influence the rate of protein synthesis. A deeper understanding of the dynamics of RNA regulation can ultimately bridge the gap between transcriptional control and protein expression. The nonlinear process of RNA-Protein Interaction (RIP), which can be viewed as the RNA analog of the better-known chromatin immunoprecipitation application (CHIP) plays a crucial role in post-transcriptional regulation of gene expression. While ChIP identifies DNA (Deoxyribonucleic Acid) targets of DNA-binding proteins in their cellular context, RIP can be used to identify specific RNA molecules associated with specific nuclear or cytoplasmic RNA-binding proteins. In this paper, a stochastic model in BioAmbients calculus for the protein synthesis and activation through RIP process is presemed.展开更多
基金supported by the National Basic Research Program of China(2010CB912801,2013CB910801)National High Technology Research and Development Program of China(2012AA022501)National Natural Science Foundation of China(31070702,31270836)
文摘Long non-coding RNAs(lncRNAs),which represent a new frontier in molecular biology,play important roles in regulating gene expression at epigenetic,transcriptional and post-transcriptional levels.More and more lncRNAs have been found to play important roles in normal cell physiological activities,and participate in the development of varieties of tumors and other diseases.Previously,we have only been able to determine the function of lncRNAs through multiple mechanisms,including genetic imprinting,chromatin remodeling,splicing regulation,mRNA decay,and translational regulation.Application of technological advances to research into the function of lncRNAs is extremely important.The major tools for exploring lncRNAs include microarrays,RNA sequencing(RNA-seq),Northern blotting,real-time quantitative reverse transcription-polymerase chain reaction(qRT-PCR),fluorescence in situ hybridization(FISH),RNA interference(RNAi),RNA-binding protein immunoprecipitation(RIP),chromatin isolation by RNA purification(ChIRP),crosslinking-immunopurification(CLIP),and bioinformatic prediction.In this review,we highlight the functions of lncRNAs,and advanced methods to research lncRNA-protein interactions.
基金National Natural Science Foundation of China,Grant/Award Numbers:81871907,81822029,81872288,82173015,81902315,81902869,81774291ShanghaiMunicipal Education Commission-Gaofeng Clinical Medicine,Grant/Award Number:20191834+5 种基金Project of Clinical Research Supporting SystemClinical Medicine First-class DisciplineShanghai Municipal Education Commission and Shanghai Education Development Foundation,Grant/Award Number:18CG16Shanghai Sailing Program,Grant/Award Number:19YF1444800Science and technology commission of Shanghai municipality project,Grant/Award Numbers:19140902600,21140902800Shanghai ChestHospital,Grant/Award Numbers:2018YNJCM01,2019YNJCM06,2021YNZYJ01,2021YNZYY01,2021YNZYY02。
文摘Background:Resistance to ferroptosis,a regulated cell death caused by irondependent excessive accumulation of lipid peroxides,has recently been linked to lung adenocarcinoma(LUAD).Intracellular antioxidant systems are required for protection against ferroptosis.The purpose of the present studywas to investigate whether and how extracellular system desensitizes LUAD cells to ferroptosis.Methods:Established human lung fibroblasts MRC-5,WI38,and human LUAD H1650,PC9,H1975,H358,A549,and H1299 cell lines,tumor and matched normal adjacent tissues of LUAD,and plasma from healthy individuals and LUAD patients were used in this study.Immunohistochemistry and immunoblotting were used to analyze protein expression,and quantitative reverse transcription-PCR was used to analyze mRNA expression.Cell viability,cell death,and the lipid reactive oxygen species generationwere measured to evaluate the responses to ferroptosis.Exosomes were observed using transmission electron microscope.The localization of arachidonic acid(AA)was detected using click chemistry labeling followed by confocal microscopy.Interactions between RNAs and proteins were detected using RNA pull-down,RNA immunoprecipitation and photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation methods.Proteomic analysis was used to investigate RNA-regulated proteins,and metabolomic analysis was performed to analyze metabolites.Cellderived xenograft,patient-derived xenograft,cell-implanted intrapulmonary LUAD mouse models and plasma/tissue specimens from LUAD patients were used to validate the molecular mechanism.Results:Plasma exosome from LUAD patients specifically reduced lipid peroxidation and desensitized LUAD cells to ferroptosis.A potential explanation is that exosomal circRNA_101093(cir93)maintained an elevation in intracellular cir93 in LUAD to modulate AA,a poly-unsaturated fatty acid critical for ferroptosisassociated increased peroxidation in the plasma membrane.Mechanistically,cir93 interacted with and increased fatty acid-binding protei
基金partially supported by National Institute of Health(R21/R33-GM078601 and R01-GM100701)National Science Foundation(MCB-1151343)in the US
文摘Elucidating protein translational regulation is crucial for understanding cellular function and drug development.A key molecule in protein translation is ribosome,which is a super-molecular complex extensively studied for more than a half century.The structure and dynamics of ribosome complexes were resolved recently thanks to the development of X-ray crystallography,Cryo-EM,and single molecule biophysics.Current studies of the ribosome have shown multiple functional states,each with a unique conformation.In this study,we analyzed the RNA-protein distances of ribosome(2.5 MDa)complexes and compared these changes among different ribosome complexes.We found that the RNA-protein distance is significantly correlated with the ribosomal functional state.Thus,the analysis of RNA-protein binding distances at important functional sites can distinguish ribosomal functional states and help understand ribosome functions.In particular,the mechanism of translational attenuation by nascent peptides and antibiotics was revealed by the conformational changes of local functional sites.
文摘Cells use various RNA (Ribonucleic Acid) regulatory mechanisms in order to temporally and coordinately influence the rate of protein synthesis. A deeper understanding of the dynamics of RNA regulation can ultimately bridge the gap between transcriptional control and protein expression. The nonlinear process of RNA-Protein Interaction (RIP), which can be viewed as the RNA analog of the better-known chromatin immunoprecipitation application (CHIP) plays a crucial role in post-transcriptional regulation of gene expression. While ChIP identifies DNA (Deoxyribonucleic Acid) targets of DNA-binding proteins in their cellular context, RIP can be used to identify specific RNA molecules associated with specific nuclear or cytoplasmic RNA-binding proteins. In this paper, a stochastic model in BioAmbients calculus for the protein synthesis and activation through RIP process is presemed.