Endometritis(inflammation of the endometrial lining) is one of the most devastating reproductive diseases in dairy cattle, resulting in substantial production loss and causing more than $650 million in lost revenue an...Endometritis(inflammation of the endometrial lining) is one of the most devastating reproductive diseases in dairy cattle, resulting in substantial production loss and causing more than $650 million in lost revenue annually in the USA.We hypothesize that alternative polyadenylation(APA) sites serve as decisive sensors for endometrium health and disease in dairy cows. Endometrial cells collected from 18 cows with purulent vaginal discharge scored 0 to 2 were used for APA profiling with our whole transcriptome termini site sequencing(WTTS-seq) method. Overall, pathogens trigger hosts to use more differentially expressed APA(DE-APA), more intronic DE-APA, more DE-APA sites per gene and more DE-genes associated with inflammation. Host CD59 molecule(CD59), Fc fragment of IgG receptor IIa(FCGR2A), lymphocyte antigen 75(LY75) and plasminogen(PLG) may serve as initial contacts or combats with pathogens on cell surface, followed by activation of nuclear receptor subfamily 1 group H member 4(NR1H4) to regulate AXL receptor tyrosine kinase(AXL), FGR proto-oncogene, Src family tyrosine kinase(FGR), HCK protooncogene, Src family tyrosine kinase(HCK) and integrin subunit beta 2(ITGB2) for anti-inflammation. This study is the first to show significance of cilium pathways in endometrium health and animal reproduction. MIR21 and MIR30A would be perfect antagonistic biomarkers for diagnosis of either inflammation or anti-inflammation. These novel findings will set precedent for future genomic studies to aid the dairy industry develop new strategies to reduce endometritis incidence and improve fertility.展开更多
Aberrant alternative polyadenylation(APA)events play an important role in cancers,but little is known about whether APA-related genetic variants contribute to the susceptibility to bladder cancer.Previous genome-wide ...Aberrant alternative polyadenylation(APA)events play an important role in cancers,but little is known about whether APA-related genetic variants contribute to the susceptibility to bladder cancer.Previous genome-wide association study performed APA quantitative trait loci(apaQTL)analyses in bladder cancer,and identified 17955 single nucleotide polymorphisms(SNPs).We found that gene symbols of APA affected by apaQTL-associated SNPs were closely correlated with cancer signaling pathways,high mutational burden,and immune infiltration.Association analysis showed that apaQTL-associated SNPs rs34402449 C>A,rs2683524 C>T,and rs11540872 C>G were significantly associated with susceptibility to bladder cancer(rs34402449:OR=1.355,95%confidence interval[CI]:1.159-1.583,P=1.33×10^(−4);rs2683524:OR=1.378,95%CI:1.164-1.632,P=2.03×10^(−4);rs11540872:OR=1.472,95%CI:1.193-1.815,P=3.06×10^(−4)).Cumulative effect analysis showed that the number of risk genotypes and smoking status were significantly associated with an increased risk of bladder cancer(P_(trend)=2.87×10^(−12)).We found that PRR13,being demonstrated the most significant effect on cell proliferation in bladder cancer cell lines,was more highly expressed in bladder cancer tissues than in adjacent normal tissues.Moreover,the rs2683524 T allele was correlated with shorter 3′untranslated regions of PRR13 and increased PRR13 expression levels.Collectively,our findings have provided informative apaQTL resources and insights into the regulatory mechanisms linking apaQTL-associated variants to bladder cancer risk.展开更多
Objective:To review alternative polyadenylation(APA)as a mechanism of gene regulation and consider potential roles for APA in prostate cancer(PCa)biology and treatment.Methods:An extensive review of mRNA polyadenylati...Objective:To review alternative polyadenylation(APA)as a mechanism of gene regulation and consider potential roles for APA in prostate cancer(PCa)biology and treatment.Methods:An extensive review of mRNA polyadenylation,APA,and PCa literature was performed.This review article introduces APA and its association with human disease,outlines the mechanisms and components of APA,reviews APA in cancer biology,and considers whether APA may contribute to PCa progression and/or produce novel biomarkers and therapeutic targets for PCa.Results:Eukaryotic mRNA 30-end cleavage and polyadenylation play a critical role in gene expression.Most human genes encode more than one polyadenylation signal,and produce more than one transcript isoform,through APA.Polyadenylation can occur throughout the gene body to generate transcripts with differing 30-termini and coding sequence.Differences in 30-untranslated regions length can modify post-transcriptional gene regulation by microRNAs and RNA binding proteins,and alter mRNA stability,translation efficiency,and subcellular localization.Distinctive APA patterns are associated with human diseases,tissue origins,and changes in cellular proliferation rate and differentiation state.APA events may therefore generate unique mRNA biomarkers or therapeutic targets in certain cancer types or phenotypic states.Conclusions:The full extent of cancer-associated and tissue-specific APA events have yet to be defined,and the mechanisms and functional consequences of APA in cancer remain incompletely understood.There is evidence that APA is active in PCa,and that it may be an untapped resource for PCa biomarkers or therapeutic targets.展开更多
hap , a novel human apoptosis inducing gene which can interact with another newly discovered apoptosis inducing gene ASY, was identified by cloning its cDNAs from human lung cell line (WI 38) cDNA library. Two major m...hap , a novel human apoptosis inducing gene which can interact with another newly discovered apoptosis inducing gene ASY, was identified by cloning its cDNAs from human lung cell line (WI 38) cDNA library. Two major mRNA species (1.8 and 2.7 kb in length, respectively) were previously identified by Northern blot analysis of poly(A) + RNA from human multiple tissues using partial hap cDNA as a probe. In the present work, the molecular mechanism accounting for the generation of the two hap transcripts were investigated. The rapid amplification of cDNA 3’\|ends (3’ RACE) technique and the sequential Southern blot analysis, in conjunction with the sequencing analysis demonstrated that the two hap transcripts derive from the alternative polyadenylation site selection: a AATAAA signal at position 1 528 1 533 nt for the 1.8 kb hap mRNA; and a AATAAA signal at position 2 375 2 380 nt for the 2.7 kb hap mRNA. Furthermore, a number of regulatory elements within hap 3’ untranslated region (3’\|UTR) were also examined.展开更多
The mRNA polyadenylation plays essential function in regulation of mRNA metabolism.Mis-regulations of mRNA polyadenylation are frequently linked with aberrant gene expression and disease progression.Under the action o...The mRNA polyadenylation plays essential function in regulation of mRNA metabolism.Mis-regulations of mRNA polyadenylation are frequently linked with aberrant gene expression and disease progression.Under the action of polyadenylate polymerase,poly(A)tail is synthesized after the polyadenylation signal(PAS)sites on the mRNAs.Alternative polyadenylation(APA)often occurs in mRNAs with multiple poly(A)sites,producing different 3'ends for transcript variants,and therefore plays important functions in gene expression regulation.In this review,we first summarize the classical process of mRNA 3'-terminal formation and discuss the length control mechanisms of poly(A)innucleus and cytoplasm.Thenwe review the research progress on alternative polyadenylation regulation and the APA site selection mechanism.Finally,we summarize the functional roles of APA in the regulation of gene expression and diseases including cancers.展开更多
Alternative polyadenylation(APA)contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases.Singlecell RNA sequencing(scRNA-seq)has enabled...Alternative polyadenylation(APA)contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases.Singlecell RNA sequencing(scRNA-seq)has enabled the profiling of APA at the single-cell level;however,the spatial information of cells is not preserved in scRNA-seq.Alternatively,spatial transcriptomics(ST)technologies provide opportunities to decipher the spatial context of the transcriptomic landscape.Pioneering studies have revealed potential spatially variable genes and/or splice isoforms;however,the pattern of APA usage in spatial contexts remains unappreciated.In this study,we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatially barcoded ST data.APA sites were identified and quantified from the ST data.In particular,an imputation model based on the k-nearest neighbors algorithm was designed to recover APA signals,and then APA genes with spatial patterns of APA usage variation were identified.By analyzing wellestablished ST data of the mouse olfactory bulb(MOB),we presented a detailed view of spatial APA usage across morphological layers of the MOB.We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers.By extending this analysis to two additional replicates of the MOB ST data,we observed that the spatial APA patterns of several genes were reproducible among replicates.stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution.This toolkit is available at https://github.com/BMILAB/stAPAminer and https://ngdc.cncb.ac.cn/biocode/tools/BT007320.展开更多
Alternative polyadenylation(APA)plays important roles in modulating mRNA stability,translation,and subcellular localization,and contributes extensively to shaping eukaryotic transcriptome complexity and proteome diver...Alternative polyadenylation(APA)plays important roles in modulating mRNA stability,translation,and subcellular localization,and contributes extensively to shaping eukaryotic transcriptome complexity and proteome diversity.Identification of poly(A)sites(pAs)on a genomewide scale is a critical step toward understanding the underlying mechanism of APA-mediated gene regulation.A number of established computational tools have been proposed to predict pAs from diverse genomic data.Here we provided an exhaustive overview of computational approaches for predicting pAs from DNA sequences,bulk RNA sequencing(RNA-seq)data,and single-cell RNA sequencing(scRNA-seq)data.Particularly,we examined several representative tools using bulk RNA-seq and scRNA-seq data from peripheral blood mononuclear cells and put forward operable suggestions on how to assess the reliability of pAs predicted by different tools.We also proposed practical guidelines on choosing appropriate methods applicable to diverse scenarios.Moreover,we discussed in depth the challenges in improving the performance of pA prediction and benchmarking different methods.Additionally,we highlighted outstanding challenges and opportunities using new machine learning and integrative multi-omics techniques,and provided our perspective on how computational methodologies might evolve in the future for non-30 untranslated region,tissuespecific,cross-species,and single-cell pA prediction.展开更多
Alternative polyadenylation(APA)is a molecular process that generates diversity at the 3′end of RNA polymeraseⅡtranscripts from over 60%of human genes.APA is derived from the existence of multiple polyadenylation si...Alternative polyadenylation(APA)is a molecular process that generates diversity at the 3′end of RNA polymeraseⅡtranscripts from over 60%of human genes.APA is derived from the existence of multiple polyadenylation signals(PAS)within the same transcript,and results in the differential inclusion of sequence information at the 3′end.While APA can occur between two PASs allowing for generation of transcripts with distinct coding potential from a single gene,most APA occurs within the untranslated region(3′UTR)and changes the length and content of these non-coding sequences.APA within the 3′UTR can have tremendous impact on its regulatory potential of the mRNA through a variety of mechanisms,and indeed this layer of gene expression regulation has profound impact on processes vital to cell growth and development.Recent studies have particularly highlighted the importance of APA dysregulation in cancer onset and progression.Here,we review the current knowledge of APA and its impacts on mRNA stability,translation,localization and protein localization.We also discuss the implications of APA dysregulation in cancer research and therapy.展开更多
N6-methyladenosine(m^(6)A),a ubiquitous internal modification of eukaryotic mRNAs,plays a vital role in almost every aspect of mRNA metabolism.However,there is little evidence documenting the role of m^(6)A in regulat...N6-methyladenosine(m^(6)A),a ubiquitous internal modification of eukaryotic mRNAs,plays a vital role in almost every aspect of mRNA metabolism.However,there is little evidence documenting the role of m^(6)A in regulating alternative polyadenylation(APA)in plants.APA is controlled by a large protein-RNA complex with many components,including CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30(CPSF30).In Arabidopsis,CPSF30 has two isoforms and the longer isoform(CPSF30-L)contains a YT512-B Homology(YTH)domain,which is unique to plants.In this study,we showed that CPSF30-L YTH domain binds to m^(6)A in v itro.In the cpsf30-2 mutant,the transcripts of many genes including several important nitrate signaling-related genes had shifts in polyadenylation sites that were correlated with m^(6)A peaks,indicating that these gene transcripts carrying m^(6)A tend to be regulated by APA.Wild-type CPSF30-L could rescue the defects in APA and nitrate metabolism in cpsf30-2,but m^(6)A-binding-defective mutants of CPSF30-L could not.Taken together,our results demonstrated that m^(6)A modification regulates APA in Arabidops is and revealed that the m^(6)A reader CPSF30-L affects nitrate signaling by controlling APA,shedding new light on the roles of the m^(6)A modification during RNA 3-end processing in nitrate metabolism.展开更多
The biological functions of the epitranscriptomic modification N^(6)-methyladenosine(m^(6)A)in plants are not fully understood.CPSF30-L is a predominant isoform of the polyadenylation factor CPSF30 and consists of CPS...The biological functions of the epitranscriptomic modification N^(6)-methyladenosine(m^(6)A)in plants are not fully understood.CPSF30-L is a predominant isoform of the polyadenylation factor CPSF30 and consists of CPSF30-S and an m^(6)A-binding YTH domain.Little is known about the biological roles of CPSF30-L and the molecular mechanism underlying its m^(6)A-binding function in alternative polyadenylation.Here,we charac-terized CPSF30-L as an Arabidopsis m^(6)A reader whose m^(6)A-binding function is required for the floral tran-sition and abscisic acid(ABA)response.We found that the m^(6)A-binding activity of CPSF30-L enhances the formation of liquid-like nuclear bodies,where CPSF30-L mainly recognizes m*A-modified far-upstream elements to control polyadenylation site choice.Deficiency of CPSF30-L lengthens the 3'untranslated region of three phenotypes-related transcripts,thereby accelerating their mRNA degradation and leading to late flowering and ABA hypersensitivity.Collectively,this study uncovers a new molecular mechanism for m^(6)A-driven phase separation and polyadenylation in plants.展开更多
Alternative polyadenylation(APA), a phenomenon that RNA molecules with different 30 ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expressi...Alternative polyadenylation(APA), a phenomenon that RNA molecules with different 30 ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expression. In the present review, we first summarized various methods prevalently adopted in APA study, mainly focused on the next-generation sequencing(NGS)-based techniques specially designed for APA identification, the related bioinformatics methods, and the strategies for APA study in single cells. Then we summarized the main findings and advances so far based on these methods, including the preferences of alternative poly A(pA) site, the biological processes involved, and the corresponding consequences. We especially categorized the APA changes discovered so far and discussed their potential functions under given conditions, along with the possible underlying molecular mechanisms. With more in-depth studies on extensive samples,more signatures and functions of APA will be revealed, and its diverse roles will gradually heave in sight.展开更多
In the sexually reproductive organisms, gametes are produced by meiosis following a limited mitotic amplification. However, the intrinsic program switching cells from mitotic to meiotic cycle is unclear.Alternative po...In the sexually reproductive organisms, gametes are produced by meiosis following a limited mitotic amplification. However, the intrinsic program switching cells from mitotic to meiotic cycle is unclear.Alternative polyadenylation(APA) is a highly conserved means of gene regulation and is achieved by the RNA 30-processing machinery to generate diverse 30 UTR profiles. In Drosophila spermatogenesis, we observed distinct profiles of transcriptome-wide 30 UTR between mitotic and meiotic cells. In mutant germ cells stuck in mitosis, 30 UTRs of hundreds of genes were consistently shifted. Remarkably, altering the levels of multiple 30-processing factors disrupted germline's progression to meiosis, indicative of APA's active role in this transition. An RNA-binding protein(RBP) Tut could directly bind 30 UTRs of 30-processing factors whose expressions were repressed in the presence of Tut-containing complex. Further,we demonstrated that this RBP complex could execute the repression post-transcriptionally by recruiting CCR4/Twin of deadenylation complex. Thus, we propose that an RBP complex regulates the dynamic APA profile to promote the mitosis-to-meiosis transition.展开更多
N^(6)-methyladenosine(m^(6)A) modification affects the post-transcriptional regulation of eukaryotic gene expression, but the underlying mechanisms and their effects in plants remain largely unknown. Here,we report th...N^(6)-methyladenosine(m^(6)A) modification affects the post-transcriptional regulation of eukaryotic gene expression, but the underlying mechanisms and their effects in plants remain largely unknown. Here,we report that the N^(6)-adenine methyltransferase-like domain-containing protein ENHANCED DOWNY MILDEW 2-LIKE(OsEDM2 L) is essential for rice(Oryza sativa L.) anther development. The osedm2 l knockout mutant showed delayed tapetal programmed cell death(PCD) and defective pollen development. OsEDM2 L interacts with the transcription factors basic helix-loop-helix 142 and TAPETUMDEGENERATIONRETARDATIONto regulate the expression of ETERNAL TAPETUM 1(EAT1), a positive regulator of tapetal PCD. Mutation of OsEDM2 L altered the transcriptomic m^(6)A landscape, and caused a distinct m^(6)A modification of the EAT1 transcript leading to dysregulation of its alternative splicing and polyadenylation, followed by suppression of the EAT1 target genes OsAP25 and OsAP37 for tapetal PCD. Therefore, OsEDM2 L is indispensable for proper messenger RNA m^(6)A modification in rice anther development.展开更多
Alternative polyadenylation(APA)is a crucial step in post-transcriptional regulation.Previous bioinformatic studies have mainly focused on the recognition of polyadenylation sites(PASs)in a given genomic sequence,whic...Alternative polyadenylation(APA)is a crucial step in post-transcriptional regulation.Previous bioinformatic studies have mainly focused on the recognition of polyadenylation sites(PASs)in a given genomic sequence,which is a binary classification problem.Recently,computational methods for predicting the usage level of alternative PASs in the same gene have been proposed.However,all of them cast the problem as a non-quantitative pairwise comparison task and do not take the competition among multiple PASs into account.To address this,here we propose a deep learning architecture,Deep Regulatory Code and Tools for Alternative Polyadenylation(DeeReCT-APA),to quantitatively predict the usage of all alternative PASs of a given gene.To accommodate different genes with potentially different numbers of PASs,DeeReCT-APA treats the problem as a regression task with a variable-length target.Based on a convolutional neural network-long short-term memory(CNN-LSTM)architecture,DeeReCT-APA extracts sequence features with CNN layers,uses bidirectional LSTM to explicitly model the interactions among competing PASs,and outputs percentage scores representing the usage levels of all PASs of a gene.In addition to the fact that only our method can quantitatively predict the usage of all the PASs within a gene,we show that our method consistently outperforms other existing methods on three different tasks for which they are trained:pairwise comparison task,highest usage prediction task,and ranking task.Finally,we demonstrate that our method can be used to predict the effect of genetic variations on APA patterns and sheds light on future mechanistic understanding in APA regulation.Our code and data are available at https://github.com/lzx325/DeeReCT-APA-repo.展开更多
In eukaryotic cells,both alternative splicing and alternative polyadenylation(APA)play essential roles in the gene regulation network.U1 small ribonucleoprotein particle(U1 snRNP)is a major component of spliceosome,an...In eukaryotic cells,both alternative splicing and alternative polyadenylation(APA)play essential roles in the gene regulation network.U1 small ribonucleoprotein particle(U1 snRNP)is a major component of spliceosome,and U1 snRNP complex can suppress proximal APA sites through crosstalking with 3end processing factors.However,here we show that both knockdown and overexpression of SNRPA,SNRPC,SNRNP70,and SNRPD2,the U1 snRNP proteins,promote the usage of proximal APA sites at the transcriptome level.SNRNP70 can drive the phase transition of PABPN1 from droplet to aggregate,which may reduce the repressive effects of PABPN1 on the proximal APA sites.Additionally,SNRNP70 can also promote the proximal APA sites by recruiting CPSF6,suggesting that the function of CPSF6 on APA is related with other RNA-binding proteins and cell context-dependent.Consequently,these results reveal that,on the contrary to U1 snRNP complex,the free proteins of U1 snRNP complex can promote proximal APA sites through the interaction with 3end processing machinery.展开更多
Background:Genome-wide association studies(GWAS)have identified thousands of genomic non-coding variants statistically associated with many human traits and diseases,including cancer.However,the functional interpretat...Background:Genome-wide association studies(GWAS)have identified thousands of genomic non-coding variants statistically associated with many human traits and diseases,including cancer.However,the functional interpretation of these non-coding variants remains a significant challenge in the post-GWAS era.Alternative polyadenylation(APA)plays an essential role in post-transcriptional regulation for most human genes.By employing different poly(A)sites,genes can either shorten or extend the 3'-UTRs that contain cu-regulatory elements such as miRNAs or RNA-binding protein binding sites.Therefore,APA can affect the mRNA stability,translation,and cellular localization of proteins.Population-scale studies have revealed many inherited genetic variants that potentially impact APA to further influence disease susceptibility and phenotypic diversity,but systematic computational investigations to delineate the connections are in their earliest states.Results:Here,we discuss the evolving definitions of the genetic basis of APA and the modern genomics tools to identify,characterize,and validate the genetic influences of APA events in human populations.We also explore the emerging and surprisingly complex molecular mechanisms that regulate APA and summarize the genetic control of APA that is associated with complex human diseases and traits.Conclusion:APA is an intermediate molecular phenotype that can translate human common non-coding variants to individual phenotypic variability and disease susceptibility.展开更多
BACKGROUND Extensive evidence has illustrated the promotive role of integrin binding sialoprotein(IBSP)in the progression of multiple cancers.However,little is known about the functions of IBSP in gastric cancer(GC)pr...BACKGROUND Extensive evidence has illustrated the promotive role of integrin binding sialoprotein(IBSP)in the progression of multiple cancers.However,little is known about the functions of IBSP in gastric cancer(GC)progression.AIM To investigate the mechanism underlying the regulatory effects of IBSP in GC progression,and the relationship between IBSP and cleavage and polyadenylation factor 6(CPSF6)in this process.METHODS The mRNA and protein expression of relevant genes were assessed through realtime quantitative polymerase chain reaction and Western blot,respectively.Cell viability was evaluated by Cell Counting Kit-8 assay.Cell invasion and migration were evaluated by Transwell assay.Pyroptosis was measured by flow cytometry.The binding between CPSF6 and IBSP was confirmed by luciferase reporter and RNA immunoprecipitation(RIP)assays.RESULTS IBSP exhibited higher expression in GC tissues and cell lines than in normal tissues and cell lines.IBSP knockdown suppressed cell proliferation,migration,and invasion but facilitated pyroptosis.In the exploration of the regulatory mechanism of IBSP,potential RNA binding proteins for IBSP were screened with catRAPID omics v2.0.The RNA-binding protein CPSF6 was selected due to its higher expression in stomach adenocarcinoma.Luciferase reporter and RIP assays revealed that CPSF6 binds to the 3’-untranslated region of IBSP and regulates its expression.Knockdown of CPSF6 inhibited cell proliferation,migration,and invasion but boosted pyroptosis.Through rescue assays,it was uncovered that the retarded GC progression mediated by CPSF6 knockdown was reversed by IBSP overexpression.CONCLUSION Our study highlighted the vital role of the CPSF6/IBSP axis in GC,suggesting that IBSP might be an effective biotarget for GC treatment.展开更多
The control of the half-life of m RNA plays a central role in normal development and in disease progression. Several pathological conditions, such as breast cancer, correlate with deregulation of the half-life of m RN...The control of the half-life of m RNA plays a central role in normal development and in disease progression. Several pathological conditions, such as breast cancer, correlate with deregulation of the half-life of m RNA encoding growth factors, oncogenes, cell cycle regulators and inflammatory cytokines that participate in cancer. Substantial stability means that a m RNA will be available for translation for a longer time, resulting in high levels of protein gene products, which may lead to prolonged responses that subsequently result in over-production of cellular mediators that participate in cancer. The stability of these m RNA is regulated at the 3'UTR level by different mechanisms involving m RNA binding proteins, micro-RNA, long non-coding RNA and alternative polyadenylation. All these events are tightly interconnected to each other and lead to steady state levels of target m RNAs. Compelling evidence also suggests that both m RNA binding proteins and regulatory RNAswhich participate to m RNA half-life regulation may be useful prognostic markers in breast cancers, pointing to a potential therapeutic approach to treatment of patients with these tumors. In this review, we summarize the main mechanisms involved in the regulation of m RNA decay and discuss the possibility of its implication in breast cancer aggressiveness and the efficacy of targeted therapy.展开更多
Transcription termination of nearly all protein-coding genes in mammals requires 3’end processing by a multiprotein complex that will cleave and polyadenylate the messenger RNA precursor.Because a variety of enzyme c...Transcription termination of nearly all protein-coding genes in mammals requires 3’end processing by a multiprotein complex that will cleave and polyadenylate the messenger RNA precursor.Because a variety of enzyme complexes intervene,3’end processing was thought to be fundamentally complex and subject to a multitude of regulatory effects.The possibility to select just one out of several polyadenylation sites,in particular,has caused much questioning and speculation.What appear to be separate mechanisms however can be combined into a defined set of rules,allowing for a relatively simple interpretation of 3’end processing.Ultimately,readiness of the terminal exon splice site determines when a transcript reaches the maturity to select a nearby polyadenylation signal.Transcriptional pausing then acts in concert,extending the timeframe during which the transcription complex is close to polyadenylation sites.Since RNA polymerase pausing is governed by the same type of sequences in bacteria and metazoans,mammalian transcription termination resembles its prokaryote counterpart more than generally thought.展开更多
Nuclear RNA processing requires dynamic and intricately regulated machinery composed of multiple enzymes and their cofactors.In this review,we summarize recent experiments using Saccharomyces cerevisiae as a model sys...Nuclear RNA processing requires dynamic and intricately regulated machinery composed of multiple enzymes and their cofactors.In this review,we summarize recent experiments using Saccharomyces cerevisiae as a model system that have yielded important insights regarding the conversion of pre-RNAs to functional RNAs,and the elimination of aberrant RNAs and unneeded intermediates from the nuclear RNA pool.Much progress has been made recently in describing the 3D structure of many elements of the nuclear degradation machinery and its cofactors.Similarly,the regulatory mechanisms that govern RNA processing are gradually coming into focus.Such advances invariably generate many new questions,which we highlight in this review.展开更多
基金supported by the National Institute of Food and Agriculture, United States Department of Agriculture (2016-67015-24470, 2018-67015-27500 (sub-contract), 2020-67015-31733 and 2022-51300-38058)funds provided for medical and biological research by the State of Washington Initiative Measure, USA (No. 171) and the Washington State University Agricultural Experiment Station (Hatch funds 1014918) received from the National Institutes for Food and Agriculture, United States Department of Agriculture。
文摘Endometritis(inflammation of the endometrial lining) is one of the most devastating reproductive diseases in dairy cattle, resulting in substantial production loss and causing more than $650 million in lost revenue annually in the USA.We hypothesize that alternative polyadenylation(APA) sites serve as decisive sensors for endometrium health and disease in dairy cows. Endometrial cells collected from 18 cows with purulent vaginal discharge scored 0 to 2 were used for APA profiling with our whole transcriptome termini site sequencing(WTTS-seq) method. Overall, pathogens trigger hosts to use more differentially expressed APA(DE-APA), more intronic DE-APA, more DE-APA sites per gene and more DE-genes associated with inflammation. Host CD59 molecule(CD59), Fc fragment of IgG receptor IIa(FCGR2A), lymphocyte antigen 75(LY75) and plasminogen(PLG) may serve as initial contacts or combats with pathogens on cell surface, followed by activation of nuclear receptor subfamily 1 group H member 4(NR1H4) to regulate AXL receptor tyrosine kinase(AXL), FGR proto-oncogene, Src family tyrosine kinase(FGR), HCK protooncogene, Src family tyrosine kinase(HCK) and integrin subunit beta 2(ITGB2) for anti-inflammation. This study is the first to show significance of cilium pathways in endometrium health and animal reproduction. MIR21 and MIR30A would be perfect antagonistic biomarkers for diagnosis of either inflammation or anti-inflammation. These novel findings will set precedent for future genomic studies to aid the dairy industry develop new strategies to reduce endometritis incidence and improve fertility.
基金The current study was supported by the National Natural Science Foundation of China(Grant Nos.82130096 and 82373537)Collaborative Innovation Center for Cancer Personalized Medicine and Priority Academic Program Development of Jiangsu Higher Education Institutions(Public Health and Preventive Medicine).
文摘Aberrant alternative polyadenylation(APA)events play an important role in cancers,but little is known about whether APA-related genetic variants contribute to the susceptibility to bladder cancer.Previous genome-wide association study performed APA quantitative trait loci(apaQTL)analyses in bladder cancer,and identified 17955 single nucleotide polymorphisms(SNPs).We found that gene symbols of APA affected by apaQTL-associated SNPs were closely correlated with cancer signaling pathways,high mutational burden,and immune infiltration.Association analysis showed that apaQTL-associated SNPs rs34402449 C>A,rs2683524 C>T,and rs11540872 C>G were significantly associated with susceptibility to bladder cancer(rs34402449:OR=1.355,95%confidence interval[CI]:1.159-1.583,P=1.33×10^(−4);rs2683524:OR=1.378,95%CI:1.164-1.632,P=2.03×10^(−4);rs11540872:OR=1.472,95%CI:1.193-1.815,P=3.06×10^(−4)).Cumulative effect analysis showed that the number of risk genotypes and smoking status were significantly associated with an increased risk of bladder cancer(P_(trend)=2.87×10^(−12)).We found that PRR13,being demonstrated the most significant effect on cell proliferation in bladder cancer cell lines,was more highly expressed in bladder cancer tissues than in adjacent normal tissues.Moreover,the rs2683524 T allele was correlated with shorter 3′untranslated regions of PRR13 and increased PRR13 expression levels.Collectively,our findings have provided informative apaQTL resources and insights into the regulatory mechanisms linking apaQTL-associated variants to bladder cancer risk.
基金The authors would like to acknowledge funding from the Department of Defense Prostate Cancer Research Program W81XWH-17-1-0581 and W81XWH-19-1-0450Shawn EL,the National Cancer Institute P30CA006973William G.Nelson,and The Patrick C.Walsh Cancer Research Fund to Shawn EL,for support of this work.
文摘Objective:To review alternative polyadenylation(APA)as a mechanism of gene regulation and consider potential roles for APA in prostate cancer(PCa)biology and treatment.Methods:An extensive review of mRNA polyadenylation,APA,and PCa literature was performed.This review article introduces APA and its association with human disease,outlines the mechanisms and components of APA,reviews APA in cancer biology,and considers whether APA may contribute to PCa progression and/or produce novel biomarkers and therapeutic targets for PCa.Results:Eukaryotic mRNA 30-end cleavage and polyadenylation play a critical role in gene expression.Most human genes encode more than one polyadenylation signal,and produce more than one transcript isoform,through APA.Polyadenylation can occur throughout the gene body to generate transcripts with differing 30-termini and coding sequence.Differences in 30-untranslated regions length can modify post-transcriptional gene regulation by microRNAs and RNA binding proteins,and alter mRNA stability,translation efficiency,and subcellular localization.Distinctive APA patterns are associated with human diseases,tissue origins,and changes in cellular proliferation rate and differentiation state.APA events may therefore generate unique mRNA biomarkers or therapeutic targets in certain cancer types or phenotypic states.Conclusions:The full extent of cancer-associated and tissue-specific APA events have yet to be defined,and the mechanisms and functional consequences of APA in cancer remain incompletely understood.There is evidence that APA is active in PCa,and that it may be an untapped resource for PCa biomarkers or therapeutic targets.
基金Sopported by the National Nature Science Foundation grant of P. R. China( 39880 0 31)
文摘hap , a novel human apoptosis inducing gene which can interact with another newly discovered apoptosis inducing gene ASY, was identified by cloning its cDNAs from human lung cell line (WI 38) cDNA library. Two major mRNA species (1.8 and 2.7 kb in length, respectively) were previously identified by Northern blot analysis of poly(A) + RNA from human multiple tissues using partial hap cDNA as a probe. In the present work, the molecular mechanism accounting for the generation of the two hap transcripts were investigated. The rapid amplification of cDNA 3’\|ends (3’ RACE) technique and the sequential Southern blot analysis, in conjunction with the sequencing analysis demonstrated that the two hap transcripts derive from the alternative polyadenylation site selection: a AATAAA signal at position 1 528 1 533 nt for the 1.8 kb hap mRNA; and a AATAAA signal at position 2 375 2 380 nt for the 2.7 kb hap mRNA. Furthermore, a number of regulatory elements within hap 3’ untranslated region (3’\|UTR) were also examined.
基金This research was supported by grants from National Natural Science Foundation of China(No.81922052,81974435,81772999)the Natural Science Foundation of Guangdong Province,China(No.2019B151502011)the Guangzhou People's Livelihood Science and Technology Project,China(No.201903010006).
文摘The mRNA polyadenylation plays essential function in regulation of mRNA metabolism.Mis-regulations of mRNA polyadenylation are frequently linked with aberrant gene expression and disease progression.Under the action of polyadenylate polymerase,poly(A)tail is synthesized after the polyadenylation signal(PAS)sites on the mRNAs.Alternative polyadenylation(APA)often occurs in mRNAs with multiple poly(A)sites,producing different 3'ends for transcript variants,and therefore plays important functions in gene expression regulation.In this review,we first summarize the classical process of mRNA 3'-terminal formation and discuss the length control mechanisms of poly(A)innucleus and cytoplasm.Thenwe review the research progress on alternative polyadenylation regulation and the APA site selection mechanism.Finally,we summarize the functional roles of APA in the regulation of gene expression and diseases including cancers.
基金supported by the National Natural Science Foundation of China(Grant Nos.T2222007 to Xiaohui Wu,61573296 to Guoli Ji,and 81901287 to Shuting Xia)the Suzhou City People’s Livelihood Science and Technology Project,China(Grant No.SYS2020086 to Shuting Xia).
文摘Alternative polyadenylation(APA)contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases.Singlecell RNA sequencing(scRNA-seq)has enabled the profiling of APA at the single-cell level;however,the spatial information of cells is not preserved in scRNA-seq.Alternatively,spatial transcriptomics(ST)technologies provide opportunities to decipher the spatial context of the transcriptomic landscape.Pioneering studies have revealed potential spatially variable genes and/or splice isoforms;however,the pattern of APA usage in spatial contexts remains unappreciated.In this study,we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatially barcoded ST data.APA sites were identified and quantified from the ST data.In particular,an imputation model based on the k-nearest neighbors algorithm was designed to recover APA signals,and then APA genes with spatial patterns of APA usage variation were identified.By analyzing wellestablished ST data of the mouse olfactory bulb(MOB),we presented a detailed view of spatial APA usage across morphological layers of the MOB.We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers.By extending this analysis to two additional replicates of the MOB ST data,we observed that the spatial APA patterns of several genes were reproducible among replicates.stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution.This toolkit is available at https://github.com/BMILAB/stAPAminer and https://ngdc.cncb.ac.cn/biocode/tools/BT007320.
基金This work was supported by the National Natural Science Foundation of China(Grant No.61871463 to XW)the Natural Science Foundation of Fujian Province of China(Grant No.2020J01047 to CY).
文摘Alternative polyadenylation(APA)plays important roles in modulating mRNA stability,translation,and subcellular localization,and contributes extensively to shaping eukaryotic transcriptome complexity and proteome diversity.Identification of poly(A)sites(pAs)on a genomewide scale is a critical step toward understanding the underlying mechanism of APA-mediated gene regulation.A number of established computational tools have been proposed to predict pAs from diverse genomic data.Here we provided an exhaustive overview of computational approaches for predicting pAs from DNA sequences,bulk RNA sequencing(RNA-seq)data,and single-cell RNA sequencing(scRNA-seq)data.Particularly,we examined several representative tools using bulk RNA-seq and scRNA-seq data from peripheral blood mononuclear cells and put forward operable suggestions on how to assess the reliability of pAs predicted by different tools.We also proposed practical guidelines on choosing appropriate methods applicable to diverse scenarios.Moreover,we discussed in depth the challenges in improving the performance of pA prediction and benchmarking different methods.Additionally,we highlighted outstanding challenges and opportunities using new machine learning and integrative multi-omics techniques,and provided our perspective on how computational methodologies might evolve in the future for non-30 untranslated region,tissuespecific,cross-species,and single-cell pA prediction.
文摘Alternative polyadenylation(APA)is a molecular process that generates diversity at the 3′end of RNA polymeraseⅡtranscripts from over 60%of human genes.APA is derived from the existence of multiple polyadenylation signals(PAS)within the same transcript,and results in the differential inclusion of sequence information at the 3′end.While APA can occur between two PASs allowing for generation of transcripts with distinct coding potential from a single gene,most APA occurs within the untranslated region(3′UTR)and changes the length and content of these non-coding sequences.APA within the 3′UTR can have tremendous impact on its regulatory potential of the mRNA through a variety of mechanisms,and indeed this layer of gene expression regulation has profound impact on processes vital to cell growth and development.Recent studies have particularly highlighted the importance of APA dysregulation in cancer onset and progression.Here,we review the current knowledge of APA and its impacts on mRNA stability,translation,localization and protein localization.We also discuss the implications of APA dysregulation in cancer research and therapy.
基金This work was supported by grants from the National Natural Science Foundation of China(31788103 to X.C.,31670247 to Y.W.,31870755 to S.L.,31801063 to Y.H.,31701096 to J.S.,31900435 to B.W.)the Chinese Academy of Sciences(Strategic Priority Research Program XDB27030201 and QYZDY-SSW-SMC022 to X.C.)+3 种基金the Guangdong Innovation Research Team Fund(2016ZT06S172 to S.L.)the Shenzhen Sci-Tech Fund(No.KYTDPT20181011104005 to S.L)the China Postdoctoral Science Foundation(2016M600143 to Y.H.)the Guangdong Science and Technology Department(2020B1212060018 and 2020B1212030004 to B.W.).
文摘N6-methyladenosine(m^(6)A),a ubiquitous internal modification of eukaryotic mRNAs,plays a vital role in almost every aspect of mRNA metabolism.However,there is little evidence documenting the role of m^(6)A in regulating alternative polyadenylation(APA)in plants.APA is controlled by a large protein-RNA complex with many components,including CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30(CPSF30).In Arabidopsis,CPSF30 has two isoforms and the longer isoform(CPSF30-L)contains a YT512-B Homology(YTH)domain,which is unique to plants.In this study,we showed that CPSF30-L YTH domain binds to m^(6)A in v itro.In the cpsf30-2 mutant,the transcripts of many genes including several important nitrate signaling-related genes had shifts in polyadenylation sites that were correlated with m^(6)A peaks,indicating that these gene transcripts carrying m^(6)A tend to be regulated by APA.Wild-type CPSF30-L could rescue the defects in APA and nitrate metabolism in cpsf30-2,but m^(6)A-binding-defective mutants of CPSF30-L could not.Taken together,our results demonstrated that m^(6)A modification regulates APA in Arabidops is and revealed that the m^(6)A reader CPSF30-L affects nitrate signaling by controlling APA,shedding new light on the roles of the m^(6)A modification during RNA 3-end processing in nitrate metabolism.
基金This work was supported by the National Natural Science Foundation of China(nos.21822702,21820102008,92053109,and 21432002)the National Basic Research Program of China(2017YFA0505201 and 2019YFA0802201).
文摘The biological functions of the epitranscriptomic modification N^(6)-methyladenosine(m^(6)A)in plants are not fully understood.CPSF30-L is a predominant isoform of the polyadenylation factor CPSF30 and consists of CPSF30-S and an m^(6)A-binding YTH domain.Little is known about the biological roles of CPSF30-L and the molecular mechanism underlying its m^(6)A-binding function in alternative polyadenylation.Here,we charac-terized CPSF30-L as an Arabidopsis m^(6)A reader whose m^(6)A-binding function is required for the floral tran-sition and abscisic acid(ABA)response.We found that the m^(6)A-binding activity of CPSF30-L enhances the formation of liquid-like nuclear bodies,where CPSF30-L mainly recognizes m*A-modified far-upstream elements to control polyadenylation site choice.Deficiency of CPSF30-L lengthens the 3'untranslated region of three phenotypes-related transcripts,thereby accelerating their mRNA degradation and leading to late flowering and ABA hypersensitivity.Collectively,this study uncovers a new molecular mechanism for m^(6)A-driven phase separation and polyadenylation in plants.
基金supported by the National Basic Research Program of China (973 Program, Grant Nos. 2013CB530700 and 2015CB943000)the National Natural Science Foundation of China (Grant Nos. 31471192 and 31521003) to TN
文摘Alternative polyadenylation(APA), a phenomenon that RNA molecules with different 30 ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expression. In the present review, we first summarized various methods prevalently adopted in APA study, mainly focused on the next-generation sequencing(NGS)-based techniques specially designed for APA identification, the related bioinformatics methods, and the strategies for APA study in single cells. Then we summarized the main findings and advances so far based on these methods, including the preferences of alternative poly A(pA) site, the biological processes involved, and the corresponding consequences. We especially categorized the APA changes discovered so far and discussed their potential functions under given conditions, along with the possible underlying molecular mechanisms. With more in-depth studies on extensive samples,more signatures and functions of APA will be revealed, and its diverse roles will gradually heave in sight.
基金supported by National Key Basic Research Program of China(No.2013CB945000)National Science Foundation of China(No.31471345)
文摘In the sexually reproductive organisms, gametes are produced by meiosis following a limited mitotic amplification. However, the intrinsic program switching cells from mitotic to meiotic cycle is unclear.Alternative polyadenylation(APA) is a highly conserved means of gene regulation and is achieved by the RNA 30-processing machinery to generate diverse 30 UTR profiles. In Drosophila spermatogenesis, we observed distinct profiles of transcriptome-wide 30 UTR between mitotic and meiotic cells. In mutant germ cells stuck in mitosis, 30 UTRs of hundreds of genes were consistently shifted. Remarkably, altering the levels of multiple 30-processing factors disrupted germline's progression to meiosis, indicative of APA's active role in this transition. An RNA-binding protein(RBP) Tut could directly bind 30 UTRs of 30-processing factors whose expressions were repressed in the presence of Tut-containing complex. Further,we demonstrated that this RBP complex could execute the repression post-transcriptionally by recruiting CCR4/Twin of deadenylation complex. Thus, we propose that an RBP complex regulates the dynamic APA profile to promote the mitosis-to-meiosis transition.
基金This work was funded by National Natural Science Foundation of China(32001519,32030080)The Major Program of Guangdong Basic and Applied Research(2019B030302006)China Postdoctoral Science Fund(2020M672653)。
文摘N^(6)-methyladenosine(m^(6)A) modification affects the post-transcriptional regulation of eukaryotic gene expression, but the underlying mechanisms and their effects in plants remain largely unknown. Here,we report that the N^(6)-adenine methyltransferase-like domain-containing protein ENHANCED DOWNY MILDEW 2-LIKE(OsEDM2 L) is essential for rice(Oryza sativa L.) anther development. The osedm2 l knockout mutant showed delayed tapetal programmed cell death(PCD) and defective pollen development. OsEDM2 L interacts with the transcription factors basic helix-loop-helix 142 and TAPETUMDEGENERATIONRETARDATIONto regulate the expression of ETERNAL TAPETUM 1(EAT1), a positive regulator of tapetal PCD. Mutation of OsEDM2 L altered the transcriptomic m^(6)A landscape, and caused a distinct m^(6)A modification of the EAT1 transcript leading to dysregulation of its alternative splicing and polyadenylation, followed by suppression of the EAT1 target genes OsAP25 and OsAP37 for tapetal PCD. Therefore, OsEDM2 L is indispensable for proper messenger RNA m^(6)A modification in rice anther development.
基金supported by the King Abdullah University of Science and Technology(KAUST)Office of Sponsored Research(OSR)(Grant Nos.URF/1/4098-01-01,BAS/1/1624-01,FCC/1/1976-18-01,FCC/1/1976-23-01,FCC/1/1976-25-01,FCC/1/1976-26-01,and FCS/1/4102-02-01)the International Cooperation Research Grant from Science and Technology Innovation Commission of Shenzhen Municipal Government,China(Grant No.GJHZ20170310161947503 to YH)the Shenzhen Science and Technology Program,China(Grant No.KQTD20180411143432337 to YH and WC).
文摘Alternative polyadenylation(APA)is a crucial step in post-transcriptional regulation.Previous bioinformatic studies have mainly focused on the recognition of polyadenylation sites(PASs)in a given genomic sequence,which is a binary classification problem.Recently,computational methods for predicting the usage level of alternative PASs in the same gene have been proposed.However,all of them cast the problem as a non-quantitative pairwise comparison task and do not take the competition among multiple PASs into account.To address this,here we propose a deep learning architecture,Deep Regulatory Code and Tools for Alternative Polyadenylation(DeeReCT-APA),to quantitatively predict the usage of all alternative PASs of a given gene.To accommodate different genes with potentially different numbers of PASs,DeeReCT-APA treats the problem as a regression task with a variable-length target.Based on a convolutional neural network-long short-term memory(CNN-LSTM)architecture,DeeReCT-APA extracts sequence features with CNN layers,uses bidirectional LSTM to explicitly model the interactions among competing PASs,and outputs percentage scores representing the usage levels of all PASs of a gene.In addition to the fact that only our method can quantitatively predict the usage of all the PASs within a gene,we show that our method consistently outperforms other existing methods on three different tasks for which they are trained:pairwise comparison task,highest usage prediction task,and ranking task.Finally,we demonstrate that our method can be used to predict the effect of genetic variations on APA patterns and sheds light on future mechanistic understanding in APA regulation.Our code and data are available at https://github.com/lzx325/DeeReCT-APA-repo.
基金supported by the National Natural Science Foundation of China(31971332 to Y.F.,91942301 and 81430099 to A.X,and 32000450 to L.C.).
文摘In eukaryotic cells,both alternative splicing and alternative polyadenylation(APA)play essential roles in the gene regulation network.U1 small ribonucleoprotein particle(U1 snRNP)is a major component of spliceosome,and U1 snRNP complex can suppress proximal APA sites through crosstalking with 3end processing factors.However,here we show that both knockdown and overexpression of SNRPA,SNRPC,SNRNP70,and SNRPD2,the U1 snRNP proteins,promote the usage of proximal APA sites at the transcriptome level.SNRNP70 can drive the phase transition of PABPN1 from droplet to aggregate,which may reduce the repressive effects of PABPN1 on the proximal APA sites.Additionally,SNRNP70 can also promote the proximal APA sites by recruiting CPSF6,suggesting that the function of CPSF6 on APA is related with other RNA-binding proteins and cell context-dependent.Consequently,these results reveal that,on the contrary to U1 snRNP complex,the free proteins of U1 snRNP complex can promote proximal APA sites through the interaction with 3end processing machinery.
基金support from the National Institutes of Health grant R01-GM134539(EJ.W).
文摘Background:Genome-wide association studies(GWAS)have identified thousands of genomic non-coding variants statistically associated with many human traits and diseases,including cancer.However,the functional interpretation of these non-coding variants remains a significant challenge in the post-GWAS era.Alternative polyadenylation(APA)plays an essential role in post-transcriptional regulation for most human genes.By employing different poly(A)sites,genes can either shorten or extend the 3'-UTRs that contain cu-regulatory elements such as miRNAs or RNA-binding protein binding sites.Therefore,APA can affect the mRNA stability,translation,and cellular localization of proteins.Population-scale studies have revealed many inherited genetic variants that potentially impact APA to further influence disease susceptibility and phenotypic diversity,but systematic computational investigations to delineate the connections are in their earliest states.Results:Here,we discuss the evolving definitions of the genetic basis of APA and the modern genomics tools to identify,characterize,and validate the genetic influences of APA events in human populations.We also explore the emerging and surprisingly complex molecular mechanisms that regulate APA and summarize the genetic control of APA that is associated with complex human diseases and traits.Conclusion:APA is an intermediate molecular phenotype that can translate human common non-coding variants to individual phenotypic variability and disease susceptibility.
文摘BACKGROUND Extensive evidence has illustrated the promotive role of integrin binding sialoprotein(IBSP)in the progression of multiple cancers.However,little is known about the functions of IBSP in gastric cancer(GC)progression.AIM To investigate the mechanism underlying the regulatory effects of IBSP in GC progression,and the relationship between IBSP and cleavage and polyadenylation factor 6(CPSF6)in this process.METHODS The mRNA and protein expression of relevant genes were assessed through realtime quantitative polymerase chain reaction and Western blot,respectively.Cell viability was evaluated by Cell Counting Kit-8 assay.Cell invasion and migration were evaluated by Transwell assay.Pyroptosis was measured by flow cytometry.The binding between CPSF6 and IBSP was confirmed by luciferase reporter and RNA immunoprecipitation(RIP)assays.RESULTS IBSP exhibited higher expression in GC tissues and cell lines than in normal tissues and cell lines.IBSP knockdown suppressed cell proliferation,migration,and invasion but facilitated pyroptosis.In the exploration of the regulatory mechanism of IBSP,potential RNA binding proteins for IBSP were screened with catRAPID omics v2.0.The RNA-binding protein CPSF6 was selected due to its higher expression in stomach adenocarcinoma.Luciferase reporter and RIP assays revealed that CPSF6 binds to the 3’-untranslated region of IBSP and regulates its expression.Knockdown of CPSF6 inhibited cell proliferation,migration,and invasion but boosted pyroptosis.Through rescue assays,it was uncovered that the retarded GC progression mediated by CPSF6 knockdown was reversed by IBSP overexpression.CONCLUSION Our study highlighted the vital role of the CPSF6/IBSP axis in GC,suggesting that IBSP might be an effective biotarget for GC treatment.
基金Supported by A fellowship from"Fondazione Umberto Veronesi" to Griseri Pthe French National Institute of Cancer(INCA)+1 种基金the French Association for Cancer Research(ARC)the Fondation de France,the Conseil Général des Alpes Maritimes,Roche France and The"Association pour la Recherche sur les Tumeurs du Rein(ARTu R)"
文摘The control of the half-life of m RNA plays a central role in normal development and in disease progression. Several pathological conditions, such as breast cancer, correlate with deregulation of the half-life of m RNA encoding growth factors, oncogenes, cell cycle regulators and inflammatory cytokines that participate in cancer. Substantial stability means that a m RNA will be available for translation for a longer time, resulting in high levels of protein gene products, which may lead to prolonged responses that subsequently result in over-production of cellular mediators that participate in cancer. The stability of these m RNA is regulated at the 3'UTR level by different mechanisms involving m RNA binding proteins, micro-RNA, long non-coding RNA and alternative polyadenylation. All these events are tightly interconnected to each other and lead to steady state levels of target m RNAs. Compelling evidence also suggests that both m RNA binding proteins and regulatory RNAswhich participate to m RNA half-life regulation may be useful prognostic markers in breast cancers, pointing to a potential therapeutic approach to treatment of patients with these tumors. In this review, we summarize the main mechanisms involved in the regulation of m RNA decay and discuss the possibility of its implication in breast cancer aggressiveness and the efficacy of targeted therapy.
基金The author is financed in part by the Spanish Government(Ministerio de Ciencia e Innovación,Grant MCIN/AEI PID2019-110574RB-I00).
文摘Transcription termination of nearly all protein-coding genes in mammals requires 3’end processing by a multiprotein complex that will cleave and polyadenylate the messenger RNA precursor.Because a variety of enzyme complexes intervene,3’end processing was thought to be fundamentally complex and subject to a multitude of regulatory effects.The possibility to select just one out of several polyadenylation sites,in particular,has caused much questioning and speculation.What appear to be separate mechanisms however can be combined into a defined set of rules,allowing for a relatively simple interpretation of 3’end processing.Ultimately,readiness of the terminal exon splice site determines when a transcript reaches the maturity to select a nearby polyadenylation signal.Transcriptional pausing then acts in concert,extending the timeframe during which the transcription complex is close to polyadenylation sites.Since RNA polymerase pausing is governed by the same type of sequences in bacteria and metazoans,mammalian transcription termination resembles its prokaryote counterpart more than generally thought.
基金Supported by The Marlene and Stewart Greenebaum Cancer Center (Toth EA)
文摘Nuclear RNA processing requires dynamic and intricately regulated machinery composed of multiple enzymes and their cofactors.In this review,we summarize recent experiments using Saccharomyces cerevisiae as a model system that have yielded important insights regarding the conversion of pre-RNAs to functional RNAs,and the elimination of aberrant RNAs and unneeded intermediates from the nuclear RNA pool.Much progress has been made recently in describing the 3D structure of many elements of the nuclear degradation machinery and its cofactors.Similarly,the regulatory mechanisms that govern RNA processing are gradually coming into focus.Such advances invariably generate many new questions,which we highlight in this review.
