Intronic polyadenylation(IPA)is an RNA 3'end processing event which has been reported to play important roles in cancer development.However,the comprehensive landscape of IPA events across various cancer types is ...Intronic polyadenylation(IPA)is an RNA 3'end processing event which has been reported to play important roles in cancer development.However,the comprehensive landscape of IPA events across various cancer types is lacking.Here,we apply IPAFinder to identify and quantify IPA events in 10,383 samples covering all 33 cancer types from The Cancer Genome Atlas(TCGA)project.We identify a total of 21,835 IPA events,almost half of which are ubiquitously expressed.We identify 2761 unique dynamically changed IPA events across cancer types.Furthermore,we observe 8855 non-redundant clinically relevant IPA events,which could potentially be used as prognostic indicators.Our analysis also reveals that dynamic IPA usage within cancer signaling pathways may affect drug response.Finally,we develop a user-friendly data portal,IPACancer Atlas(http://www.tingni-lab.com/Pancan_IPA),to search and explore IPAs in cancer.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
The majority of eukaryotic genes produce multiple mRNA isoforms with distinct 3＇ ends through a process called mRNA alternative polyadenylation （APA）. Recent studies have demonstrated that APA is dynamically regula...The majority of eukaryotic genes produce multiple mRNA isoforms with distinct 3＇ ends through a process called mRNA alternative polyadenylation （APA）. Recent studies have demonstrated that APA is dynamically regulated during development and in response to environmental stimuli. A number of mechanisms have been described for APA regulation. In this review, we attempt to integrate all the known mechanisms into a unified model. This model not only explains most of previous results, but also provides testable predictions that will improve our understanding of the mechanistic details of APA regulation. Finally, we briefly discuss the known and putative functions of APA regulation.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
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
hap, a novel human apoptosis-inducing gene which can interact with another newly discovered apoptosis-inducing geneASY, was identified, by cloning its cDNAs from human lung cell line (WI-38) cDNA library. Two major mR...hap, a novel human apoptosis-inducing gene which can interact with another newly discovered apoptosis-inducing geneASY, 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 partialhap cDNA as a probe. In the present work, the molecular mechanism accounting for the generation of the twohap 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 twohap transcripts derive from the alternative polyadenylation site selection: a AATAAA signal at position 1 528–1 533 nt for the 1.8 kbhap mRNA: and a AATAAA signal at position 2 375–2 380 nt for the 2.7 kbhap mRNA. Furthermore, a number of regulatory elements withinhap 3′-untranslated region (3′-UTR) were also examined.展开更多
Solute carrier family 27 member 5(SLC27A5/FATP5)is a liver-specific metabolic enzyme that plays a crucial role in fatty acid transport and bile acid metabolism.Deficiency of SLC27A5 promotes the progression of hepatoc...Solute carrier family 27 member 5(SLC27A5/FATP5)is a liver-specific metabolic enzyme that plays a crucial role in fatty acid transport and bile acid metabolism.Deficiency of SLC27A5 promotes the progression of hepatocellular carcinoma(HCC)and is strongly asso-ciated with a poor prognosis.SLC27A5 exhibits noncanonical functions beyond its metabolic role;however,its specific mechanisms in hepatocarcinogenesis remain elusive and are there-fore investigated in this study.Immunoprecipitation-mass spectrometry analysis showed that SLC27A5-interacting proteins were significantly enriched in alternative polyadenylation(APA).RNA-sequencing data provided evidence that SLC27A5 plays a global role in regulating APA events in HCC.Mechanistically,SLC27A5 facilitates the usage of the proximal polyadeny-lation site of METTL14 by downregulating the expression of the APA-associated factor PABPC1,resulting in the shortening of the METTL14-30UTR and the conversion of METTL14-UL to METTL14-US.In contrast to METTL14-UL,METTL14-US escapes the inhibitory effect of miRNA targeting,leading to increased METTL14 expression.METTL14-US upregulation by SLC27A5 sup-pressed the stemness of HCC.Therefore,low levels of SLC27A5 and METTL14 may serve as reli-able biomarkers for identifying poor prognosis in patients with HCC.In conclusion,SLC27A5/PABPC1 inhibits HCC stemness via APA-regulated expression of METTL14,providing potential avenues for the development of novel therapeutic strategies.展开更多
In recent years,posttranscriptional cellular processes such as alternative splicing,messenger RNA(mRNA)decay and translational control have emerged as important regulatory layers required for fine-tuning the inflammat...In recent years,posttranscriptional cellular processes such as alternative splicing,messenger RNA(mRNA)decay and translational control have emerged as important regulatory layers required for fine-tuning the inflammatory response in coordination with transcriptional regulation.However,among these posttranscriptional mechanisms,very little is known regarding the role of alternative polyadenylation(APA),a process that generates transcripts with different 3'ends,in modulating gene expression during inflammation.In a paper published on this topic,Chen and coworkers provided evidence indicating that alternative polyadenylation promotes macrophage inflammatory functions by modulating the expression of genes involved in the autophagy pathway[1].展开更多
Somatic variants in the cancer genome influence gene expression through diverse mechanisms depending on their specific locations.However,a systematic evaluation of the effects of somatic variants located in 3'untr...Somatic variants in the cancer genome influence gene expression through diverse mechanisms depending on their specific locations.However,a systematic evaluation of the effects of somatic variants located in 3'untranslated regions(3'UTRs)on alternative polyadenylation(APA)of m RNA remains lacking.In this study,we analyze 10,199 tumor samples across 32 cancer types and identify 1333 somatic single nucleotide variants(SNVs)associated with abnormal 3'UTR APA.Mechanistically,these 3'UTR SNVs can alter cisregulatory elements,such as the poly(A)signal and UGUA motif,leading to changes in APA.Minigene assays confirm that 3'UTR SNVs in multiple genes,including RPS23 and CHTOP,induce aberrant APA.Among affected genes,62 exhibit differential stability between tandem 3'UTR isoforms,including HSPA4and UCK2,validated by experimental assays.Finally,we establish that SNV-related abnormal APA usage serves as an additional layer of expression regulation for tumor-suppressor gene HMGN2 in breast cancer.Collectively,this study reveals 3'UTR APA as a critical mechanism mediating the functional impact of somatic noncoding variants in human cancers.展开更多
Under warm temperatures,plants adjust their morphologies for environmental adaption via precise gene expression regulation.However,the function and regulation of alternative polyadenylation(APA),an important fine-tuni...Under warm temperatures,plants adjust their morphologies for environmental adaption via precise gene expression regulation.However,the function and regulation of alternative polyadenylation(APA),an important fine-tuning of gene expression,remains unknown in plant thermomorphogenesis.In this study,we found that SUMOylation,a critical post-translational modification,is induced by a long-term treat-ment at warm temperatures via a SUMO ligase SIZ1 in Arabidopsis.Disruption of SIZ1 altered the global usage of polyadenylation signals and affected the APA dynamic of thermomorphogenesis-related genes.CPSF100,a key subunit of the CPSF complex for polyadenylation regulation,is SUMOylated by SIZ1.Importantly,we demonstrated that SUMOylation is essential for the function of CPSF1oo in genome-wide polyadenylation site choice during thermomorphogenesis.Further analyses revealed that the SUMO conjugation on CPSF100 attenuates its interaction with two isoforms of its partner CPSF30,increasing the nuclear accumulation of CPsF1oo for polyadenylation regulation.In summary,our study uncovers a regulatory mechanism of APA via SiZ1-mediated SUMOylation in plant thermomorpho-genesis.展开更多
Generally shortened 3′UTR due to alternative polyadenylation(APA)is widely observed in cancer,but its regulation mechanisms for cancer are not well characterized.Here,with profiling of APA in colorectal cancer tissue...Generally shortened 3′UTR due to alternative polyadenylation(APA)is widely observed in cancer,but its regulation mechanisms for cancer are not well characterized.Here,with profiling of APA in colorectal cancer tissues and poly(A)signal editing,we firstly identified that the shortened 3′UTR of CTNNIBP1 in colorectal cancer promotes cell proliferation and migration.We found that liquid-liquid phase separation(LLPS)of PABPN1 is reduced albeit with higher expression in cancer,and the reduction of LLPS leads to the shortened 3′UTR of CTNNBIP1and promotes cell proliferation and migration.Notably,the splicing factor SNRPD2 upregulated in colorectal cancer,can interact with glutamic-proline(EP)domain of PABPN1,and then disrupt LLPS of PABPN1,which attenuates the repression effect of PABPN1 on the proximal poly(A)sites.Our results firstly reveal a new regulation mechanism of APA by disruption of LLPS of PABPN1,suggesting that regulation of APA by interfering LLPS of 3′end processing factor may have the potential as a new way for the treatment of cancer.展开更多
Macrophage hyperactivation is a hallmark of inflammatory diseases,yet the role of alternative polyadenylation(APA)of mRNAs in regulating innate immunity remains unclear.In this study,we focused on 3’UTR-APA and demon...Macrophage hyperactivation is a hallmark of inflammatory diseases,yet the role of alternative polyadenylation(APA)of mRNAs in regulating innate immunity remains unclear.In this study,we focused on 3’UTR-APA and demonstrated that Nudt21,a crucial RNA-binding component of the 3’UTR-APA machinery,is significantly upregulated in various inflammatory conditions.By utilizing myeloid-specific Nudt21-deficient mice,we revealed a protective effect of Nudt21 depletion against colitis and severe hyperinflammation,primarily through diminished production of proinflammatory cytokines.Notably,Nudt21 regulates the mRNA stability of key autophagy-related genes,Map1lc3b and Ulk2,by mediating selective 3’UTR polyadenylation in activated macrophages.As a result,Nudt21-deficient macrophages display increased autophagic activity,which leads to reduced cytokine secretion.Our findings highlight an unexplored role of Nudt21-mediated 3’UTR-APA in modulating macrophage autophagy and offer new insights into the modulation of inflammation and disease progression.展开更多
Alternative polyadenylation(APA)is an essential post-transcriptional process that produces mature mRNA isoforms by regulating the usage of polyadenylation sites(PASs).APA is involved in lymphocyte activation;however,i...Alternative polyadenylation(APA)is an essential post-transcriptional process that produces mature mRNA isoforms by regulating the usage of polyadenylation sites(PASs).APA is involved in lymphocyte activation;however,its role throughout the entire differentiation trajectory remains elusive.Here,we analyzed single-cell 3'-end transcriptome data from healthy subjects to construct a dynamic-APA landscape from hematopoietic stem and progenitor cells(HSPCs)to terminally differentiated lymphocytes.This analysis covered 19973 cells of 12 clusters from five lineages(B cells,CD4^(+)T cells,CD8^(+)T cells,natural killer cells,and plasmacytoid dendritic cells).A total of 2364 genes exhibited differential 3'-untranslated region(3'UTR)PAS usage,and 3021 genes displayed differential intronic cleavage during lymphoid differentiation.We observed a global trend of 3'UTR shortening during lymphoid differentiation.Nevertheless,specific events of both 3'UTR shortening and lengthening were also identified within each cluster.The APA patterns delineated three differentiation stages:HSPCs,precursor cells,and mature cells.Moreover,we demonstrated that the conversion of naïve T cells to memory T cells was accompanied by dynamic APA in transcription factor-encoding genes(TCF7 and NFATC2IP),immune function-related genes(BCL2,CD5,CD28,GOLT1B,and TMEM59),and protein ubiquitination-related genes(UBE2G1,YPEL5,and SUMO3).These findings expand our understanding of the underlying molecular mechanisms of APA and facilitate studies on the regulatory role of APA in lymphoid hematopoiesis.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
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
Tomato(Solanum lycopersicum)is an extensively cultivated vegetable,and its growth and fruit quality can be significantly impaired by low temperatures.The widespread presence of N^(6)-methyladenosine(m^(6)A)modificatio...Tomato(Solanum lycopersicum)is an extensively cultivated vegetable,and its growth and fruit quality can be significantly impaired by low temperatures.The widespread presence of N^(6)-methyladenosine(m^(6)A)modification on RNA is involved in a diverse range of stress response processes.There is a significant knowledge gap regarding the precise roles of m^(6)A modification in tomato,particularly for cold stress response.Here,we assessed the m^(6)A modification landscape of S.lycopersicum'Micro-Tom'leaves in response to low-temperature stress.Furthermore,we investigated the potential relationship among m^(6)A modification,transcriptional regulation,alternative polyadenylation events,and protein translation via MeRIP-seq,RNA-seq,and protein mass spectrometry.After omic date analysis,11378 and 10735 significant m^(6)A peak associated genes were identified in the control and cold treatment tomato leaves,respectively.Additionally,we observed a UGUACAK(K=G/U)motif under both conditions.Differential m^(6)A site associated genes most likely play roles in protein translation regulatory pathway.Besides directly altering gene expression levels,m^(6)A also leads to differential poly(A)site usage under low-temperature.Finally,24 important candidate genes associated with cold stress were identified by system-level multi-omic analysis.Among them,m^(6)A modification levels were increased in SBPase(Sedoheptulose-1,7-bisphosphatase,Solyc05g052600.4)mRNA,causing distal poly(A)site usage,downregulation of mRNA expression level,and increased protein abundance.Through these,tomato leaves try to maintain normal photo synthetic carbon assimilation and nitro gen metabolism under low-temperature condition.The comprehensive investigation of the m^(6)A modification landscape and multi-omics analysis provide valuable insights into the epigenetic regulatory mechanisms in tomato cold stress response.展开更多
Background:Nudix Hydrolase 21(NUDT21)is crucial for the regulation of alternative polyadenylation,with its reduced expression frequently resulting in a shortened mRNA 3′untranslated region(UTR),thereby enhancing the ...Background:Nudix Hydrolase 21(NUDT21)is crucial for the regulation of alternative polyadenylation,with its reduced expression frequently resulting in a shortened mRNA 3′untranslated region(UTR),thereby enhancing the protein levels of downstream genes.Although NUDT21 is widely recognized for its tumor-suppressive function in various cancers,its involvement in colorectal cancer(CRC)remains poorly understood.Methods:The expression of NUDT21 in CRC and adjacent normal tissues was analyzed through qPCR,Western blot,and immunohistochemistry(IHC).Additionally,we investigated the correlation between NUDT21 expression and patient prognosis.With Cell Counting Kit-8 assay and Transwell assay,we detected the exact role of NUDT21 in the development and progress of CRC.We used RNA-Seq analysis to explore the downstream target gene of NUDT21.Meanwhile,DaPars analysis revealed the Hippo pathway as a critical pathway in CRC progress.Western blotting and luciferase assays were used to investigate the specific mechanisms by which NUDT21 regulates the Hippo pathway.In addition,the interaction between NUDT21 and TAZ was confirmed by co-immunoprecipitation and the correlation between the two expressions was verified by IHC.Results:In CRC,elevated NUDT21 expression has been identified as a predictor of poor prognosis,as well as a promoter of CRC cell proliferation and migration.Combined with RNA-seq and DaPars analyses,we identified the Hippo pathway as an important downstream target of NUDT21 in CRC.NUDT21 knockdown significantly downregulated the YAP,TAZ,and TEAD1 protein levels.Mechanistically,shortening of the 3′UTR of TAZ by NUDT21 knockdown suppressed TAZ protein expression.A positive correlation was observed between NUDT21 and TAZ proteins in CRC.Conclusion:NUDT21 plays a pro-tumorigenic role in CRC by upregulating TAZ protein expression,revealing a new regulatory mechanism of the Hippo pathway and providing insight into the biological effect of mRNA 3′UTR shortening.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
基金This work was financially supported by the National Natural Science Foundation of China(92249302,32370592)the National Key Research and Development Program of China(2023YFC3603300,2021YFA0909300).
文摘Intronic polyadenylation(IPA)is an RNA 3'end processing event which has been reported to play important roles in cancer development.However,the comprehensive landscape of IPA events across various cancer types is lacking.Here,we apply IPAFinder to identify and quantify IPA events in 10,383 samples covering all 33 cancer types from The Cancer Genome Atlas(TCGA)project.We identify a total of 21,835 IPA events,almost half of which are ubiquitously expressed.We identify 2761 unique dynamically changed IPA events across cancer types.Furthermore,we observe 8855 non-redundant clinically relevant IPA events,which could potentially be used as prognostic indicators.Our analysis also reveals that dynamic IPA usage within cancer signaling pathways may affect drug response.Finally,we develop a user-friendly data portal,IPACancer Atlas(http://www.tingni-lab.com/Pancan_IPA),to search and explore IPAs in cancer.
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Project supported by the National Institutes of Health (NIH) (No.R01 GM090056),USA
文摘The majority of eukaryotic genes produce multiple mRNA isoforms with distinct 3＇ ends through a process called mRNA alternative polyadenylation （APA）. Recent studies have demonstrated that APA is dynamically regulated during development and in response to environmental stimuli. A number of mechanisms have been described for APA regulation. In this review, we attempt to integrate all the known mechanisms into a unified model. This model not only explains most of previous results, but also provides testable predictions that will improve our understanding of the mechanistic details of APA regulation. Finally, we briefly discuss the known and putative functions of APA regulation.
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 geneASY, 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 partialhap cDNA as a probe. In the present work, the molecular mechanism accounting for the generation of the twohap 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 twohap transcripts derive from the alternative polyadenylation site selection: a AATAAA signal at position 1 528–1 533 nt for the 1.8 kbhap mRNA: and a AATAAA signal at position 2 375–2 380 nt for the 2.7 kbhap mRNA. Furthermore, a number of regulatory elements withinhap 3′-untranslated region (3′-UTR) were also examined.
基金supported by the National Key Research and Development Program of China(No.2023YFC2306800)The National Natural Science Foundation of China(No.82272975,82073251,82304288)+5 种基金Natural Science Foundation of Chongqing(No.CSTB2024NSCQ-KJFZMSX0016)the Innovative and Entrepreneurial Team of Chongqing Talents PlanChongqing Medical Scientific Research Project,China(Joint Project of Chongqing Health Commission and Science and Technology Bureau,No.2023DBXM007)the Future Medical Youth Innovation Team of Chongqing Medical University(China)(No.W0036,W0101)Senior Medical Talents Program of Chongqing for Young and Middle-aged(China)the Kuanren Talents Program and Joint Project of Pinnacle Disciplinary Group of the Second Affiliated Hospital of Chongqing Medical University(China).
文摘Solute carrier family 27 member 5(SLC27A5/FATP5)is a liver-specific metabolic enzyme that plays a crucial role in fatty acid transport and bile acid metabolism.Deficiency of SLC27A5 promotes the progression of hepatocellular carcinoma(HCC)and is strongly asso-ciated with a poor prognosis.SLC27A5 exhibits noncanonical functions beyond its metabolic role;however,its specific mechanisms in hepatocarcinogenesis remain elusive and are there-fore investigated in this study.Immunoprecipitation-mass spectrometry analysis showed that SLC27A5-interacting proteins were significantly enriched in alternative polyadenylation(APA).RNA-sequencing data provided evidence that SLC27A5 plays a global role in regulating APA events in HCC.Mechanistically,SLC27A5 facilitates the usage of the proximal polyadeny-lation site of METTL14 by downregulating the expression of the APA-associated factor PABPC1,resulting in the shortening of the METTL14-30UTR and the conversion of METTL14-UL to METTL14-US.In contrast to METTL14-UL,METTL14-US escapes the inhibitory effect of miRNA targeting,leading to increased METTL14 expression.METTL14-US upregulation by SLC27A5 sup-pressed the stemness of HCC.Therefore,low levels of SLC27A5 and METTL14 may serve as reli-able biomarkers for identifying poor prognosis in patients with HCC.In conclusion,SLC27A5/PABPC1 inhibits HCC stemness via APA-regulated expression of METTL14,providing potential avenues for the development of novel therapeutic strategies.
文摘In recent years,posttranscriptional cellular processes such as alternative splicing,messenger RNA(mRNA)decay and translational control have emerged as important regulatory layers required for fine-tuning the inflammatory response in coordination with transcriptional regulation.However,among these posttranscriptional mechanisms,very little is known regarding the role of alternative polyadenylation(APA),a process that generates transcripts with different 3'ends,in modulating gene expression during inflammation.In a paper published on this topic,Chen and coworkers provided evidence indicating that alternative polyadenylation promotes macrophage inflammatory functions by modulating the expression of genes involved in the autophagy pathway[1].
基金financially supported by the National Key R&D Program of China(2023YFC3603300,2021YFA0909300)National Natural Science Foundation of China(92249302,32370592,32400437)China Postdoctoral Science Foundation(BX20230073 and 2023M740709)。
文摘Somatic variants in the cancer genome influence gene expression through diverse mechanisms depending on their specific locations.However,a systematic evaluation of the effects of somatic variants located in 3'untranslated regions(3'UTRs)on alternative polyadenylation(APA)of m RNA remains lacking.In this study,we analyze 10,199 tumor samples across 32 cancer types and identify 1333 somatic single nucleotide variants(SNVs)associated with abnormal 3'UTR APA.Mechanistically,these 3'UTR SNVs can alter cisregulatory elements,such as the poly(A)signal and UGUA motif,leading to changes in APA.Minigene assays confirm that 3'UTR SNVs in multiple genes,including RPS23 and CHTOP,induce aberrant APA.Among affected genes,62 exhibit differential stability between tandem 3'UTR isoforms,including HSPA4and UCK2,validated by experimental assays.Finally,we establish that SNV-related abnormal APA usage serves as an additional layer of expression regulation for tumor-suppressor gene HMGN2 in breast cancer.Collectively,this study reveals 3'UTR APA as a critical mechanism mediating the functional impact of somatic noncoding variants in human cancers.
基金supported by grants from the Major Program of Guangdong Basic and Applied Research(2019B030302006)the National Natural Science Foundation of China(32000449,32270292,32270344,32270752,and 32170593)+3 种基金the China Postdoctoral Science Foundation(2020M672674)the Program for Changjang Scholars,the Natural Science Foundation of Guangdong Province,China(2024A1515011497,2020B1515020007,and 2024A1515011071)the Guangdong Provincial Pearl River Talent Plan(2019QN01N108)the National Science Foundation of USA(2347540).
文摘Under warm temperatures,plants adjust their morphologies for environmental adaption via precise gene expression regulation.However,the function and regulation of alternative polyadenylation(APA),an important fine-tuning of gene expression,remains unknown in plant thermomorphogenesis.In this study,we found that SUMOylation,a critical post-translational modification,is induced by a long-term treat-ment at warm temperatures via a SUMO ligase SIZ1 in Arabidopsis.Disruption of SIZ1 altered the global usage of polyadenylation signals and affected the APA dynamic of thermomorphogenesis-related genes.CPSF100,a key subunit of the CPSF complex for polyadenylation regulation,is SUMOylated by SIZ1.Importantly,we demonstrated that SUMOylation is essential for the function of CPSF1oo in genome-wide polyadenylation site choice during thermomorphogenesis.Further analyses revealed that the SUMO conjugation on CPSF100 attenuates its interaction with two isoforms of its partner CPSF30,increasing the nuclear accumulation of CPsF1oo for polyadenylation regulation.In summary,our study uncovers a regulatory mechanism of APA via SiZ1-mediated SUMOylation in plant thermomorpho-genesis.
基金supported by the National Key Research and Development Program of China(2022YFA1103900,2017YFC1308800)the National Natural Science Foundation of China(31971332,32000450,91942301,81430099)+5 种基金the National Basic Research Program of China(2013CB917801)the National High-tech Research and Development Program of China(863 Program)(2012AA02A520)Basic and Applied Basic Research Foundation of Guangdong Province(2020A1515010293)the Fundamental Research Funds for the Central Universities,Sun Yat-sen University(2021qntd26)the National Key Clinical Discipline([2012]649)the Program of Guangdong Provincial Clinical Research Center for Digestive Diseases(2020B1111170004)。
文摘Generally shortened 3′UTR due to alternative polyadenylation(APA)is widely observed in cancer,but its regulation mechanisms for cancer are not well characterized.Here,with profiling of APA in colorectal cancer tissues and poly(A)signal editing,we firstly identified that the shortened 3′UTR of CTNNIBP1 in colorectal cancer promotes cell proliferation and migration.We found that liquid-liquid phase separation(LLPS)of PABPN1 is reduced albeit with higher expression in cancer,and the reduction of LLPS leads to the shortened 3′UTR of CTNNBIP1and promotes cell proliferation and migration.Notably,the splicing factor SNRPD2 upregulated in colorectal cancer,can interact with glutamic-proline(EP)domain of PABPN1,and then disrupt LLPS of PABPN1,which attenuates the repression effect of PABPN1 on the proximal poly(A)sites.Our results firstly reveal a new regulation mechanism of APA by disruption of LLPS of PABPN1,suggesting that regulation of APA by interfering LLPS of 3′end processing factor may have the potential as a new way for the treatment of cancer.
基金supported by the National Natural Science Foundation of China(No.82325024,82341017,82350112,82030042 and 32070917 to H.-B.L.)the Ministry of Science and Technology of China(No.2021YFA1100800 to H.-B.L.)the Shanghai Municipal Health Commission(No.2022XD047 and 2022JC001 to H.-B.L.).
文摘Macrophage hyperactivation is a hallmark of inflammatory diseases,yet the role of alternative polyadenylation(APA)of mRNAs in regulating innate immunity remains unclear.In this study,we focused on 3’UTR-APA and demonstrated that Nudt21,a crucial RNA-binding component of the 3’UTR-APA machinery,is significantly upregulated in various inflammatory conditions.By utilizing myeloid-specific Nudt21-deficient mice,we revealed a protective effect of Nudt21 depletion against colitis and severe hyperinflammation,primarily through diminished production of proinflammatory cytokines.Notably,Nudt21 regulates the mRNA stability of key autophagy-related genes,Map1lc3b and Ulk2,by mediating selective 3’UTR polyadenylation in activated macrophages.As a result,Nudt21-deficient macrophages display increased autophagic activity,which leads to reduced cytokine secretion.Our findings highlight an unexplored role of Nudt21-mediated 3’UTR-APA in modulating macrophage autophagy and offer new insights into the modulation of inflammation and disease progression.
基金supported by the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences(2021-I2M-1-040 to F.W.)the National Key Research and Development Program of China(2021YFA1102400 to F.W.,2019YFA0111700 to X.W.)the National Natural Science Foundation of China(82022001 and 81970103 to F.W.,82070111 to Y.Z.).
文摘Alternative polyadenylation(APA)is an essential post-transcriptional process that produces mature mRNA isoforms by regulating the usage of polyadenylation sites(PASs).APA is involved in lymphocyte activation;however,its role throughout the entire differentiation trajectory remains elusive.Here,we analyzed single-cell 3'-end transcriptome data from healthy subjects to construct a dynamic-APA landscape from hematopoietic stem and progenitor cells(HSPCs)to terminally differentiated lymphocytes.This analysis covered 19973 cells of 12 clusters from five lineages(B cells,CD4^(+)T cells,CD8^(+)T cells,natural killer cells,and plasmacytoid dendritic cells).A total of 2364 genes exhibited differential 3'-untranslated region(3'UTR)PAS usage,and 3021 genes displayed differential intronic cleavage during lymphoid differentiation.We observed a global trend of 3'UTR shortening during lymphoid differentiation.Nevertheless,specific events of both 3'UTR shortening and lengthening were also identified within each cluster.The APA patterns delineated three differentiation stages:HSPCs,precursor cells,and mature cells.Moreover,we demonstrated that the conversion of naïve T cells to memory T cells was accompanied by dynamic APA in transcription factor-encoding genes(TCF7 and NFATC2IP),immune function-related genes(BCL2,CD5,CD28,GOLT1B,and TMEM59),and protein ubiquitination-related genes(UBE2G1,YPEL5,and SUMO3).These findings expand our understanding of the underlying molecular mechanisms of APA and facilitate studies on the regulatory role of APA in lymphoid hematopoiesis.
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 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financially supported by the National Natural Science Foundation of China(Grant Nos.32202518 and 32070601)Shandong University of Technology PhD Start-up Fund(418097)。
文摘Tomato(Solanum lycopersicum)is an extensively cultivated vegetable,and its growth and fruit quality can be significantly impaired by low temperatures.The widespread presence of N^(6)-methyladenosine(m^(6)A)modification on RNA is involved in a diverse range of stress response processes.There is a significant knowledge gap regarding the precise roles of m^(6)A modification in tomato,particularly for cold stress response.Here,we assessed the m^(6)A modification landscape of S.lycopersicum'Micro-Tom'leaves in response to low-temperature stress.Furthermore,we investigated the potential relationship among m^(6)A modification,transcriptional regulation,alternative polyadenylation events,and protein translation via MeRIP-seq,RNA-seq,and protein mass spectrometry.After omic date analysis,11378 and 10735 significant m^(6)A peak associated genes were identified in the control and cold treatment tomato leaves,respectively.Additionally,we observed a UGUACAK(K=G/U)motif under both conditions.Differential m^(6)A site associated genes most likely play roles in protein translation regulatory pathway.Besides directly altering gene expression levels,m^(6)A also leads to differential poly(A)site usage under low-temperature.Finally,24 important candidate genes associated with cold stress were identified by system-level multi-omic analysis.Among them,m^(6)A modification levels were increased in SBPase(Sedoheptulose-1,7-bisphosphatase,Solyc05g052600.4)mRNA,causing distal poly(A)site usage,downregulation of mRNA expression level,and increased protein abundance.Through these,tomato leaves try to maintain normal photo synthetic carbon assimilation and nitro gen metabolism under low-temperature condition.The comprehensive investigation of the m^(6)A modification landscape and multi-omics analysis provide valuable insights into the epigenetic regulatory mechanisms in tomato cold stress response.
基金funded by grants from the National Natural Science Foundation of China(82073056)the Shanghai Pujiang Program(19PJ1407600).
文摘Background:Nudix Hydrolase 21(NUDT21)is crucial for the regulation of alternative polyadenylation,with its reduced expression frequently resulting in a shortened mRNA 3′untranslated region(UTR),thereby enhancing the protein levels of downstream genes.Although NUDT21 is widely recognized for its tumor-suppressive function in various cancers,its involvement in colorectal cancer(CRC)remains poorly understood.Methods:The expression of NUDT21 in CRC and adjacent normal tissues was analyzed through qPCR,Western blot,and immunohistochemistry(IHC).Additionally,we investigated the correlation between NUDT21 expression and patient prognosis.With Cell Counting Kit-8 assay and Transwell assay,we detected the exact role of NUDT21 in the development and progress of CRC.We used RNA-Seq analysis to explore the downstream target gene of NUDT21.Meanwhile,DaPars analysis revealed the Hippo pathway as a critical pathway in CRC progress.Western blotting and luciferase assays were used to investigate the specific mechanisms by which NUDT21 regulates the Hippo pathway.In addition,the interaction between NUDT21 and TAZ was confirmed by co-immunoprecipitation and the correlation between the two expressions was verified by IHC.Results:In CRC,elevated NUDT21 expression has been identified as a predictor of poor prognosis,as well as a promoter of CRC cell proliferation and migration.Combined with RNA-seq and DaPars analyses,we identified the Hippo pathway as an important downstream target of NUDT21 in CRC.NUDT21 knockdown significantly downregulated the YAP,TAZ,and TEAD1 protein levels.Mechanistically,shortening of the 3′UTR of TAZ by NUDT21 knockdown suppressed TAZ protein expression.A positive correlation was observed between NUDT21 and TAZ proteins in CRC.Conclusion:NUDT21 plays a pro-tumorigenic role in CRC by upregulating TAZ protein expression,revealing a new regulatory mechanism of the Hippo pathway and providing insight into the biological effect of mRNA 3′UTR shortening.
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.
