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.
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.
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.
The sessile nature of plants confines their responsiveness to changing environmental conditions.Gene expression regulation becomes a paramount mechanism for plants to adjust their physiological and morphological behaviors.Alternative polyadenylation(APA)is known for its capacity to augment transcriptome diversity and plasticity,thereby furnishing an additional set of tools for modulating gene expression.APA has also been demonstrated to exhibit intimate associations with plant stress responses.In this study,we review APA dynamic features and consequences in plants subjected to both biotic and abiotic stresses.These stresses include adverse environmental stresses,and pathogenic attacks,such as cadmium toxicity,high salt,hypoxia,oxidative stress,cold,heat shock,along with bacterial,fungal,and viral infections.We analyzed the overarching research framework employed to elucidate plant APA response and the alignment of polyadenylation site transitions with the modulation of gene expression levels within the ambit of each stress condition.We also proposed a general APA model where transacting factors,including poly(A)factors,epigenetic regulators,RNA m6A modification factors,and phase separation proteins,assume pivotal roles in APA related transcriptome plasticity during stress response in plants.
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.
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.
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.
