Alternative polyadenylation and the stress response

Gender associations between phthalate exposure and biomarkers of oxidative stress: A prospective cohort study

Previous epidemiologic research has shown that phthalate exposure in pregnant women is related to adverse birth outcomes in a sex-specific manner. However, the biological mechanism of phthalate exposure that causes these birth outcomes remains poorly defined. In this research, we investigated the association between phthalate exposure and placental oxidative stress in a large population-based cohort study, aiming to initially explore the relationship between phthalate exposure and gene expression in placental oxidative stress in a sex-specific manner. Quantitative PCR was performed to measure the expression of placental inflammatory mRNAs (HO-1, HIF1α, and GRP78) in 2469 placentae. The multiple linear regression models were used to investigate the associations between mRNA and urinary phthalate monoesters. Phthalate metabolites monomethyl phthalate (MMP) and mono-n-butyl phthalate (MBP) were positively correlated with higher HIF1α expression in placentae of male fetuses (p < .05). Mono-benzyl phthalate (MBzP) increased the expression of HO-1, HIF1α, and GRP78 in placentae of male fetuses, and mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) up-regulated the expression of HIF1α and GRP78. Additionally, mono-(2-ethyl-5-oxohexyl) phthalate (MEOHP) was negatively correlated with HO-1, HIF1α, and GRP78 in placentae of female fetuses. Maternal phthalate exposure was associated with oxidative stress variations in placental tissues. The associations were closer in the placentas of male fetuses than in that of female ones. The placenta oxidative stress is worth further investigation as a potential mediator of maternal exposure-induced disease risk in children.

Isoform Switching Regulates the Response to Ionizing Radiation Through SRSF1

PURPOSE

This study investigated how isoform switching affects the cellular response to ionizing radiation (IR), an understudied area despite its relevance to radiation therapy in cancer treatment. We aimed to identify changes in transcript isoform expression post-IR exposure and the proteins mediating these changes, with a focus on their potential to modulate radiosensitivity.

METHODS AND MATERIALS

Using RNA sequencing, we analyzed the B-cell lines derived from 10 healthy individuals at 3 timepoints, applying the mixture of isoforms algorithm to quantify alternative splicing. We examined RNA binding protein motifs within the sequences of IR-responsive isoforms and validated the serine/arginine-rich splicing factor 1 (SRSF1) as a predominant mediator through RNA immunoprecipitation. We further investigated the effects of SRSF1 on radiosensitivity by RNA interference and by analyzing publicly available data on patients with cancer.

RESULTS

We identified ∼1900 radiation-responsive alternatively spliced isoforms. Many isoforms were differentially expressed without changes in their overall gene expression. Over a third of these transcripts underwent exon skipping, while others used proximal last exons. These IR-responsive isoforms tended to be shorter transcripts missing vital domains for preventing apoptosis and promoting cell division but retaining those necessary for DNA repair. Our combined computational, genetic, and molecular analyses identified the proto-oncogene SRSF1 as a mediator of these radiation-induced isoform-switching events that promote apoptosis. After exposure to DNA double-strand break-inducing agents, SRSF1 expression decreased. A reduction in SRSF1 increased radiosensitivity in vitro and among patients with cancer.

CONCLUSIONS

We establish a pivotal role for isoform switching in the cellular response to IR and propose SRSF1 as a promising biomarker for assessing radiation therapy effectiveness.

Fates and functions of RNA-binding proteins under stress

Exposure to stress activates a well-orchestrated set of changes in gene expression programs that allow the cell to cope with and adapt to the stress, or undergo programmed cell death. RNA-protein interactions, mediating all aspects of post-transcriptional regulation of gene expression, play crucial roles in cellular stress responses. RNA-binding proteins (RBPs), which interact with sequence/structural elements in RNAs to control the steps of RNA metabolism, have therefore emerged as central regulators of post-transcriptional responses to stress. Following exposure to a variety of stresses, the dynamic alterations in the RNA-protein interactome enable cells to respond to intracellular or extracellular perturbations by causing changes in mRNA splicing, polyadenylation, stability, translation, and localization. As RBPs play a central role in determining the cellular proteome both qualitatively and quantitatively, it has become increasingly evident that their abundance, availability, and functions are also highly regulated in response to stress. Exposure to stress initiates a series of signaling cascades that converge on post-translational modifications (PTMs) of RBPs, resulting in changes in their subcellular localization, association with stress granules, extracellular export, proteasomal degradation, and RNA-binding activities. These alterations in the fate and function of RBPs directly impact their post-transcriptional regulatory roles in cells under stress. Adopting the ubiquitous RBP HuR as a prototype, three scenarios illustrating the changes in nuclear-cytoplasmic localization, RNA-binding activity, export and degradation of HuR in response to inflammation, genotoxic stress, and heat shock depict the complex and interlinked regulatory mechanisms that control the fate and functions of RBPs under stress. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

Heat shock induces alternative polyadenylation through dynamic DNA methylation-regulated chromatin looping

Alternative cleavage and polyadenylation (APA) is a gene regulatory mechanism used by cells under stress to upregulate proteostasis-promoting transcripts, but how cells achieve this remains poorly understood. Previously, we elucidated a DNA methylation-regulated APA mechanism, in which gene body DNA methylation enhances distal poly(A) isoform expression by blocking CTCF binding and chromatin loop formation at APA control regions. We hypothesized that DNA methylation-regulated APA is one mechanism cells employ to induce proteostasis-promoting poly(A) isoforms. At the DNAJB6 co-chaperone gene locus, acute heat shock resulted in binding of stress response transcription factors HSF1, ATF6, and YY1 at the APA control region and an increase in the expression of the proximal poly(A) isoform known to prevent protein aggregation. Furthermore, TET1 was recruited to rapidly demethylate DNA, facilitating CTCF binding and chromatin loop formation, thereby reinforcing preferential proximal poly(A) isoform expression. As cells recovered, the transcription factors vacated the APA control region, and DNMT1 was recruited to remethylate the region. This process resolved chromatin looping and reset the poly(A) isoform expression pattern. Our findings unveil an epigenetic mechanism enabling cells to dynamically modulate poly(A) isoforms in response to stress while shedding light on the interplay between DNA methylation, transcription factors, and chromatin looping.

Eriocheir sinensis feminization-1c (Fem-1c) and Its Predicted miRNAs Involved in Sexual Development and Regulation

Feminization-1c (Fem-1c) is important for sex differentiation in the model organism Caenorhabditis elegans. In our previous study, the basic molecular characteristics of the Fem-1c gene (EsFem-1c) in Eriocheir sinensis (Henri Milne Edwards, 1854) were cloned to determine the relationship with sex differentiation. In this study, the genomic sequence of EsFem-1c contained five exons and four introns, with an exceptionally long 3'UTR sequence. The qRT-PCR results of EsFem-1c demonstrated lower tissue expression in the androgenic gland of the intersex crab than the normal male crab, implying that EsFem-1c plays a role in crab AG development. RNA interference experiments and morphological observations of juvenile and mature crabs indicated that EsFem-1c influences sexual development in E. sinensis. A dual-luciferase reporter assay disclosed that tcf-miR-315-5p effectively inhibits the translation of the EsFem-1c gene, influencing male development. An intriguing finding was that miRNA tcf-miR-307 could increase EsFem-1c expression by binding to the alternative splicing region with a length of 248 bp (ASR-248) in the 3'UTR sequence. The present research contributes to a better understanding of the molecular regulation mechanism of EsFem-1c and provides a resource for future studies of the miRNA-mediated regulation of sexual development and regulation in E. sinensis.

Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions

Rapid plastic response to environmental changes, which involves extremely complex underlying mechanisms, is crucial for organismal survival during many ecological and evolutionary processes such as those in global change and biological invasions. Gene expression is among the most studied molecular plasticity, while co- or posttranscriptional mechanisms are still largely unexplored. Using a model invasive ascidian Ciona savignyi, we studied multidimensional short-term plasticity in response to hyper- and hyposalinity stresses, covering the physiological adjustment, gene expression, alternative splicing (AS), and alternative polyadenylation (APA) regulations. Our results demonstrated that rapid plastic response varied with environmental context, timescales, and molecular regulatory levels. Gene expression, AS, and APA regulations independently acted on different gene sets and corresponding biological functions, highlighting their nonredundant roles in rapid environmental adaptation. Stress-induced gene expression changes illustrated the use of a strategy of accumulating free amino acids under high salinity and losing/reducing them during low salinity to maintain the osmotic homoeostasis. Genes with more exons were inclined to use AS regulations, and isoform switches in functional genes such as SLC2a5 and Cyb5r3 resulted in enhanced transporting activities by up-regulating the isoforms with more transmembrane regions. The extensive 3'-untranslated region (3'UTR) shortening through APA was induced by both salinity stresses, and APA regulation predominated transcriptomic changes at some stages of stress response. The findings here provide evidence for complex plastic mechanisms to environmental changes, and thereby highlight the importance of systemically integrating different levels of regulatory mechanisms in studying initial plasticity in evolutionary trajectories.

The emerging roles of CFIm25 (NUDT21/CPSF5) in human biology and disease

The mammalian cleavage factor I subunit CFIm25 (NUDT21) binds to the UGUA sequences of precursor RNAs. Traditionally, CFIm25 is known to facilitate 3' end formation of pre-mRNAs resulting in the formation of polyadenylated transcripts. Recent studies suggest that CFIm25 may be involved in the cyclization and hence generation of circular RNAs (circRNAs) that contain UGUA motifs. These circRNAs act as competing endogenous RNAs (ceRNAs) that disrupt the ceRNA-miRNA-mRNA axis. Other emerging roles of CFIm25 include regulating both alternative splicing and alternative polyadenylation (APA). APA generates different sized transcripts that may code for different proteins, or more commonly transcripts that code for the same protein but differ in the length and sequence content of their 3' UTRs (3' UTR-APA). CFIm25 mediated global changes in 3' UTR-APA affect human physiology including spermatogenesis and the determination of cell fate. Deregulation of CFIm25 and changes in 3' UTR-APA have been implicated in several human diseases including cancer. In many cancers, CFIm25 acts as a tumor suppressor. However, there are some cancers where CFIm25 has the opposite effect. Alterations in CFIm25-driven 3' UTR-APA may also play a role in neural dysfunction and fibrosis. CFIm25 mediated 3' UTR-APA changes can be used to generate specific signatures that can be used as potential biomarkers in development and disease. Due to the emerging role of CFIm25 as a regulator of the aforementioned RNA processing events, modulation of CFIm25 levels may be a novel viable therapeutic approach. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease.

The Dynamic Poly(A) Tail Acts as a Signal Hub in mRNA Metabolism

In eukaryotes, mRNA metabolism requires a sophisticated signaling system. Recent studies have suggested that polyadenylate tail may play a vital role in such a system. The poly(A) tail used to be regarded as a common modification at the 3' end of mRNA, but it is now known to be more than just that. It appears to act as a platform or hub that can be understood in two ways. On the one hand, polyadenylation and deadenylation machinery constantly regulates its dynamic activity; on the other hand, it exhibits the ability to recruit RNA-binding proteins and then interact with diverse factors to send various signals to regulate mRNA metabolism. In this paper, we outline the main complexes that regulate the dynamic activities of poly(A) tails, explain how these complexes participate polyadenylation/deadenylation process and summarize the diverse signals this hub emit. We are trying to make a point that the poly(A) tail can metaphorically act as a "flagman" who is supervised by polyadenylation and deadenylation and sends out signals to regulate the orderly functioning of mRNA metabolism.

Global 3'-UTRome of porcine immature Sertoli cells altered by acute heat stress

Alternative polyadenylation (APA) affects the composition of cis-elements in 3'-untranslated region (3'-UTR), to regulate gene expression and localization, and subsequently the downstream biological processes. Acute heat stress could change rapidly the cellular transcriptome, however the underlying molecular changes are less explored. Here, we systematically catalogued the global 3'-UTRome dynamics, by analyzing our previously reported transcriptome sequencing data of porcine immature Sertoli (iST) cells before (Control group), acute heat stress treatment at 43 °C for 0.5h (HS0.5 group), and 36h recovery culture (HS0.5-R36h group) after acute heat stress treatment. After three group comparisons (HS0.5 vs. Control, HS0.5-R36 vs. HS0.5, and HS0.5-R36 vs. Control), DaPars (dynamic analysis of alternative polyadenylation) identified 639, 464 and 290 mRNAs, and APAtrap (a tool to identify APA sites and detect changes of APA site usage) identified 713, 518 and 321 mRNAs, with significantly different 3'-UTRs (Padj.≤0.05), respectively. These genes with different 3'-UTR patterns were mainly enriched in P53, glycolysis/gluconeogenesis, HIF-1, apoptosis, PI3K-Akt and AMPK signaling pathways. Further analysis identified that average 3'-UTR lengths of Acss2, Inpp1 and Nr1h4 were more than 140 nt longer (HS0.5-R36 vs. HS0.5), and contained different cis-elements (PAS, CPE and microRNA binding sites). Moreover, Hsp70.2, Inhbb and Dhrs were identified to have extremely different 3'-UTR abundances. Further 3'RACE assays validated several 3'-UTRs of Nr1h4, and RT-qPCR confirmed the abundance changes of different 3'-UTR isoforms for Nr1h4 and Hsp70.2. Our findings provide useful information and resources to further uncover the molecular role of 3'-UTR, in regulating the response of porcine iST cells to acute heat stress.

Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response

Full-length transcriptome sequencing with long reads is a powerful tool to analyze transcriptional and post-transcriptional events; however, it has not been applied on soybean (Glycine max). Here, a comparative full-length transcriptome analysis was performed on soybean genotype 09-138 infected with soybean cyst nematode (SCN, Heterodera glycines) race 4 (SCN4, incompatible reaction) and race 5 (SCN5, compatible reaction) using Oxford Nanopore Technology. Each of 9 full-length samples collected 8 days post inoculation with/without nematodes generated an average of 6.1 GB of clean data and a total of 65,038 transcript sequences. After redundant transcripts were removed, 1,117 novel genes and 41,096 novel transcripts were identified. By analyzing the sequence structure of the novel transcripts, a total of 28,759 complete open reading frame (ORF) sequences, 5,337 transcription factors, 288 long non-coding RNAs, and 40,090 novel transcripts with function annotation were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) revealed that growth hormone, auxin-activated signaling pathway and multidimensional cell growth, and phenylpropanoid biosynthesis pathway were enriched by infection with both nematode races. More DEGs associated with stress response elements, plant-hormone signaling transduction pathway, and plant-pathogen interaction pathway with more upregulation were found in the incompatible reaction with SCN4 infection, and more DEGs with more upregulation involved in cell wall modification and carbohydrate bioprocess were detected in the compatible reaction with SCN5 infection when compared with each other. Among them, overlapping DEGs with a quantitative difference was triggered. The combination of protein-protein interaction with DEGs for the first time indicated that nematode infection activated the interactions between transcription factor WRKY and VQ (valine-glutamine motif) to contribute to soybean defense. The knowledge of the SCN-soybean interaction mechanism as a model will present more understanding of other plant-nematode interactions.

Implications of Poly(A) Tail Processing in Repeat Expansion Diseases

Repeat expansion diseases are a group of more than 40 disorders that affect mainly the nervous and/or muscular system and include myotonic dystrophies, Huntington’s disease, and fragile X syndrome. The mutation-driven expanded repeat tract occurs in specific genes and is composed of tri- to dodeca-nucleotide-long units. Mutant mRNA is a pathogenic factor or important contributor to the disease and has great potential as a therapeutic target. Although repeat expansion diseases are quite well known, there are limited studies concerning polyadenylation events for implicated transcripts that could have profound effects on transcript stability, localization, and translation efficiency. In this review, we briefly present polyadenylation and alternative polyadenylation (APA) mechanisms and discuss their role in the pathogenesis of selected diseases. We also discuss several methods for poly(A) tail measurement (both transcript-specific and transcriptome-wide analyses) and APA site identification—the further development and use of which may contribute to a better understanding of the correlation between APA events and repeat expansion diseases. Finally, we point out some future perspectives on the research into repeat expansion diseases, as well as APA studies.

Cigarette smoking-associated isoform switching and 3' UTR lengthening via alternative polyadenylation

Cigarette smoking induces a profound transcriptomic and systemic inflammatory response. Previous studies have focused on gene level differential expression of smoking, but the genome-wide effects of smoking on alternative isoform regulation have not yet been described. We conducted RNA sequencing in whole-blood samples of 454 current and 767 former smokers in the COPDGene Study, and we analyzed the effects of smoking on differential usage of isoforms and exons. At 10% FDR, we detected 3167 differentially expressed genes, 945 differentially used isoforms and 160 differentially used exons. Isoform switch analysis revealed widespread 3' UTR lengthening associated with cigarette smoking. The lengthening of these 3' UTRs was consistent with alternative usage of distal polyadenylation sites, and these extended 3' UTR regions were significantly enriched with functional sequence elements including microRNA and RNA-protein binding sites. These findings warrant further studies on alternative polyadenylation events as potential biomarkers and novel therapeutic targets for smoking-related diseases.

A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells

Background

Temperature change affects the myriad of concurrent cellular processes in a non-uniform, disruptive manner. While endothermic organisms minimize the challenge of ambient temperature variation by keeping the core body temperature constant, cells of many ectothermic species maintain homeostatic function within a considerable temperature range. The cellular mechanisms enabling temperature acclimation in ectotherms are still poorly understood. At the transcriptional level, the heat shock response has been analyzed extensively. The opposite, the response to sub-optimal temperature, has received lesser attention in particular in animal species. The tissue specificity of transcriptional responses to cool temperature has not been addressed and it is not clear whether a prominent general response occurs. Cis-regulatory elements (CREs), which mediate increased transcription at cool temperature, and responsible transcription factors are largely unknown.

Results

The ectotherm Drosophila melanogaster with a presumed temperature optimum around 25 °C was used for transcriptomic analyses of effects of temperatures at the lower end of the readily tolerated range (14–29 °C). Comparative analyses with adult flies and cell culture lines indicated a striking degree of cell-type specificity in the transcriptional response to cool. To identify potential cis-regulatory elements (CREs) for transcriptional upregulation at cool temperature, we analyzed temperature effects on DNA accessibility in chromatin of S2R+ cells. Candidate cis-regulatory elements (CREs) were evaluated with a novel reporter assay for accurate assessment of their temperature-dependency. Robust transcriptional upregulation at low temperature could be demonstrated for a fragment from the pastrel gene, which expresses more transcript and protein at reduced temperatures. This CRE is controlled by the JAK/STAT signaling pathway and antagonizing activities of the transcription factors Pointed and Ets97D.

Conclusion

Beyond a rich data resource for future analyses of transcriptional control within the readily tolerated range of an ectothermic animal, a novel reporter assay permitting quantitative characterization of CRE temperature dependence was developed. Our identification and functional dissection of the pst_E1 enhancer demonstrate the utility of resources and assay. The functional characterization of this CoolUp enhancer provides initial mechanistic insights into transcriptional upregulation induced by a shift to temperatures at the lower end of the readily tolerated range.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08057-4.

Regulation, diversity and function of MECP2 exon and 3'UTR isoforms

The methyl-CpG-binding protein 2 (MECP2) is a critical global regulator of gene expression. Mutations in MECP2 cause neurodevelopmental disorders including Rett syndrome (RTT). MECP2 exon 2 is spliced into two alternative messenger ribonucleic acid (mRNA) isoforms encoding MECP2-E1 or MECP2-E2 protein isoforms that differ in their N-termini. MECP2-E2, isolated first, was used to define the general roles of MECP2 in methyl-deoxyribonucleic acid (DNA) binding, targeting of transcriptional regulatory complexes, and its disease-causing impact in RTT. It was later found that MECP2-E1 is the most abundant isoform in the brain and its exon 1 is also mutated in RTT. MECP2 transcripts undergo alternative polyadenylation generating mRNAs with four possible 3'untranslated region (UTR) lengths ranging from 130 to 8600 nt. Together, the exon and 3'UTR isoforms display remarkable abundance disparity across cell types and tissues during development. These findings indicate discrete means of regulation and suggest that protein isoforms perform non-overlapping roles. Multiple regulatory programs have been explored to explain these disparities. DNA methylation patterns of the MECP2 promoter and first intron impact MECP2-E1 and E2 isoform levels. Networks of microRNAs and RNA-binding proteins also post-transcriptionally regulate the stability and translation efficiency of MECP2 3'UTR isoforms. Finally, distinctions in biophysical properties in the N-termini between MECP2-E1 and E2 lead to variable protein stabilities and DNA binding dynamics. This review describes the steps taken from the discovery of MECP2, the description of its key functions, and its association with RTT, to the emergence of evidence revealing how MECP2 isoforms are differentially regulated at the transcriptional, post-transcriptional and post-translational levels.

Alternative 3' UTRs play a widespread role in translation-independent mRNA association with the endoplasmic reticulum

Transcripts encoding membrane and secreted proteins are known to associate with the endoplasmic reticulum (ER) through translation. Here, using cell fractionation, polysome profiling, and 3' end sequencing, we show that transcripts differ substantially in translation-independent ER association (TiERA). Genes in certain functional groups, such as cell signaling, tend to have significantly higher TiERA potentials than others, suggesting the importance of ER association for their mRNA metabolism, such as localized translation. The TiERA potential of a transcript is determined largely by size, sequence content, and RNA structures. Alternative polyadenylation (APA) isoforms can have distinct TiERA potentials because of changes in transcript features. The widespread 3' UTR lengthening in cell differentiation leads to greater transcript association with the ER, especially for genes that are capable of expressing very long 3' UTRs. Our data also indicate that TiERA is in dynamic competition with translation-dependent ER association, suggesting limited space on the ER for mRNA association.

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

Liriodendron chinense is an economically and ecologically important deciduous tree species. Although the reference genome has been revealed, alternative polyadenylation (APA), transcription factors (TFs), long non-coding RNAs (lncRNAs), and co-expression networks of tissue-specific genes remain incompletely annotated. In this study, we used the bracts, petals, sepals, stamens, pistils, leaves, and shoot apex of L. chinense as materials for hybrid sequencing. On the one hand, we improved the annotation of the genome. We detected 13,139 novel genes, 7,527 lncRNAs, 1,791 TFs, and 6,721 genes with APA sites. On the other hand, we found that tissue-specific genes play a significant role in maintaining tissue characteristics. In total, 2,040 tissue-specific genes were identified, among which 9.2% of tissue-specific genes were affected by APA, and 1,809 tissue-specific genes were represented in seven specific co-expression modules. We also found that bract-specific hub genes were associated plant defense, leaf-specific hub genes were involved in energy metabolism. Moreover, we also found that a stamen-specific hub TF Lchi25777 may be involved in the determination of stamen identity, and a shoot-apex-specific hub TF Lchi05072 may participate in maintaining meristem characteristic. Our study provides a landscape of APA, lncRNAs, TFs, and tissue-specific gene co-expression networks in L. chinense that will improve genome annotation, strengthen our understanding of transcriptome complexity, and drive further research into the regulatory mechanisms of tissue-specific genes.

Regulation of the Ysh1 endonuclease of the mRNA cleavage/polyadenylation complex by ubiquitin-mediated degradation

Mutation of the essential yeast protein Ipa1 has previously been demonstrated to cause defects in pre-mRNA 3' end processing and growth, but the mechanism underlying these defects was not clear. In this study, we show that the ipa1-1 mutation causes a striking depletion of Ysh1, the evolutionarily conserved endonuclease subunit of the 19-subunit mRNA Cleavage/Polyadenylation (C/P) complex, but does not decrease other C/P subunits. YSH1 overexpression rescues both the growth and 3' end processing defects of the ipa1-1 mutant. YSH1 mRNA level is unchanged in ipa1-1 cells, and proteasome inactivation prevents Ysh1 loss and causes accumulation of ubiquitinated Ysh1. Ysh1 ubiquitination is mediated by the Ubc4 ubiquitin-conjugating enzyme and Mpe1, which in addition to its function in C/P, is also a RING ubiquitin ligase. In summary, Ipa1 affects mRNA processing by controlling the availability of the C/P endonuclease and may represent a regulatory mechanism that could be rapidly deployed to facilitate reprogramming of cellular responses.

Alternative polyadenylation of mRNA and its role in cancer

Alternative polyadenylation (APA) is a molecular process that generates diversity at the 3′ end of RNA polymerase II transcripts 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.