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Molecular Cell Sep 2022Alternative polyadenylation (APA) enhances gene regulatory potential by increasing the diversity of mRNA transcripts. 3' UTR shortening through APA correlates with...
Alternative polyadenylation (APA) enhances gene regulatory potential by increasing the diversity of mRNA transcripts. 3' UTR shortening through APA correlates with enhanced cellular proliferation and is a widespread phenomenon in tumor cells. Here, we show that the ubiquitously expressed transcription factor Sp1 binds RNA in vivo and is a common repressor of distal poly(A) site usage. RNA sequencing identified 2,344 genes (36% of the total mapped mRNA transcripts) with lengthened 3' UTRs upon Sp1 depletion. Sp1 preferentially binds the 3' UTRs of such lengthened transcripts and inhibits cleavage at distal sites by interacting with the subunits of the core cleavage and polyadenylation (CPA) machinery. The 3' UTR lengths of Sp1 target genes in breast cancer patient RNA-seq data correlate with Sp1 expression levels, implicating Sp1-mediated APA regulation in modulating tumorigenic properties. Taken together, our findings provide insights into the mechanism for dynamic APA regulation by unraveling a previously unknown function of the DNA-binding transcription factor Sp1.
Topics: 3' Untranslated Regions; Humans; Poly A; Polyadenylation; RNA, Messenger; Sp1 Transcription Factor; Zinc
PubMed: 35914531
DOI: 10.1016/j.molcel.2022.06.031 -
Transcription 2022The processing of the proximal and distal poly(A) sites in alternative polyadenylation (APA) has long been thought to independently occur on pre-mRNAs during... (Review)
Review
The processing of the proximal and distal poly(A) sites in alternative polyadenylation (APA) has long been thought to independently occur on pre-mRNAs during transcription. However, a recent study by our groups demonstrated that the proximal sites for many genes could be activated sequentially following the distal ones, suggesting a multi-cleavage-same-transcript mode beyond the canonical one-cleavage-per-transcript view. Here, we review the established mechanisms for APA regulation and then discuss the additional insights into APA regulation from the perspective of sequential polyadenylation, resulting in a unified leverage model for understanding the mechanisms of regulated APA.
Topics: Polyadenylation; Gene Expression Regulation
PubMed: 36004392
DOI: 10.1080/21541264.2022.2114776 -
Nature Structural & Molecular Biology Jan 2022Analogous to alternative splicing, alternative polyadenylation (APA) has long been thought to occur independently at proximal and distal polyA sites. Using...
Analogous to alternative splicing, alternative polyadenylation (APA) has long been thought to occur independently at proximal and distal polyA sites. Using fractionation-seq, we unexpectedly identified several hundred APA genes in human cells whose distal polyA isoforms are retained in chromatin/nuclear matrix and whose proximal polyA isoforms are released into the cytoplasm. Global metabolic PAS-seq and Nanopore long-read RNA-sequencing provide further evidence that the strong distal polyA sites are processed first and the resulting transcripts are subsequently anchored in chromatin/nuclear matrix to serve as precursors for further processing at proximal polyA sites. Inserting an autocleavable ribozyme between the proximal and distal polyA sites, coupled with a Cleave-seq approach that we describe here, confirms that the distal polyA isoform is indeed the precursor to the proximal polyA isoform. Therefore, unlike alternative splicing, APA sites are recognized independently, and in many cases, in a sequential manner. This provides a versatile strategy to regulate gene expression in mammalian cells.
Topics: 3' Untranslated Regions; Alternative Splicing; HeLa Cells; Humans; Introns; Nuclear Matrix; Poly A; Polyadenylation; RNA; RNA Polymerase II
PubMed: 35013598
DOI: 10.1038/s41594-021-00709-z -
Philosophical Transactions of the Royal... Nov 2018Post-transcriptional addition of poly(A) tails to the 3' end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of... (Review)
Review
Post-transcriptional addition of poly(A) tails to the 3' end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of life. Although an enzyme with poly(A)-adding activity was discovered in more than 50 years ago, its existence and role in prokaryotic RNA metabolism were neglected for many years. As a result, it was not until 1992 that poly(A) polymerase I was purified to homogeneity and its gene was finally identified. Further work revealed that, similar to its role in surveillance of aberrant nuclear RNAs of eukaryotes, the addition of poly(A) tails often destabilizes prokaryotic RNAs and their decay intermediates, thus facilitating RNA turnover. Moreover, numerous studies carried out over the last three decades have shown that polyadenylation greatly contributes to the control of prokaryotic gene expression by affecting the steady-state level of diverse protein-coding and non-coding transcripts including antisense RNAs involved in plasmid copy number control, expression of toxin-antitoxin systems and bacteriophage development. Here, we review the main findings related to the discovery of polyadenylation in prokaryotes, isolation, and characterization and regulation of bacterial poly(A)-adding activities, and discuss the impact of polyadenylation on prokaryotic mRNA metabolism and gene expression.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
Topics: Bacteria; Poly A; Polyadenylation; Prokaryotic Cells; RNA
PubMed: 30397102
DOI: 10.1098/rstb.2018.0166 -
Wiley Interdisciplinary Reviews. RNA 2011Although the first poly(A) polymerase (PAP) was discovered in Escherichia coli in 1962, the study of polyadenylation in bacteria was largely ignored for the next 30... (Review)
Review
Although the first poly(A) polymerase (PAP) was discovered in Escherichia coli in 1962, the study of polyadenylation in bacteria was largely ignored for the next 30 years. However, with the identification of the structural gene for E. coli PAP I in 1992, it became possible to analyze polyadenylation using both biochemical and genetic approaches. Subsequently, it has been shown that polyadenylation plays a multifunctional role in prokaryotic RNA metabolism. Although the bulk of our current understanding of prokaryotic polyadenylation comes from studies on E. coli, recent limited experiments with Cyanobacteria, organelles, and Archaea have widened our view on the diversity, complexity, and universality of the polyadenylation process. For example, the identification of polynucleotide phosphorylase (PNPase), a reversible phosphorolytic enzyme that is highly conserved in bacteria, as an additional PAP in E. coli caught everyone by surprise. In fact, PNPase has now been shown to be the source of post-transcriptional RNA modifications in a wide range of cells of prokaryotic origin including those that lack a eubacterial PAP homolog. Accordingly, the past few years have witnessed increased interest in the mechanism and role of post-transcriptional modifications in all species of prokaryotic origin. However, the fact that many of the poly(A) tails are very short and unstable as well as the presence of polynucleotide tails has posed significant technical challenges to the scientific community trying to unravel the mystery of polyadenylation in prokaryotes. This review discusses the current state of knowledge regarding polyadenylation and its functions in bacteria, organelles, and Archaea.
Topics: Animals; Archaea; Bacteria; Base Sequence; Humans; Models, Biological; Molecular Sequence Data; Organelles; Polyadenylation; Quality Control; RNA Stability
PubMed: 21344039
DOI: 10.1002/wrna.51 -
Journal of Experimental & Clinical... Feb 2021Occurring in over 60% of human genes, alternative polyadenylation (APA) results in numerous transcripts with differing 3'ends, thus greatly expanding the diversity of... (Review)
Review
Occurring in over 60% of human genes, alternative polyadenylation (APA) results in numerous transcripts with differing 3'ends, thus greatly expanding the diversity of mRNAs and of proteins derived from a single gene. As a key molecular mechanism, APA is involved in various gene regulation steps including mRNA maturation, mRNA stability, cellular RNA decay, and protein diversification. APA is frequently dysregulated in cancers leading to changes in oncogenes and tumor suppressor gene expressions. Recent studies have revealed various APA regulatory mechanisms that promote the development and progression of a number of human diseases, including cancer. Here, we provide an overview of four types of APA and their impacts on gene regulation. We focus particularly on the interaction of APA with microRNAs, RNA binding proteins and other related factors, the core pre-mRNA 3'end processing complex, and 3'UTR length change. We also describe next-generation sequencing methods and computational tools for use in poly(A) signal detection and APA repositories and databases. Finally, we summarize the current understanding of APA in cancer and provide our vision for future APA related research.
Topics: 3' Untranslated Regions; Animals; Computational Biology; Databases, Genetic; Gene Expression Regulation, Neoplastic; Humans; Neoplasms; Poly A; Polyadenylation; RNA Precursors; RNA Stability; RNA, Messenger; RNA-Binding Proteins; Signal Transduction
PubMed: 33526057
DOI: 10.1186/s13046-021-01852-7 -
Plant Science : An International... Nov 2022Recent years have seen an explosion of interest in the subject of alternative polyadenylation in plants. Connections between the polyadenylation complex and numerous... (Review)
Review
Recent years have seen an explosion of interest in the subject of alternative polyadenylation in plants. Connections between the polyadenylation complex and numerous developmental and stress responses are well-established. However, those that link stimuli with the functioning of the polyadenylation complex are less well understood. To this end, it is imperative to clearly delineate the roles of the polyadenylation complex in both plant growth AND alternative polyadenylation. It is also necessary to understand the ways by which other molecular processes may contribute to alternative polyadenylation. This review discusses these issues, with a focus on instances that reveal mechanisms by which mRNA polyadenylation may be regulated. Insights from from characterizations of mutants affected in the polyadenylation complex are discussed, as are the limitations of such characterizations when it comes to teasing out cause and effect. These limitations encourage explorations to other processes that are beyond the core polyadenylation complex. Two such processes that sculpt the plant transcriptome - transcription termination and the epigenetic control of transposon activity - also contribute to regulated poly(A) site choice. These subjects define "the right places" - molecular mechanisms that contribute to the wide-ranging control of gene expression via mRNA polyadenylation.
Topics: Humans; Plants; Poly A; Polyadenylation; RNA, Messenger; Transcriptome
PubMed: 36007628
DOI: 10.1016/j.plantsci.2022.111430 -
Nucleus (Austin, Tex.) 2014Polyadenylation is the RNA processing step that completes the maturation of nearly all eukaryotic mRNAs. It is a two-step nuclear process that involves an... (Review)
Review
Polyadenylation is the RNA processing step that completes the maturation of nearly all eukaryotic mRNAs. It is a two-step nuclear process that involves an endonucleolytic cleavage of the pre-mRNA at the 3'-end and the polymerization of a polyadenosine (polyA) tail, which is fundamental for mRNA stability, nuclear export and efficient translation during development. The core molecular machinery responsible for the definition of a polyA site includes several recognition, cleavage and polyadenylation factors that identify and act on a given polyA signal present in a pre-mRNA, usually an AAUAAA hexamer or similar sequence. This mechanism is tightly regulated by other cis-acting elements and trans-acting factors, and its misregulation can cause inefficient gene expression and may ultimately lead to disease. The majority of genes generate multiple mRNAs as a result of alternative polyadenylation in the 3'-untranslated region. The variable lengths of the 3' untranslated regions created by alternative polyadenylation are a recognizable target for differential regulation and clearly affect the fate of the transcript, ultimately modulating the expression of the gene. Over the past few years, several studies have highlighted the importance of polyadenylation and alternative polyadenylation in gene expression and their impact in a variety of physiological conditions, as well as in several illnesses. Abnormalities in the 3'-end processing mechanisms thus represent a common feature among many oncological, immunological, neurological and hematological disorders, but slight imbalances can lead to the natural establishment of a specific cellular state. This review addresses the key steps of polyadenylation and alternative polyadenylation in different cellular conditions and diseases focusing on the molecular effectors that ensure a faultless pre-mRNA 3' end formation.
Topics: 3' Untranslated Regions; Gene Expression Regulation, Developmental; Genetic Diseases, Inborn; Humans; Poly A; Polyadenylation; RNA Stability; RNA, Messenger
PubMed: 25484187
DOI: 10.4161/nucl.36360 -
Annual Review of Biochemistry 1997The 3'-ends of both prokaryotic and eukaryotic mRNA are polyadenylated, but the poly(A) tracts of prokaryotic mRNA are generally shorter, ranging from 15 to 60 adenylate... (Review)
Review
The 3'-ends of both prokaryotic and eukaryotic mRNA are polyadenylated, but the poly(A) tracts of prokaryotic mRNA are generally shorter, ranging from 15 to 60 adenylate residues and associated with only 2-60% of the molecules of a given mRNA species. The sites of polyadenylation of bacterial mRNA are diverse and include the 3'-ends of primary transcripts, the sites of endonucleolytic processing in the 3' untranslated and intercistronic regions, and sites within the coding regions of mRNA degradation products. The diversity of polyadenylation sites suggests that mRNA polyadenylation in prokaryotes is a relatively indiscriminate process that can occur at all mRNA's 3'-ends and does not require specific consensus sequences as in eukaryotes. Two poly(A) polymerases have been identified in Escherichia coli. They are encoded by unlinked genes, neither of which is essential for growth, suggesting significant functional overlap. Polyadenylation promotes the degradation of a regulatory RNA that inhibits the replication of bacterial plasmids and may play a similar role in the degradation of mRNA. However, under certain conditions, poly(A) tracts may lead to mRNA stabilization. Their ability to bind S1 ribosomal protein suggests that poly(A) tracts may also play a role in mRNA translation.
Topics: Archaea; Bacteria; Poly A; Polynucleotide Adenylyltransferase; RNA, Messenger
PubMed: 9242905
DOI: 10.1146/annurev.biochem.66.1.173 -
International Journal of Molecular... May 2018Facioscapulohumeral dystrophy (FSHD) is characterized by the contraction of the D4Z4 array located in the sub-telomeric region of the chromosome 4, leading to the... (Review)
Review
Facioscapulohumeral dystrophy (FSHD) is characterized by the contraction of the D4Z4 array located in the sub-telomeric region of the chromosome 4, leading to the aberrant expression of the DUX4 transcription factor and the mis-regulation of hundreds of genes. Several therapeutic strategies have been proposed among which the possibility to target the polyadenylation signal to silence the causative gene of the disease. Indeed, defects in mRNA polyadenylation leads to an alteration of the transcription termination, a disruption of mRNA transport from the nucleus to the cytoplasm decreasing the mRNA stability and translation efficiency. This review discusses the polyadenylation mechanisms, why alternative polyadenylation impacts gene expression, and how targeting polyadenylation signal may be a potential therapeutic approach for FSHD.
Topics: Gene Expression Regulation; Gene Silencing; Polyadenylation; RNA, Messenger
PubMed: 29751519
DOI: 10.3390/ijms19051347