scholarly journals The RS Domain of Human CFIm68 Plays a Key Role in Selection Between Alternative Sites of Pre-mRNA Cleavage and Polyadenylation

2017 ◽  
Author(s):  
Jessica G. Hardy ◽  
Michael Tellier ◽  
Shona Murphy ◽  
Chris J. Norbury
Keyword(s):  
Molecular Mechanisms ◽  
Alternative Polyadenylation ◽  
Hek293 Cells ◽  
Translation Efficiency ◽  
Mrna Isoforms ◽  
Protein Coding ◽  
Mrna Cleavage ◽  
Cleavage And Polyadenylation ◽  
Alternative Sites

AbstractMany eukaryotic protein-coding genes give rise to alternative mRNA isoforms with identical protein-coding capacities but which differ in the extents of their 3´ untranslated regions (3´UTRs), due to the usage of alternative sites of pre-mRNA cleavage and polyadenylation. By governing the presence of regulatory 3´UTR sequences, this type of alternative polyadenylation (APA) can significantly influence the stability, localisation and translation efficiency of mRNA. Though a variety of molecular mechanisms for APA have been proposed, previous studies have identified a pivotal role for the multi-subunit cleavage factor I (CFIm) in this process in mammals. Here we show that, in line with previous reports, depletion of the CFIm 68 kDa subunit (CFIm68) by CRISPR/Cas9-mediated gene disruption in HEK293 cells leads to a shift towards the use of promoter-proximal poly(A) sites. Using these cells as the basis for a complementation assay, we show that CFIm68 lacking its arginine/serine-rich (RS) domain retains the ability to form a nuclear complex with other CFIm subunits, but selectively lacks the capacity to restore polyadenylation at promoter-distal sites. In addition, nanoparticle-mediated analysis indicates that the RS domain is extensively phosphorylated in vivo. Overall, these results suggest that the CFIm68 RS domain makes a key regulatory contribution to APA.

scholarly journals Seeking a Role for Translational Control by Alternative Polyadenylation in Saccharomyces cerevisiae

2021 ◽  
Vol 9 (9) ◽  
pp. 1885
Author(s):  
Rachael E. Turner ◽  
Traude H. Beilharz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Translational Control ◽  
Model Organism ◽  
Alternative Polyadenylation ◽  
Ribosome Profiling ◽  
Translation Efficiency ◽  
Mrna Isoforms ◽  
Cleavage And Polyadenylation ◽  
Made In

Alternative polyadenylation (APA) represents an important mechanism for regulating isoform-specific translation efficiency, stability, and localisation. Though some progress has been made in understanding its consequences in metazoans, the role of APA in the model organism Saccharomyces cerevisiae remains a relative mystery because, despite abundant studies on the translational state of mRNA, none differentiate mRNA isoforms’ alternative 3′-end. This review discusses the implications of alternative polyadenylation in S. cerevisiae using other organisms to draw inferences. Given the foundational role that research in this yeast has played in the discovery of the mechanisms of cleavage and polyadenylation and in the drivers of APA, it is surprising that such an inference is required. However, because advances in ribosome profiling are insensitive to APA, how it impacts translation is still unclear. To bridge the gap between widespread observed APA and the discovery of any functional consequence, we also provide a review of the experimental techniques used to uncover the functional importance of 3′ UTR isoforms on translation.

scholarly journals Regulation, diversity and function of MECP2 exon and 3′UTR isoforms

2020 ◽  
Vol 29 (R1) ◽  
pp. R89-R99
Author(s):  
Deivid Carvalho Rodrigues ◽  
Marat Mufteev ◽  
James Ellis
Keyword(s):  
Dna Binding ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Alternative Polyadenylation ◽  
Cell Types ◽  
Protein Isoforms ◽  
Translation Efficiency ◽  
Mrna Isoforms ◽  
Exon 2 ◽  
Messenger Ribonucleic Acid

Abstract 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.

scholarly journals Cell Cycle Kinase Polo Is Controlled by a Widespread 3′ Untranslated Region Regulatory Sequence inDrosophila melanogaster

2019 ◽  
Vol 39 (15) ◽  
Author(s):  
Marta S. Oliveira ◽  
Jaime Freitas ◽  
Pedro A. B. Pinto ◽  
Ana de Jesus ◽  
Joana Tavares ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Drosophila Melanogaster ◽  
Untranslated Region ◽  
Molecular Mechanisms ◽  
Alternative Polyadenylation ◽  
Upstream Sequence ◽  
Sequence Element ◽  
Content Type ◽  
Cell Cycle Kinase

ABSTRACTAlternative polyadenylation generates transcriptomic diversity, although the physiological impact and regulatory mechanisms involved are still poorly understood. The cell cycle kinase Polo is controlled by alternative polyadenylation in the 3′ untranslated region (3′UTR), with critical physiological consequences. Here, we characterized the molecular mechanisms required forpoloalternative polyadenylation. We identified a conserved upstream sequence element (USE) close to thepoloproximal poly(A) signal. Transgenic flies without this sequence show incorrect selection ofpolopoly(A) signals with consequent downregulation of Polo expression levels and insufficient/defective activation of Polo kinetochore targets Mps1 and Aurora B. Deletion of the USE results in abnormal mitoses in neuroblasts, revealing a role for this sequencein vivo. We found that Hephaestus binds to the USE RNA and thathephaestusmutants display defects inpoloalternative polyadenylation concomitant with a striking reduction in Polo protein levels, leading to mitotic errors and aneuploidy. Bioinformatic analyses show that the USE is preferentially localized upstream of noncanonical polyadenylation signals inDrosophila melanogastergenes. Taken together, our results revealed the molecular mechanisms involved inpoloalternative polyadenylation, with remarkable physiological functions in Polo expression and activity at the kinetochores, and disclosed a newin vivofunction for USEs inDrosophila melanogaster.

scholarly journals The C. elegans 3’-UTRome V2: an updated genomic resource to study 3’-UTR biology

2019 ◽  
Author(s):  
HS Steber ◽  
C Gallante ◽  
S O’Brien ◽  
P.-L Chiu ◽  
M Mangone
Keyword(s):  
Living Organism ◽  
Regulatory Elements ◽  
Untranslated Regions ◽  
High Quality ◽  
Protein Coding ◽  
C Elegans ◽  
Mrna Cleavage ◽  
Entire Collection ◽  
Cleavage And Polyadenylation ◽  
Genomic Resource

ABSTRACT3’-Untranslated Regions (3’-UTRs) of mRNAs emerged as central regulators of cellular function as they contain important but poorly-characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode C. elegans is ideal to study these interactions since it possesses a well-defined 3’-UTRome. In order to improve its annotation, we have used a genomics approach to download raw transcriptome data for 1,088 transcriptome datasets corresponding to the entire collection of C. elegans trancriptomes from 2015 to 2018 from the Sequence Read Archive at the NCBI. We then extracted and mapped high-quality 3’-UTR data at ultra-deep coverage. Here we describe and release to the community the updated version of the worm 3’-UTRome, which we named 3’-UTRome v2. This resource contains high-quality 3’-UTR data mapped at single base ultra-resolution for 23,084 3’-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this dataset to study and probe principles of mRNA cleavage and polyadenylation in C. elegans. The worm 3’-UTRome v2 represents the most comprehensive and high-resolution 3’-UTR dataset available in C. elegans and provides a novel resource to investigate the mRNA cleavage and polyadenylation reaction, 3’-UTR biology and miRNA targeting in a living organism.

scholarly journals A functional non-coding RNA is produced from xbp-1 mRNA

2020 ◽  
Author(s):  
Xiao Liu ◽  
Jean-Denis Beaudoin ◽  
Carrie Ann Davison ◽  
Sara G. Kosmaczewski ◽  
Benjamin I. Meyer ◽  
...  
Keyword(s):  
Axon Regeneration ◽  
Biologically Active ◽  
Protein Coding ◽  
Unfolded Protein ◽  
Mrna Cleavage ◽  
Non Coding Rna ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Fine Tune

AbstractThe xbp-1 mRNA encodes the XBP-1 transcription factor, a critical part of the unfolded protein response. Here we report that an RNA fragment produced from xbp-1 mRNA cleavage is a biologically active non-coding RNA (ncRNA) in Caenorhabditis elegans neurons, providing the first example of ncRNA derived from mRNA cleavage. We show that the xbp-1 ncRNA is crucial for axon regeneration in vivo, and that it acts independently of the protein-coding function of the xbp-1 transcript. Structural analysis indicates that the function of the xbp-1 ncRNA depends on a single RNA stem; and this stem forms only in the cleaved xbp-1 ncRNA fragment. Disruption of this stem abolishes the non-coding but not coding function of the endogenous xbp-1 transcript. Thus, cleavage of the xbp-1 mRNA bifurcates it into a coding and a non-coding pathway; modulation of the two pathways may allow neurons to fine-tune their response to injury and other stresses.Graphic abstract

scholarly journals Precise removal of Calm1 long 3′ UTR isoform by CRISPR-Cas9 genome editing impairs dorsal root ganglion development in mice

2019 ◽  
Author(s):  
Hannah N. Gruner ◽  
Bongmin Bae ◽  
Maebh Lynch ◽  
Daniel Oliver ◽  
Kevin So ◽  
...  
Keyword(s):  
Dorsal Root Ganglion ◽  
Genome Editing ◽  
Neural Development ◽  
Dorsal Root ◽  
Physiological Role ◽  
Mrna Isoforms ◽  
A Genome ◽  
Mouse Tissues ◽  
Cleavage And Polyadenylation

AbstractMost mammalian genes are subject to Alternative cleavage and PolyAdenylation (APA), often resulting in alternative length 3′ UTR isoforms. Thousands of extended or long 3′ UTR variants are preferentially expressed in neuron-enriched tissues of metazoans. However, the in vivo functions of these long 3′ UTR isoforms are largely unknown. Calmodulin 1 (Calm1) is a key integrator of calcium signaling that is required for correct neural development. Calm1 generates short (Calm1-S) and long 3′ UTR (Calm1-L) mRNA isoforms via APA. We found Calm1-S to be broadly expressed across mouse tissues, whereas Calm1-L expression was largely restricted to neural tissues, including the dorsal root ganglion (DRG). Using CRISPR-Cas9 genome editing, a series of mouse deletion lines were generated that successfully eliminated expression of Calm1-L while maintaining expression of Calm1-S. One of these lines, Calm1Δ3′ UTR, carried a 163 bp deletion surrounding the distal polyA site. Examination of Calm1Δ3′ UTR embryos revealed disrupted development of the DRG. In Calm1Δ3′ UTR DRG explant cultures undergoing axon outgrowth, we observed a dramatic increase in axon fasciculation. These results demonstrate a physiological role for Calm1-L in DRG development, and more generally, establish a genome-editing strategy to study in vivo functions of long 3′ UTR isoforms.Author SummaryMore than half of all human genes generate alternative mRNA isoforms which differ in the length of their 3’ Untranslated regions (3’ UTRs). Through a process called Alternative Cleavage and Polyadenylation thousands of broadly expressed genes preferentially express long 3’ UTR variants in brain tissues whereas their short 3’ UTR counterparts are more broadly expressed. A challenge to study the functions of these transcripts has been to generate loss of function mutant animals that lack a long 3’ UTR isoform but maintain expression of the corresponding short 3’ UTR isoform. Here, we used the precise, rapid, and efficient approach of CRISPR genome-editing to generate long 3’ UTR mutant mice. These mice, which do not express the long 3’ UTR of the Calmodulin 1 (Calm1) gene, exhibit impairment in the development of sensory neurons, including increased fasciculation of axons and aberrant cell body migration. This finding is important because it provides conclusive genetic evidence for a neural function of a long 3’ UTR isoform in an animal. The CRISPR genome-editing approach used here can be applied to the study of neuron-enriched long 3’ UTR isoforms, which number in the thousands and have largely unexplored functions.

scholarly journals FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Caryn R Hale ◽  
Kirsty Sawicka ◽  
Kevin Mora ◽  
John J Fak ◽  
Jin Joo Kang ◽  
...  
Keyword(s):  
Cell Body ◽  
Pyramidal Neurons ◽  
Neuronal Cell ◽  
Alternative Polyadenylation ◽  
Cell Type ◽  
Mrna Isoforms ◽  
Protein Coding ◽  
Ca1 Pyramidal Neurons ◽  
Synaptic Functions ◽  
Cell Type Specific

Neurons rely on translation of synaptic mRNAs in order to generate activity-dependent changes in plasticity. Here we develop a strategy combining compartment-specific CLIP and TRAP in conditionally tagged mice to precisely define the ribosome-bound dendritic transcriptome of CA1 pyramidal neurons. We identify CA1 dendritic transcripts with differentially localized mRNA isoforms generated by alternative polyadenylation and alternative splicing, including many which have altered protein-coding capacity. Among dendritic mRNAs, FMRP targets were found to be overrepresented. Cell-type specific FMRP-CLIP and TRAP in microdissected CA1 neuropil revealed 383 dendritic FMRP targets and suggests that FMRP differentially regulates functionally distinct modules in CA1 dendrites and cell bodies. FMRP regulates ~15-20% of mRNAs encoding synaptic functions and 10% of chromatin modulators, in the dendrite and cell body, respectively. In the absence of FMRP, dendritic FMRP targets had increased ribosome association, consistent with a function for FMRP in synaptic translational repression. Conversely, downregulation of FMRP targets involved in chromatin regulation in cell bodies and suggest a role for FMRP in stabilizing mRNAs containing stalled ribosomes in this compartment. Together, the data support a model in which FMRP regulates the translation and expression of synaptic and nuclear proteins within different compartments of a single neuronal cell type.

scholarly journals Elevated Expression of the RNA-Binding Protein IGF2BP1 Enhances the Mrna Stability and Translation Efficiency of INHBA to Promote the Invasion and Migration of Esophageal Squamous Cancer Cells

2021 ◽  
Author(s):  
Juan-Juan Wang ◽  
Ding-Xiong Chen ◽  
Yu Zhang ◽  
Yan Cai ◽  
Xin Xu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Rna Binding ◽  
Mrna Level ◽  
Rna Stability ◽  
Translation Efficiency ◽  
Invasion And Migration ◽  
Frequent Event ◽  
Elevated Expression ◽  
And Migration

Abstract Background: The mechanisms underlying the occurrence and development of esophageal squamous cell carcinoma (ESCC) remains to be elucidated. The present study aims to investigate the roles and implications of IGF2BP1 overexpression in ESCC.Methods: IGF2BP1 protein expression in ESCC samples was assessed by immunohistochemistry (IHC), and the mRNA abundance of IGF2BP1 and INHBA was analyzed with TCGA datasets and by RNA in situ hybridization (RISH). Cell viability, migration, invasion and in vivo metastasis assays were performed to explore the roles of IGF2BP1 overexpression in ESCC. RNA immunoprecipitation sequencing (RIP-seq) and mass spectrometry were applied to identify the target RNAs and interacting proteins of IGF2BP1, respectively. RIP-PCR, RNA pulldown, immunofluorescence (IF), gene-specific m6A PCR and RNA stability assays were used to uncover the molecular mechanisms underlying the malignant phenotypes of ESCC cells caused by IGF2BP1 dysregulation. The methylation level of the IGF2BP1 promoter region was detected by methylation-specific PCR (MSP-PCR). BTYNB, a small molecular inhibitor was evaluated for its inhibitory effect on the malignant phenotypes of ESCC cells.Results: IGF2BP1 overexpression was detected in ESCC tissues and associated with the depth of tumor invasion. Knockdown of IGF2BP1 inhibited ESCC cell invasion and migration as well as tumor metastasis. Mechanistically, we observed that IGF2BP1 bound and stabilized INHBA mRNA and then enhanced the translation of INHBA, leading to the activation of Smad2/3 signaling, thus promoting malignant phenotypes. The mRNA level of INHBA was upregulated in ESCC tissues as well. Furthermore, IGF2BP1 interacted with G3BP stress granule assembly factor 1 (G3BP1) and activated the INHBA-Smad signaling. BTYNB abolished this activated signaling and significantly attenuated the malignant phenotypes of ESCC cells. In addition, IGF2BP1 mRNA expression in ESCC cells was negatively correlated with the level of its promoter methylation.Conclusions: Elevated expression of IGF2BP1 is a frequent event in ESCC tissues and might be a candidate biomarker for the disease. IGF2BP1 overexpression promotes the invasion and migration of ESCC cells by activating the INHBA-TGF-β-Smad2/3 pathway, providing a potential therapeutic target for ESCC patients with high expression of IGF2BP1.

scholarly journals Cleavage factor Im (CFIm) as a regulator of alternative polyadenylation

2016 ◽  
Vol 44 (4) ◽  
pp. 1051-1057 ◽  
Author(s):  
Jessica G. Hardy ◽  
Chris J. Norbury
Keyword(s):  
Cleavage Site ◽  
Current Knowledge ◽  
Alternative Polyadenylation ◽  
Potential Contribution ◽  
Protein Coding ◽  
Site Use ◽  
Cleavage And Polyadenylation ◽  
Regulatory Potential ◽  
Mammalian Protein ◽  
Candidate Regulator

Most mammalian protein coding genes are subject to alternative cleavage and polyadenylation (APA), which can generate distinct mRNA 3′UTRs with differing regulatory potential. Although this process has been intensely studied in recent years, it remains unclear how and to what extent cleavage site selection is regulated under different physiological conditions. The cleavage factor Im (CFIm) complex is a core component of the mammalian cleavage machinery, and the observation that its depletion causes transcriptome-wide changes in cleavage site use makes it a key candidate regulator of APA. This review aims to summarize current knowledge of the CFIm complex, and explores the evidence surrounding its potential contribution to regulation of APA.

scholarly journals Systematic identification of functional SNPs interrupting 3’ UTR polyadenylation signals

2019 ◽  
Author(s):  
Eldad David Shulman ◽  
Ran Elkon
Keyword(s):  
Gene Expression ◽  
Nuclear Export ◽  
Cellular Localization ◽  
Alternative Polyadenylation ◽  
Regulatory Elements ◽  
Translation Efficiency ◽  
Protein Coding ◽  
A Site ◽  
The Impact ◽  
Main Variant

AbstractAlternative polyadenylation (APA) is emerging as a widespread regulatory layer as the majority of human protein-coding genes contain several polyadenylation (p(A)) sites in their 3’ UTRs. By generating isoforms with different 3’ UTR length, APA potentially affects mRNA stability, translation efficiency, nuclear export, and cellular localization. Polyadenylation sites are regulated by adjacent RNA cis-regulatory elements, the principals among them are the polyadenylation signal (PAS) AAUAAA and its main variant AUUAAA, typically located ~20- nt upstream of the p(A) site. Mutations in PAS and other auxiliary poly(A) cis-elements in the 3’ UTR of several genes have been shown to cause human Mendelian diseases, and to date, only a few common SNPs that regulate APA were associated with complex diseases. Here, we systematically searched for SNPs that affect gene expression and human traits by modulation of 3’ UTR APA. Focusing on the variants most likely to exert the strongest effect, we identified 2,305 SNPs that interrupt the canonical PAS or its main variant. Implementing pA-QTL tests using GTEx RNA-seq data, we identified 139 PAS SNPs significantly associated with the usage of their p(A) site. As expected, PAS-interrupting alleles were significantly linked with decreased cleavage at their p(A) site and the consequential 3’ UTR lengthening. As an indication for a functional effect of these PAS SNPs on gene expression, 65 of the pA-QTLs were also detected as eQTLs of the same gene in the same tissue. Furthermore, we observed that PAS-interrupting alleles linked with 3’ UTR lengthening were also strongly associated with decreased gene expression, pointing that shorter isoforms generated by APA are generally more stable than longer ones. Last, indicative of the impact of PAS SNPs on human phenotypes, 53 pA-QTLs overlapped GWAS SNPs that are significantly linked with human traits.

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