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Location of polyadenylation sites within 3’ untranslated regions is linked to biological function in yeast

ABSTRACT: Location of polyadenylation sites within 3’ untranslated regions is linked to biological function in yeast

PROVIDER: PRJNA1132142 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29712955.fastq.gz	Fastqsanger.gz
	SRR29712956.fastq.gz	Fastqsanger.gz

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Location of polyadenylation sites within 3’ untranslated regions is linked to biological function in yeast

Project description:Expression of a typical yeast gene results in ~50 3’ mRNA isoforms that are distinguished by the locations of poly(A) sites within the 3’ untranslated regions (3’ UTRs).The location of poly(A) sites with respect to the translational termination codon varies considerably among genes, but it is unknown whether this has any functional significance.Using hierarchical clustering of 3’ UTRs, we identify eight classes ofS. cerevisiaegenes based on their poly(A) site locations within 3’ UTRs.Genes involved in related biological functions (GO categories) are uniquely over-represented in six of these classes.Similar analysis ofS. pombegenes reveals three classes of 3’ UTRs, all of which show over-representation of functionally related genes.Remarkably,S. cerevisiaeandS. pombehomologs have similar patterns of poly(A) site locations.These observations suggest that the location of poly(A) sites within 3’ UTRs has biological significance.

2024-10-15 | GSE271512 | GEO

Mapping 3’ untranslated regions reveal compromised alternative polyadenylation in human right ventricle failure

Project description:Right ventricular failure (RVF) impacts the prognosis of pulmonary arterial hypertension (PAH). Alternative polyadenylation (APA) generates transcript diversity and is implicated in diseases, including left heart failure. However, understanding genome-wide polyadenylation maps in RVF patients with PAH is limited, with no studies investigating RVF-specific APA events. This study mapped 3' untranslated regions (3'UTRs) to explore APA dynamics in RVF development, comparing healthy donors and RVF from patients with PAH.

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Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

Project description:The 3' untranslated regions (3' UTRs) of mRNAs contain cis-acting elements for posttranscriptional regulation of gene expression. Here, we report that mouse genes tend to express mRNAs with longer 3' UTRs as embryonic development progresses. This global regulation is controlled by alternative polyadenylation and coordinates with initiation of organogenesis and aspects of embryonic development, including morphogenesis, differentiation, and proliferation. Using myogenesis of C2C12 myoblast cells as a model, we recapitulated this process in vitro and found that 3' UTR lengthening is likely caused by weakening of mRNA polyadenylation activity. Because alternative 3' UTR sequences are typically longer and have higher AU content than constitutive ones, our results suggest that lengthening of 3' UTR can significantly augment posttranscriptional control of gene expression during embryonic development, such as microRNA-mediated regulation. Two biological replicates of C2C12 growth and differentiation conditions, repesctively

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Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during C2C12 differentiation

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Mapping 3’ untranslated regions reveal compromised alternative polyadenylation in human right ventricle failure

Project description:Mapping 3’ untranslated regions reveal compromised alternative polyadenylation in human right ventricle failure

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Argonaute Binding within 3’-Untranslated Regions Does Not Predict Gene Repression

Project description:Despite two decades of study, the full scope of RNAi in mammalian cells has remained obscure. Here we combine: 1) Knockout of argonaute (AGO) variants; 2) RNA sequencing analysis of gene expression changes; and 3) Enhanced Crosslinking Immunoprecipitation Sequencing (eCLIP-seq) using anti-AGO2 antibody to identify potential microRNA (miRNA) binding sites. We find that knocking out AGO1, AGO2, and AGO3 are necessary to achieve full impact on gene expression. eCLIP-seq reveals several hundred significant AGO2 associations within 3’-untranslated regions. The standard mechanism of miRNA action would suggest that these associations repress gene expression. Contrary to this expectation, associations between AGO and RNA are poorly correlated with gene repression in wild-type versus knockout cells. Many clusters are associated with increased gene expression in wild-type versus knock out cells, including the strongest cluster within the MYC 3’-UTR. Our results suggest that assumptions about miRNA action should be re-examined.

2020-05-27 | GSE146688 | GEO

Argonaute Binding within 3’-Untranslated Regions Does Not Predict Gene Repression

Project description:Argonaute Binding within 3’-Untranslated Regions Does Not Predict Gene Repression

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5' Untranslated regions tune Toxoplasma translation [MPRA]

Project description:5' Untranslated regions tune Toxoplasma translation [MPRA]

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5' Untranslated regions tune Toxoplasma translation [Ribosome Profiling]

Project description:5' Untranslated regions tune Toxoplasma translation [Ribosome Profiling]

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Dehydration stress extends mRNA 3' untranslated regions with noncoding RNA functions in Arabidopsis

Project description:The 3' untranslated regions (3' UTRs) of mRNAs play important roles in the regulation of mRNA localization, translation, and stability. Alternative cleavage and polyadenylation (APA) generates mRNAs with different 3' UTRs, but the involvement of this process in stress response has not been clarified. Here, we report that a subset of stress-related genes exhibits 3' UTR extensions of their mRNAs during dehydration stress. These extended 3' UTRs have characteristics of long noncoding RNAs and likely do not interact with miRNAs. Functional studies using T-DNA insertion mutants reveal that they can function as antisense transcripts to repress expression levels of sense genes from the opposite strand, or can activate the transcription of downstream genes from the same strand. Poly(A) signal analysis reveal that mRNAs with 3' UTR extensions have weaker poly(A) signals than mRNAs without 3' UTR extensions. Finally, we show that their biogenesis is partially dependent on a trans-acting factor FPA. Taken together, we report that dehydration stress could induce mRNA 3' UTR extensions, and elucidate a novel function for these stress-induced 3' UTR extensions as long noncoding RNAs in the regulation of their neighboring genes.

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