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

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

PROVIDER: PRJNA611621 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11276900.fastq.gz	Fastqsanger.gz
	SRR11276901.fastq.gz	Fastqsanger.gz
	SRR11276902.fastq.gz	Fastqsanger.gz
	SRR11276903.fastq.gz	Fastqsanger.gz
	SRR11276904.fastq.gz	Fastqsanger.gz

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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 poorly predicts gene repression.

Project description:Despite two decades of study, the full scope of RNAi in mammalian cells has remained obscure. Here we combine: (i) Knockout of argonaute (AGO) variants; (ii) RNA sequencing analysis of gene expression changes and (iii) 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 together are necessary to achieve full impact on steady state levels of mRNA. eCLIP-seq located AGO2 protein associations within 3'-untranslated regions. The standard mechanism of miRNA action would suggest that these associations should 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 steady state levels of mRNA 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.

| S-EPMC7367155 | biostudies-literature

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

Peptides encoded by 5’ untranslated regions mediate pain sensitization

Project description:Peptides encoded by 5’ untranslated regions mediate pain sensitization

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Peptides encoded by 5’ untranslated regions mediate pain sensitization

Project description:Nociceptors are neurons responsible for the detection of pain producing stimuli. Persistent changes in their activity, termed plasticity, benefit survival through injury avoidance and are regulated on a translational basis. Yet, the mRNAs whose translation facilitates plasticity are unknown. Here, we apply ribosome profiling to dorsal root ganglion and identify a small number of transcripts that are selectively translated in response to plasticity mediators. Among them are Arc and Fos, genes implicated in episodic learning in the brain. We demonstrate that the ribosomal S6 kinase 1 is responsible for their production in nociceptors. Blocking S6 driven translation also reduces pain associated behavioral responses in vivo. In addition to translation of coding regions of mRNA, we detect pervasive ribosome occupancy in 5’ untranslated regions. We find that peptides encoded by open reading frames in the 5’ untranslated regions of Calca and Egr2 increase neuronal excitability in vitro and are sufficient to induce pain-like behaviors in vivo. Together, our findings uncover new targets of translational control that drive changes in plasticity and suggest new mechanisms for targeted pain therapeutics that disrupt pain signaling.

2020-02-01 | GSE117043 | GEO

miRNAs associated with the different human Argonaute proteins

Project description:microRNAs (miRNAs) are small non-coding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3’ untranslated region (UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer-independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected. Examination of miRNAs associated with endogenous human Ago1-4 in HeLa cells

2013-03-29 | E-GEOD-45506 | biostudies-arrayexpress

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

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

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Argonaute protein binding Met-tRNAiMet represses translation initiation

Project description:Initiation factor 2 (eIF2) delivering the initiator methionine transfer RNA (Met-tRNAiMet) to the ribosome is a conserved key step in translation initiation. Argonaute (Ago) proteins were initially identified as eukaryotic translation initiation factor 2C,2 (EIF2C2). In the past 2 decades, Argonaute were extensively studied as a core component of RNA induced gene silencing, although various model raised the exact mechanism of Ago in translation repression remains elusive. Here we found Ago protein directly bind Met- tRNAiMet independent of miRNA binding, which interfere the formation of the ternary complex eIF2–GTP–Met- tRNAiMet. Ago proteins can solely inhibit protein synthesis via competing tRNAiMet with eIF2. Our findings elucidate a physical link between Ago and tRNAiMet and provide mechanistic insight into translation repression by Ago proteins.

2022-02-01 | GSE181004 | GEO

Nuclear Localization of Argonaute is affected by Cell Density and May Relieve Repression by microRNAs

Project description:Nuclear Localization of Argonaute is affected by Cell Density and May Relieve Repression by microRNAs

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PREDICT 2

Project description:PREDICT 2

| PRJEB75460 | ENA