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Argonaute immunoprecipitation reveals mis-annotation of human microRNAs

ABSTRACT: Argonaute immunoprecipitation reveals mis-annotation of human microRNAs

PROVIDER: PRJNA764930 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15997656.fastq.gz	Fastqsanger.gz
	SRR15997657.fastq.gz	Fastqsanger.gz
	SRR15997658.fastq.gz	Fastqsanger.gz
	SRR15997659.fastq.gz	Fastqsanger.gz
	SRR15997660.fastq.gz	Fastqsanger.gz

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Argonaute immunoprecipitation reveals mis-annotation of human microRNAs [miRNA-seq]

Project description:MicroRNAs (miRNAs) form the sequence recognition component of the RNA-induced silencing complex (RISC), bringing Argonaute (AGO) and other RISC-associated proteins to target transcripts where they mediate post-transcriptional gene silencing. High-throughput sequencing has helped to catalogue several thousand human miRNAs, as well as a plethora of other small RNAs derived from larger transcripts. Here, we take a closer inspection of sequencing data derived from cellular fractionation and AGO-RNA immunoprecipitation and find that a subset of small RNAs, despite being denoted as miRNAs, are in fact almost exclusively nuclear and do not associate with AGO. Experimental validation of a select number of these small RNAs also fails to show endogenous miRNA-like activity, suggesting they are degradation products from larger transcripts that have been mis-annotated. Despite this, the presumed miRNA functions of almost 20 of these have collectively been the subject of several hundred publications, emphasising the need to filter unlikely miRNA candidates from sequencing data and large miRNA-sequence repositories.

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Argonaute immunoprecipitation reveals mis-annotation of human microRNAs

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-04-23 | GSE184535 | GEO

Identifying mRNA Sequence Elements for Target Recognition by Human Argonaute Proteins

Project description:It is commonly known that mammalian microRNAs guide the RNA-induced silencing complex (RISC) to target mRNAs through the seed-pairing rule. However, recent experiments by co-immunoprecipitating the argonaute proteins (AGOs), the central catalytic component of RISC, have consistently revealed extensive AGO-associated mRNAs lacking seed complementarity with microRNAs. We herein test the hypothesis that AGO has its own binding preference within target mRNAs, independent of guide microRNAs. By systematically analyzing the data from in vivo cross-linking experiments with human AGOs, we have identified a structurally accessible and evolutionarily conserved region (~10 nucleotides) that alone can accurately predict AGO-mRNA associations, independent of the presence of microRNA binding sites. Within this region, we further identified an enriched motif that is also consistently present in several independent AGO-immunoprecipitation datasets. We used RNAcompete to enumerate the RNA-binding preference of human AGO2 to all possible 7-mer RNA sequences, and validated our motif in vitro. These findings reveal a novel function of AGOs as sequence-specific RNA-binding proteins, which may aid microRNAs in recognizing their targets with high specificity. Here, we analyze the RNA-binding preference of human Argonaute 2 protein using RNAcompete assay

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Project description:MicroRNAs (miRNAs) together with Argonaute (AGO) proteins form the core of the RNA-induced silencing complex (RISC) to regulate gene expression of their target RNAs post-transcriptionally. Argonaute proteins are subjected to intensive regulation via various post-translational modifications that can affect their stability, silencing efficacy and specificity for targeted gene regulation. We report here that in C. elegans, two conserved serine/threonine kinases - Casein Kinase 1 alpha 1 (CK1A1) and Casein Kinase 2 (CK2) - regulate a highly conserved phosphorylation cluster of 4 Serine residues (S988:S998) on the miRNA-specific AGO protein ALG-1. We show that CK1A1 phosphorylates ALG-1 at sites S992 and S995, while CK2 phosphorylates ALG-1 at sites S988 and S998. Furthermore, we demonstrate that phospho-mimicking mutants of the entire S988:S998 cluster rescue the various developmental defects observed upon depleting CK1A1 and CK2. In humans, we show that CK1A1 also acts as a priming kinase of this cluster on AGO2. Altogether, our data suggest that phosphorylation of AGO within the cluster by CK1A1 and CK2 is required for efficient miRISC-target RNA binding and silencing

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