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Argonaute immunoprecipitation reveals mis-annotation of human microRNAs [HITS-CLIP]

ABSTRACT: Argonaute immunoprecipitation reveals mis-annotation of human microRNAs [HITS-CLIP]

PROVIDER: PRJNA764932 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15997474.fastq.gz	Fastqsanger.gz
	SRR15997475.fastq.gz	Fastqsanger.gz
	SRR15997476.fastq.gz	Fastqsanger.gz
	SRR15997477.fastq.gz	Fastqsanger.gz
	SRR15997478.fastq.gz	Fastqsanger.gz

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Argonaute immunoprecipitation reveals mis-annotation of human microRNAs [HITS-CLIP]

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

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

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Argonaute HITS-CLIP in wild-type and APOBEC1-deficient BMDMs

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HITS–CLIP reveals Argonaute 1-associated MicroRNAs and Target Sites in Schistosoma japonicum

Project description:In this study, we isolated and identified the small RNAs associated with the S. japonicum Argonaute protein, SjAgo1, by HITS-CLIP combined with bioinformatic analysis. These data reveal a genome-wide miRNA-mRNA interaction map in S. japonicum in vivo, which will help us understand the complex gene regulation network in this pathogen and thereby facilitate to develop novel approaches against Schistosomiasis.

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Camk2a-neuron specific FLAG-Ago HITS-CLIP

Project description:The HITS-CLIP procedure was used to detect miRNA mediated Argonaute (Ago) binding in Camk2a mouse neurons.

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Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts.

Project description:High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) allows for high resolution, genome-wide mapping of RNA-binding proteins. We found that substantial mispriming during reverse transcription results in the overrepresentation of sequences complementary to the primer used for reverse transcription. Up to 45% of peaks in publicly available HITS-CLIP libraries are attributable to this artifact, and the majority of libraries have detectable levels of mispriming. We also found that standard techniques for validating miRNA-target interactions fail to differentiate between artifactual peaks and physiologically relevant peaks. Here, we present a modification to the HITS-CLIP protocol that effectively eliminates this artifact. Argonaute HITS-CLIP on the MCF-7 breast cancer cell line treated with 17Î²-estradiol for 0, 6 or 24 hours using a nested reverse transcriptions pimer and protected or unprotected reverse PCR primers for library amplification.

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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