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Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [4_Cnot shRNA-seq]

ABSTRACT: Here, we show that embryonic stem cells (ESCs) and muscle stem cells contain high levels of nuclear AGO proteins and that in ESCs nuclear AGO2 protein activity is sufficient to allow for differentiation. Transcriptome-wide mapping of binding sites at nucleotide resolution revealed that nuclear AGO2 expands its target sequence repertoire in a miRNA-dependent manner to include intronic sequences to induce post-transcriptional gene silencing

ORGANISM(S): Mus musculus

PROVIDER: GSE108798 | GEO | 2018/08/31

REPOSITORIES: GEO

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Nuclear miRNA-mediated gene silencing dependent on Argonaute proteins is required for embryonic stem cell differentiation [6_chr_seq]

Project description:Here, we show that embryonic stem cells (ESCs) and muscle stem cells contain high levels of nuclear AGO proteins and that in ESCs nuclear AGO2 protein activity is sufficient to allow for differentiation. Transcriptome-wide mapping of binding sites at nucleotide resolution revealed that nuclear AGO2 expands its target sequence repertoire in a miRNA-dependent manner to include intronic sequences to induce post-transcriptional gene silencing

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Argonaute proteins couple chromatin silencing to alternative splicing (exon array)

Project description:While Argonaute (AGO) proteins play a major role in transcriptional gene silencing (TGS) in many organisms, their role in the nucleus of somatic mammalian cells remains elusive. Here, we have purified AGO1 and AGO2 chromatin-embedded complexes, and found these proteins associated with previously described partners, but also with chromatin modifiers and, rather unexpectedly, with different splicing factors. Using the CD44 gene as a model for alternative splicing, we show that both AGO1 and AGO2 are required for Protein Kinase C (PKC)-dependent variant exon inclusion. AGO proteins facilitate the spliceosome recruitment and modulate the elongation rate of RNA polymerase II (RNAPII). The recruitment of AGO proteins to CD44 transcribed region is dependent on both the endonuclease Dicer and the chromodomain-containing protein HP1g, and results in locally increased levels of histone H3 lysine 9 (H3K9) methylation on variant exons. Genome wide analysis of splicing in either AGO2 or Dicer null cells showed that the two proteins have similar effects on many splicing events. Finally, sRNAs associated with nuclear AGO2 are mostly in sense orientation relative to protein-coding genes, supporting a role for intragenic antisense non-coding RNAs in the recruitment AGO and splicing factors. Together, our data demonstrate for the first time that the endogenous RNAi pathway is involved in alternative splicing decisions, unravelling a new model in which AGO proteins couple RNAPII elongation and chromatin modification. Study of AGO2 or Dicer knock-out on gene expression and splicing regulation in MEF cells Transcriptome analysis of AGO2 and Dicer null MEF cells on GeneChipM-BM-. Mouse Exon 1.0 ST Arrays (Affymetrix). Dicer null MEF cells and wild-type MEF cells were from M. Otsuka. AGO2 null MEF cells were from A. Tarakhovsky. Experiment has been done in experimental triplicates. 9 Total samples were analyzed.

2012-09-10 | E-GEOD-39746 | biostudies-arrayexpress

Argonaute proteins couple chromatin silencing to alternative splicing (RNA IP-Seq)

Project description:While Argonaute (AGO) proteins play a major role in transcriptional gene silencing (TGS) in many organisms, their role in the nucleus of somatic mammalian cells remains elusive. Here, we have purified AGO1 and AGO2 chromatin-embedded complexes, and found these proteins associated with previously described partners, but also with chromatin modifiers and, rather unexpectedly, with different splicing factors. Using the CD44 gene as a model for alternative splicing, we show that both AGO1 and AGO2 are required for Protein Kinase C (PKC)-dependent variant exon inclusion. AGO proteins facilitate the spliceosome recruitment and modulate the elongation rate of RNA polymerase II (RNAPII). The recruitment of AGO proteins to CD44 transcribed region is dependent on both the endonuclease Dicer and the chromodomain-containing protein HP1g, and results in locally increased levels of histone H3 lysine 9 (H3K9) methylation on variant exons. Genome wide analysis of splicing in either AGO2 or Dicer null cells showed that the two proteins have similar effects on many splicing events. Finally, sRNAs associated with nuclear AGO2 are mostly in sense orientation relative to protein-coding genes, supporting a role for intragenic antisense non-coding RNAs in the recruitment AGO and splicing factors. Together, our data demonstrate for the first time that the endogenous RNAi pathway is involved in alternative splicing decisions, unravelling a new model in which AGO proteins couple RNAPII elongation and chromatin modification. Deep sequencing of small RNAs (approx. 15-80 nucleotides) bound to either cytoplasmic or chromatin-associated AGO2 complex.

2012-09-10 | E-GEOD-39748 | biostudies-arrayexpress

Argonaute proteins couple chromatin silencing to alternative splicing (exon array)

2012-09-10 | GSE39746 | GEO

Argonaute proteins couple chromatin silencing to alternative splicing (RNA IP-Seq)

2012-09-10 | GSE39748 | GEO

Sites for Argonaute Binding within Human Nuclear RNA and their Impact on Alternative Splicing

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