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| Status |
Public on Sep 10, 2012 |
| Title |
Argonaute proteins couple chromatin silencing to alternative splicing (exon array) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
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
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| Overall design |
Transcriptome analysis of AGO2 and Dicer null MEF cells on GeneChip® 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.
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| Contributor(s) |
Ameyar-Zazoua M, Muchardt C, Harel-Bellan A, Batsché E |
| Citation(s) |
22961379 |
| Submission date |
Jul 30, 2012 |
| Last update date |
Mar 06, 2018 |
| Contact name |
Eric Batsche |
| Phone |
(33)1 44 27 34 77
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| Organization name |
IBPS - Institut Biologie Paris Seine
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| Department |
B2A Biological Adaptation and Ageing - UMR8256 CNRS
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| Lab |
Epigenetics and RNA metabolism in human diseases
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| Street address |
7-9, Quai Saint Bernard
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| City |
Paris |
| ZIP/Postal code |
75006 |
| Country |
France |
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| Platforms (2) |
| GPL6096 |
[MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [transcript (gene) version] |
| GPL6193 |
[MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [probe set (exon) version] |
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| Samples (18)
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| GSM978467 |
array1 for AGO2 knock-out in MEF cells, biological (gene) rep1 |
| GSM978468 |
array2 for AGO2 knock-out in MEF cells, biological (gene) rep2 |
| GSM978469 |
array3 for AGO2 knock-out in MEF cells, biological (gene) rep3 |
| GSM978470 |
array1 for Dicer knock-out in MEF cells, biological (gene) rep1 |
| GSM978471 |
array2 for Dicer knock-out in MEF cells, biological (gene) rep2 |
| GSM978472 |
array3 for Dicer knock-out in MEF cells, biological (gene) rep3 |
| GSM978473 |
array1 for wild-type MEF cells, biological (gene) rep1 |
| GSM978474 |
array2 for wild-type MEF cells, biological (gene) rep2 |
| GSM978475 |
array3 for wild-type MEF cells, biological (gene) rep3 |
| GSM978476 |
array1 for AGO2 knock-out in MEF cells, biological (exon) rep1 |
| GSM978477 |
array2 for AGO2 knock-out in MEF cells, biological (exon) rep2 |
| GSM978478 |
array3 for AGO2 knock-out in MEF cells, biological (exon) rep3 |
| GSM978479 |
array1 for Dicer knock-out in MEF cells, biological (exon) rep1 |
| GSM978480 |
array2 for Dicer knock-out in MEF cells, biological (exon) rep2 |
| GSM978481 |
array3 for Dicer knock-out in MEF cells, biological (exon) rep3 |
| GSM978482 |
array1 for wild-type MEF cells, biological (exon) rep1 |
| GSM978483 |
array2 for wild-type MEF cells, biological (exon) rep2 |
| GSM978484 |
array3 for wild-type MEF cells, biological (exon) rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE39749 |
Argonaute proteins couple chromatin silencing to alternative splicing |
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| Relations |
| BioProject |
PRJNA171691 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE39746_RAW.tar |
410.6 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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