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Series GSE76248 Query DataSets for GSE76248
Status Public on Apr 06, 2018
Title MiCEE: a ncRNA-protein complex mediates epigenetic silencing and nucleolus organization
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary The majority of the eukaryotic genome is transcribed into non-coding RNAs (ncRNAs), which are important regulators of different biological processes in the cell nucleus as part of the machinery controlling chromatin structure. However, the full extent of ncRNAs function has remained elusive. Here we deciphered the function of the microRNA Mirlet7d as a key regulator of the expression of bi-directionally transcribed genes. We found that nuclear Mirlet7d binds ncRNAs expressed from these genes. The Mirlet7d-ncRNA duplexes are further bound by C1D, which in turn targets the RNA exosome complex and EZH2 to the bi-directionally active loci. The exosome degrades the ncRNAs, whereas EZH2 induces heterochromatin and transcriptional silencing. Moreover, this multicomponent RNA-protein complex, which we called MiCEE, tethers the regulated genes to the perinucleolar region, thereby being required for proper nucleolus organization. Our study demonstrates that the MiCEE complex mediates epigenetic silencing of bi-directionally expressed genes and global genome organization.

Overall design RNA_Seq Data from MLE-12 cells:
i) Investigate the effect of Mirlet7d gain-of-function on the RNA population in the nucleus of the cell.
ii) Pulldown experiment to identify the RNAs that interact with Mirlet7d in the nucleus of the cell.
RNA-seq after Mirlet7d-Pulldown, RNA-seq after Mirlet7d-GOF, Mirlet7d-ChIRP-seq and small_RNA_Seq from MLE-12 cells
Citation(s) 29867223
Submission date Dec 22, 2015
Last update date Oct 07, 2023
Contact name Guillermo Barreto
Organization name CNRS Director of Research
Department Campus Biologie-Santé. Faculté de Médecine
Lab Laboratoire IMoPA. UMR 7365 CNRS
Street address 9, Avenue de la Forêt de Haye ‐ BP 20199
City Nancy Cedex
ZIP/Postal code 54505
Country France
Platforms (2)
GPL18635 Ion Torrent Proton (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (12)
GSM1977639 Nuclear_RNA_seq_Mirlet7d_GOF
GSM1977640 Nuclear_RNA_seq_Random_GOF
GSM1977641 Mirlet7d_Input
BioProject PRJNA306722
SRA SRP067683

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Supplementary file Size Download File type/resource
GSE76248_RAW.tar 257.1 Mb (http)(custom) TAR (of BED, BEDGRAPH, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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