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| Status |
Public on May 24, 2022 |
| Title |
The lncRNA RUS shapes gene expression program towards neurogenesis [ChIRP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The evolution of brain complexity correlates with an increased expression of long, non-coding (lnc) RNAs in neuronal tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during neurogenesis. We present a first functional characterization of the lncRNA LINC01322, which we term RUS for 'RNA upstream of Slitrk3'. The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases along with neuronal markers during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation, with arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner.
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| Overall design |
Chromatin Isolation by RNA Purification (ChIRP) of RUS bound chromatin binding sites using two independent probe sets (odd & even) and an input control (3 replicates per condition).
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| Contributor(s) |
Schneider MF, Müller V, Müller S, Lichtenthaler S, Scheuermann J, Becker PB |
| Citation(s) |
35688487 |
| Submission date |
Feb 10, 2022 |
| Last update date |
Jul 14, 2022 |
| Contact name |
Marius Frederik Schneider |
| E-mail(s) |
Marius.Schneider@med.uni-muenchen.de
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| Organization name |
Biomedical center munich - LMU
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| Department |
molecular biology
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| Lab |
Becker
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| Street address |
Großhaderner Str. 9
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| City |
Planegg-Martinsried |
| State/province |
Bayern |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (9)
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| GSM5888608 |
NSCs, input, rep2 |
| GSM5888609 |
NSCs, even, rep2 |
| GSM5888610 |
NSCs, odd, rep2 |
| GSM5888611 |
NSCs, input, rep3 |
| GSM5888612 |
NSCs, even, rep3 |
| GSM5888613 |
NSCs, odd, rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE196528 |
The lncRNA RUS shapes gene expression program towards neurogenesis |
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| Relations |
| BioProject |
PRJNA805253 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE196527_RAW.tar |
661.1 Mb |
(http)(custom) |
TAR (of BEDGRAPH) |
| GSE196527_RUS_rep1.bedgraph.gz |
43.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE196527_RUS_rep2.bedgraph.gz |
1.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE196527_RUS_rep3.bedgraph.gz |
4.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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