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| Status |
Public on Jan 09, 2019 |
| Title |
LncRNAs and open chromatin regions constitute midbrain dopaminergic neuron- specific molecular signatures |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Midbrain dopaminergic (DA) neurons are involved in diverse neurological functions, including control of movements, emotions or reward. In return, their dysfunctions cause severe clinical manifestations in humans, such as the appearance of motor and cognitive symptoms in Parkinson’s Disease. The physiology and pathophysiology of these neurons are widely studied, mostly with respect to molecular mechanisms implicating protein-coding genes. In contrast, the contribution of non-coding elements of the genome to DA neurons function is poorly investigated.
In this study, we isolated DA neurons from E14.5 ventral mesencephalons, and used RNA-seq and ATAC-seq to establish and describe the repertoires of long non-coding RNAs (lncRNAs) and putative DNA regulatory regions, such as enhancers, specific to this neuronal population. We identified 990 novel lncRNAs out of 1,363 expressed in DA neurons, and most of them were not found in hindbrain serotonergic (5-HT) neurons, indicating a high degree of cell-specificity. This feature was also observed regarding open chromatin regions, as 39% of the ATAC-seq peaks from the DA repertoire were not detected in the 5-HT neurons.
Our work provides for the first time DA-specific catalogues of non-coding elements of the genome that will undoubtedly participate in deepening our knowledge regarding DA neuronal development and dysfunctions.
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| Overall design |
comparison of Lnc-RNA expression and genome structure by ATAC-seq in 2 cell types.
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| Contributor(s) |
Gendron J, Colace-Sauty C, Beaume N, Cartonnet H, Guegan J, Ulveling D, Pardanaud-Glavieux C, Moszer I, Cheval H, Ravassard P |
| Citation(s) |
30723217 |
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| Submission date |
Jan 09, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Philippe Ravassard |
| E-mail(s) |
philippe.ravassard@icm-institute.org
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| Organization name |
Brain & Spine Institute
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| Street address |
47, boulevard de l'Hôpital
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| City |
Paris |
| ZIP/Postal code |
75013 |
| Country |
France |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (11)
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| GSM2938851 |
RNA-seq_serotoninergic neurons sample 1 |
| GSM2938852 |
RNA-seq_serotoninergic neurons sample 2 |
| GSM2938853 |
RNA-seq_serotoninergic neurons sample 3 |
| GSM2938854 |
ATAC-seq_dopaminergic neuron sample 1 |
| GSM2938855 |
ATAC-seq_dopaminergic neuron sample 2 |
| GSM2938856 |
ATAC-seq_dopaminergic neuron sample 3 |
| GSM2938857 |
ATAC-seq_serotoninergic neurons sample 1 |
| GSM2938858 |
ATAC-seq_serotoninergic neurons sample 2 |
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| Relations |
| BioProject |
PRJNA430414 |
| SRA |
SRP131090 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE108917_5HT_FPKM_allTranscripts.xlsx |
17.6 Mb |
(ftp)(http) |
XLSX |
| GSE108917_DA_FPKM_allTranscripts.xlsx |
18.2 Mb |
(ftp)(http) |
XLSX |
| GSE108917_RAW.tar |
8.4 Mb |
(http)(custom) |
TAR (of BROADPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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