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| Status |
Public on Feb 25, 2015 |
| Title |
Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity |
| Organisms |
Mus musculus; Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Circular RNAs (circRNAs), formed by the atypical head-to-tail splicing of exons, have re-emerged as a potentially interesting RNA species given recent reports of a surprising diversity and abundance of circRNA in organisms ranging from worm to human. Here, using deep RNA sequencing, we profiled different RNA species in mouse and observed that circRNAs are significantly enriched in neural tissue, relative to other tissues.
Using PacBio sequencing, we determined, for the first time, the circular structure of this population of circRNAs as well as their full-length sequences. We discovered that a disproportionate fraction of the brain circRNA population is derived from host genes that code for synaptic proteins.
Moreover, based on the separate profiling of the RNAs localized in neuronal cell bodies and neuropil (enriched in axons and dendrites), we found that, on average, circular RNAs are more enriched in the neuropil than their host gene mRNA isoforms. Using high resolution in situ hybridization we, for the first time, directly visualized circRNA punctae in the dendrites of neurons.
The host gene origin and location of the circRNA in neurons suggest the possibility that circRNAs might participate in the regulation of synaptic function and plasticity. Consistent with this idea, we observed via profiling at different developmental stages, that the abundance of many circular RNAs changes abruptly at a time corresponding to synaptogenesis.
In addition, following a homeostatic downscaling of neuronal activity many circRNAs exhibit significant up or down-regulation. These data indicate that brain circRNAs are positioned to respond to and regulate synaptic function.
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| Overall design |
Circular RNA profiling in 13 different samples in mice and four samples in rat, using Illumina sequencing
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| Contributor(s) |
You X, Vlatkovic I, Babic A, Will T, Epstein I, Wei S |
| Citation(s) |
25714049 |
| Submission date |
Oct 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xintian Arthur YOU |
| Organization name |
Max-Delbrueck-Center for Molecular Medicine
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| Street address |
Robert-Roessle-str. 10
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| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platforms (4)
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| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL18694 |
Illumina HiSeq 2500 (Rattus norvegicus) |
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| Samples (35)
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| Relations |
| BioProject |
PRJNA262902 |
| SRA |
SRP048593 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61991_PacBio_CCS.fa.gz |
1.4 Mb |
(ftp)(http) |
FA |
| GSE61991_mouse_TPM.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE61991_mouse_circRNA_CBR.bed.txt.gz |
212.1 Kb |
(ftp)(http) |
TXT |
| GSE61991_mouse_circRNA_MEA.bed.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE61991_mouse_circRNA_TPM.txt.gz |
751.5 Kb |
(ftp)(http) |
TXT |
| GSE61991_rat_TPM.txt.gz |
923.3 Kb |
(ftp)(http) |
TXT |
| GSE61991_rat_circRNA_CBR.bed.gz |
214.7 Kb |
(ftp)(http) |
BED |
| GSE61991_rat_circRNA_MEA.bed.gz |
584.3 Kb |
(ftp)(http) |
BED |
| GSE61991_rat_circRNA_TPM.txt.gz |
305.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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