|
| Status |
Public on Nov 03, 2021 |
| Title |
An expansion of genomic regulatory complexity underlies vertebrate neuronal diversity |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
The proper assembly and function of the mammalian nervous system requires the generation of a uniquely diverse population of neurons. Neuronal identity can be viewed as a cell-type-specific combination of broadly expressed effector genes (e.g. receptors, cytoskeletal proteins, adhesion molecules, ion channels, neurotransmitters) that collectively define neuronal morphology, connectivity, and function. How countless, partially overlapping, yet cell-type-specific patterns of gene expression are controlled at the genomic level remains poorly understood. Using primary and stem cell-derived motor neurons, we mapped enhancer-promoter interactions, revealing that motor neuron enhancers are distributed across large chromatin domains, instead of clustered as super-enhancers previously described in other tissues. The distributed enhancers converge on promoters to regulate both neuronal cell-type- and cell-stage-specific patterns of gene expression. Distributed dynamic enhancers are not a unique property of motor neurons, but are broadly employed in the regulation of gene expression throughout the nervous system. Together, our findings establish that neuronal genes are associated with expanded non-coding genomic domains, accommodating large numbers of independent cell-type- and cell-stage-specific regulatory elements. This regulatory system facilitates the implementation of complex gene expression programs underlying the expansion in the cellular diversity of the vertebrate central nervous system.
|
| |
|
| Overall design |
Genomic maps of regulatory elements in different neuronal cell types
|
| |
|
| Contributor(s) |
Closser M, Wichterle H |
| Citation(s) |
34727520 |
| |
| Submission date |
May 06, 2020 |
| Last update date |
Nov 06, 2021 |
| Contact name |
Michael Closser |
| E-mail(s) |
mc3394@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Street address |
630 W 168th St
|
| City |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (35)
|
|
| Relations |
| BioProject |
PRJNA630707 |
| SRA |
SRP260268 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE149971_Isl1_Lhx3.interacting.mngenes.txt.gz |
38.6 Kb |
(ftp)(http) |
TXT |
| GSE149971_MN.Promoter.Enhancer.Interactions.txt.gz |
109.7 Kb |
(ftp)(http) |
TXT |
| GSE149971_RAW.tar |
90.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE149971_broad_neuronal_genes_table2.txt.gz |
10.5 Kb |
(ftp)(http) |
TXT |
| GSE149971_e10_5_MN_ATAC_peaks.txt.gz |
2.0 Mb |
(ftp)(http) |
TXT |
| GSE149971_e13_5_MN_ATAC_peaks.txt.gz |
2.0 Mb |
(ftp)(http) |
TXT |
| GSE149971_e14_5_SN_ATAC_peaks.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
| GSE149971_es_neuron_expression_data.txt.gz |
233.8 Kb |
(ftp)(http) |
TXT |
| GSE149971_invitro_MN_ATAC_Med1_K27ac_enhancers.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE149971_invitro_MN_ATAC_peaks.txt.gz |
3.8 Mb |
(ftp)(http) |
TXT |
| GSE149971_invitro_MN_H3K27ac_ChIP_peaks.txt.gz |
947.1 Kb |
(ftp)(http) |
TXT |
| GSE149971_invitro_MN_Med1_ChIP_peaks.txt.gz |
912.6 Kb |
(ftp)(http) |
TXT |
| GSE149971_model_organisms_7species.xlsx |
2.9 Mb |
(ftp)(http) |
XLSX |
| GSE149971_mouse_intergenic_genomic_features.txt.gz |
519.8 Kb |
(ftp)(http) |
TXT |
| GSE149971_orthologue_data_table5.txt.gz |
143.1 Kb |
(ftp)(http) |
TXT |
| GSE149971_orthologue_genes_table4.txt.gz |
3.9 Kb |
(ftp)(http) |
TXT |
| GSE149971_top500_chiapet_genes_table3.txt.gz |
9.0 Kb |
(ftp)(http) |
TXT |
| GSE149971_top500_tissue_specific_genes_table1.txt.gz |
43.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...