 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 12, 2018 |
| Title |
Genome-wide CRISPR-Cas9 interrogation of splicing networks reveals a mechanism for recognition of autism-misregulated neuronal microexons [CRISPR screen] |
| Organisms |
Mus musculus; synthetic construct |
| Experiment type |
Other
|
| Summary |
Alternative splicing has critical roles in diverse cellular, developmental and pathological processes. However, the full repertoires of factors that control individual splicing events are not known. We describe a CRISPR-based screening strategy for the systematic identification of genes that control 3-27 nt microexons with functions in nervous system development and that are commonly disrupted in autism. Besides known regulators including nSR100/Srrm4, Rbfox and Ptbp1, approximately 200 additional genes impact microexon splicing. These genes are enriched in genetic links to autism. Two of the screen hits, Srsf11 and Rnps1, preferentially regulate Srrm4-dependent microexons relative to other exons. These factors form mutually stabilizing interactions with Srrm4 that bridge upstream intronic enhancer elements and exonic sequences to activate microexon splicing. Our study thus presents a system for the genome-wide definition of splicing regulatory networks and further reveals a mechanism for the recognition of microexons with critical roles in nervous system development and disorders.
|
| |
|
| Overall design |
sgRNA sequencing in N2A cells expressing a fluorescent splicing reporter and infected with a CRISPR loss-of-function library, unsorted cells or sorted based on reporter
|
| |
|
| Contributor(s) |
Gonatopoulos-Pournatzis T, Wu M, Braunschweig U, Roth J, Han H, Best A, Raj B, Aregger M, O'Hanlon D, Ellis JD, Calarco JA, Moffat J, Gingras A, Blencowe BJ |
| Citation(s) |
30388412 |
| |
| Submission date |
Apr 02, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Ulrich Braunschweig |
| Organization name |
University of Toronto
|
| Department |
Donnelly Centre
|
| Lab |
Benjamin J. Blencowe
|
| Street address |
160 College Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5S 3E1 |
| Country |
Canada |
| |
|
| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19424 |
Illumina NextSeq 500 (synthetic construct) |
|
| Samples (49)
|
| GSM3073829 |
Brie library plasmid prep |
| GSM3073830 |
Shank2 splicing reporter, unsorted cells after infection (T0) |
| GSM3073831 |
Shank2 splicing reporter, unsorted cells, replicate 1 (T15) |
| GSM3073832 |
Shank2 splicing reporter, unsorted cells, replicate 2 (T17) |
| GSM3073833 |
Shank2 splicing reporter, unsorted cells, replicate 3 (T9) |
| GSM3073834 |
Shank2 splicing reporter, unsorted cells, replicate 4 (T22) |
| GSM3073835 |
Shank2 splicing reporter, unsorted cells, replicate 5 (T24) |
| GSM3073836 |
Shank2 splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 1 (T15) |
| GSM3073837 |
Shank2 splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 2 (T17) |
| GSM3073838 |
Shank2 splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 3 (T9) |
| GSM3073839 |
Shank2 splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 4 (T22) |
| GSM3073840 |
Shank2 splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 5 (T24) |
| GSM3073841 |
Shank2 splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 1 (T15) |
| GSM3073842 |
Shank2 splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 2 (T17) |
| GSM3073843 |
Shank2 splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 3 (T9) |
| GSM3073844 |
Shank2 splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 4 (T22) |
| GSM3073845 |
Shank2 splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 5 (T24) |
| GSM3073846 |
Mef2d splicing reporter, unsorted cells after infection (T0) |
| GSM3073847 |
Mef2d splicing reporter, unsorted cells, replicate 1 (T9) |
| GSM3073848 |
Mef2d splicing reporter, unsorted cells, replicate 2 (T16) |
| GSM3073849 |
Mef2d splicing reporter, unsorted cells, replicate 3 (T16) |
| GSM3073850 |
Mef2d splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 1 (T9) |
| GSM3073851 |
Mef2d splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 2 (T16) |
| GSM3073852 |
Mef2d splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 3 (T16) |
| GSM3073853 |
Mef2d splicing reporter, sorted cells with 2% highest EGFP/mCherry, replicate 4 (T16) |
| GSM3073854 |
Mef2d splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 1 (T9) |
| GSM3073855 |
Mef2d splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 2 (T16) |
| GSM3073856 |
Mef2d splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 3 (T16) |
| GSM3073857 |
Mef2d splicing reporter, sorted cells with 2% lowest EGFP/mCherry, replicate 4 (T16) |
| GSM3073858 |
Mef2d splicing reporter, sorted cells with 30% highest EGFP/mCherry, replicate 1 (T9) |
| GSM3073859 |
Mef2d splicing reporter, sorted cells with 30% highest EGFP/mCherry, replicate 2 (T11) |
| GSM3073860 |
Mef2d splicing reporter, sorted cells with 30% highest EGFP/mCherry, replicate 3 (T16) |
| GSM3073861 |
Mef2d splicing reporter, sorted cells with 30% highest EGFP/mCherry, replicate 4 (T18) |
| GSM3073862 |
Mef2d splicing reporter, sorted cells with 30% highest EGFP/mCherry, replicate 5 (T18) |
| GSM3073863 |
Mef2d splicing reporter, sorted cells with 30% lowest EGFP/mCherry, replicate 1 (T9) |
| GSM3073864 |
Mef2d splicing reporter, sorted cells with 30% lowest EGFP/mCherry, replicate 2 (T11) |
| GSM3073865 |
Mef2d splicing reporter, sorted cells with 30% lowest EGFP/mCherry, replicate 3 (T16) |
| GSM3073866 |
Mef2d splicing reporter, sorted cells with 30% lowest EGFP/mCherry, replicate 4 (T18) |
| GSM3073867 |
Mef2d splicing reporter, sorted cells with 30% lowest EGFP/mCherry, replicate 5 (T18) |
| GSM3073868 |
Srrm4 expression reporter, unsorted cells after infection (T0) |
| GSM3073869 |
Srrm4 expression reporter, unsorted cells, replicate 1 (T16) |
| GSM3073870 |
Srrm4 expression reporter, unsorted cells, replicate 2 (T16) |
| GSM3073871 |
Srrm4 expression reporter, unsorted cells, replicate 3 (T18) |
| GSM3073872 |
Srrm4 expression reporter, sorted cells with 2% highest EGFP, replicate1 (T16) |
| GSM3073873 |
Srrm4 expression reporter, sorted cells with 2% highest EGFP, replicate2 (T16) |
| GSM3073874 |
Srrm4 expression reporter, sorted cells with 2% highest EGFP, replicate3 (T18) |
| GSM3073875 |
Srrm4 expression reporter, sorted cells with 2% lowest EGFP, replicate1 (T16) |
| GSM3073876 |
Srrm4 expression reporter, sorted cells with 2% lowest EGFP, replicate2 (T16) |
| GSM3073877 |
Srrm4 expression reporter, sorted cells with 2% lowest EGFP, replicate3 (T18) |
|
| This SubSeries is part of SuperSeries: |
| GSE112601 |
Genome-wide CRISPR-Cas9 interrogation of splicing networks reveals a mechanism for recognition of autism-misregulated neuronal microexons |
|
| Relations |
| BioProject |
PRJNA448435 |
| SRA |
SRP136944 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE112599_Counts_Mef2d_UB180328.tab.gz |
3.2 Mb |
(ftp)(http) |
TAB |
| GSE112599_Counts_Shank2_UB180328.tab.gz |
2.5 Mb |
(ftp)(http) |
TAB |
| GSE112599_Counts_Srrm4_UB180328.tab.gz |
2.0 Mb |
(ftp)(http) |
TAB |
| GSE112599_MAGeCK.scores.xlsx |
5.2 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...