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| Status |
Public on Jan 01, 2016 |
| Title |
Gene expression analyses of HB9-GFP D2 mMN cultures following Pbx1 exon 7 inclusion |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
PTBP1 and PTBP2 control alternative splicing programs during neuronal development, but the cellular functions of most PTBP1/2-regulated isoforms remain unknown. We show that PTBP1 guides developmental gene expression by regulating the transcription factor Pbx1. We identify exons that are differentially spliced when mouse embryonic stem cells (ESCs) differentiate into neuronal progenitor cells (NPCs) and neurons, and transition from PTBP1 to PTBP2 expression. We define those exons controlled by PTBP1 in ESCs and NPCs by RNA-seq analysis after PTBP1 depletion and PTBP1 crosslinking-immunoprecipitation. We find that PTBP1 represses Pbx1 exon 7 and the expression of its neuronal isoform Pbx1a in ESC. Using CRISPR-Cas9 to delete regulatory elements for exon 7, we induce Pbx1a expression in ESCs, finding that this activates transcription of specific neuronal genes including known Pbx1 targets. Thus PTBP1 controls the activity of Pbx1 and suppresses its neuronal transcriptional program prior to differentiation.
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| Overall design |
HB9-GFP mESC were transiently transfected with Cas9 and guide RNA sequences to generate heterozygous deletions at the Pbx1 intron 6 locus (Pbx1 I6 +/-). Wild type and (n=3) or Pbx1 I6 +/- (n=5) clones were differentiated in MN media. Samples were harvested at Day 2 of differentiation, and poly-A RNA was isolated for RNA-sequencing and gene expression analyses.
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| Contributor(s) |
Linares AJ |
| Citation(s) |
26705333 |
| |
| Submission date |
Jul 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chia-ho Lin |
| E-mail(s) |
CHIAHOLI@g.UCLA.EDU
|
| Organization name |
UCLA
|
| Lab |
BLACK LAB
|
| Street address |
6577 MRL. 675 CHARLES E YOUNG DR. SOUTH
|
| City |
LOS ANGELES |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE71179 |
The splicing regulator PTBP1 controls the activity of the transcription factor Pbx1 during neuronal differentiation |
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| Relations |
| BioProject |
PRJNA289755 |
| SRA |
SRP061079 |
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