10.5061/DRYAD.CV39V
Li, Qin
University of California Los Angeles
Zheng, Sika
University of California Los Angeles
Han, Areum
University of California Los Angeles
Lin, Chia-Ho
University of California Los Angeles
Stoilov, Peter
West Virginia University
Fu, Xiang-Dong
University of California Los Angeles
Black, Douglas L.
University of California Los Angeles
Data from: The splicing regulator PTBP2 controls a program of embryonic
splicing required for neuronal maturation
Dryad
dataset
2015
neuronal development
microarray
Alternative splicing
RNA binding protein
Mus musculus
Neuron
RNAseq
2015-01-14T00:00:00Z
2015-01-14T00:00:00Z
en
https://doi.org/10.7554/eLife.01201
6625530 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
We show that the splicing regulator PTBP2 controls a genetic program
essential for neuronal maturation. Depletion of PTBP2 in developing mouse
cortex leads to degeneration of these tissues over the first three
postnatal weeks, a time when the normal cortex expands and develops mature
circuits. Cultured Ptbp2−/− neurons exhibit the same initial viability as
wild type, with proper neurite outgrowth and marker expression. However,
these mutant cells subsequently fail to mature and die after a week in
culture. Transcriptome-wide analyses identify many exons that share a
pattern of mis-regulation in the mutant brains, where isoforms normally
found in adults are precociously expressed in the developing embryo. These
transcripts encode proteins affecting neurite growth, pre- and
post-synaptic assembly, and synaptic transmission. Our results define a
new genetic regulatory program, where PTBP2 acts to temporarily repress
expression of adult protein isoforms until the final maturation of the
neuron.
Li et al. Supplemental File 1: Table 1. Exons validated by RT/PCR.Table S1
for Li et al. A variety of exons showing differences in splicing between
wild type and Ptbp2 nestin-KO brain at embryonic day 18 were subjected to
further analysis by RT/PCR. These included exons identified by MJAY array,
RNAseq, and exons previously reported to be PTBP targets. Gene names, exon
coordinates, and percent spliced in values (PSI) are listed. Genome
coordinates are for mm9.Supplemental File 1 Table S1 RT-PCR validated E18
exons.docxLi et al. Supplemental File 2: Table 2. Splicing Changes
Identified by Exon Junction Microarray.RNA from WT and Ptbp2-NestinKO E18
pups was analyzed on Affymetrix MJAY arrays (see Methods). Splicing events
yielding Sepscores greater than 0.345 are listed.Supplemental File 2
Table_S2_MJAY Array_top_Splicing_events_by_SepScore.xlsLi et al.
Supplemental File 3: Table 3. Splicing Changes Identified by RNAseq
analysis in Ptbp2-NesKO mice.RNAseq reads from E18 WT and NesKO mice were
subjected to Splicetrap analysis (see Methods). Events with a change in
PSI of greater than 10% are shown with genome coordinates, read numbers,
and coverage statistics.Supplemental File 3 Table
S3_nestin_nptbko_SpliceTrap_psi_over10percent_with_pvalues.xlsLi et al.
Supplemental File 4: Table 4. Gene Ontology Analysis of Functional or
Process Enrichment for Genes Showing Splicing Changes in Ptbp2-NesKO
mice.Enrichments are relative to all genes expressed in wildtype brain at
E18.Supplemental File 4 Table_S4_GO_analysis_nestin_splicetrap_exons.xlsLi
et al. Supplemental File 5: Table 5. Expression changes in Ptbp2-NesKO
mice.Genes showing overall expression changes were identified by Cuffdiff
analysis.Supplemental File 5
Table_S5_cuffdiff_NesKOvWT_expression_change_V3.xlsLi et al. Supplemental
File 6: Table 6. Gene Ontology analysis of genes up-regulated in
Ptbp2-NesKO mice.Genes showing a two-fold or greater increase in
expression in the KO relative to WT were analyzed for functional or
process enrichment relative to all genes expressed in wildtype
brain.Supplemental File 6 Table_S6_gene_ontology_2_fold_upregulated
transcripts_v2.xlsLi et al. Supplemental File 7: Table 7. Gene Ontology
analysis of genes down-regulated in Ptbp2-NesKO mice.Genes showing
two-fold or greater reduced expression in the KO relative to WT were
analyzed for functional or process enrichment relative to all genes
expressed in wildtype brain.Supplemental File 7
Table_S7_gene_ontology_2_fold_change_down_regulated_transcripts_v2.xlsLi
et al. Supplemental File 8: Table 8. Splicing Changes Identified by RNAseq
analysis in Ptbp2-EmxKO mice.RNAseq reads from P1 WT and EmxKO mice were
subjected to Splicetrap analysis (see Methods). Events with a change in
PSI of greater than 10% are shown with genome coordinates, read numbers,
and coverage statistics.Supplemental File 8
Table_S8_Emx_P1_SpliceTrap_psi_over10percent_with_pvalues.xls