Transcriptomics

Dataset Information

7

Transcriptomic Analysis of PNN- and ESRP1-regulation in Human Corneal Epithelial Cells


ABSTRACT: Pnn depletion in developing mouse corneal epithelium led to disrupted alternative splicing of multiple ESRP-regulated epithelial-type exons. In human corneal epithelial cells (HCET), ESRP1 and PNN displayed close localization in and around nuclear speckles and their physical association in protein complexes was identified. In this study, gene expression profiling was performed to identify PNN- and ESRP1-regulated alternative pre-mRNA splicing in human corneal epithelial cells. Immortalized human corneal epithelial cells harboring doxycycline-inducible shRNA against PNN or ESRP1 were created. Whole transcriptome array analysis on ESRP1 or PNN knockdown HCET cells revealed clear alterations in transcript level and splicing pattern of specific subsets of genes with significant overlaps in their candidate targets. Our data suggest that ESRP1 and PNN modulate alternative splicing of a specific subset of exons, but not general splicing events. ESRP1 and PNN may together participate in the regulation of epithelial-specific splicing program in a genome-wide fashion. Parental HCET, shRNA-PNN HCET, and shRNA-ESRP1 HCET cells were cultured for 3 days with/without doxycycline. Total RNA was isolated from four biological replicates of each sample group and then subjected to hGlue3_0 transcriptome array analysis.

ORGANISM(S): Homo sapiens  

SUBMITTER: Jian-Liang Li   Maria C Lopez  Jeong H Joo  Stephen P Sugrue  Henry V Baker  Creg P Correia  Jian L Li 

PROVIDER: E-GEOD-41996 | ArrayExpress | 2013-01-24

SECONDARY ACCESSION(S): GSE41996PRJNA179187

REPOSITORIES: GEO, ArrayExpress

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Publications

Transcriptomic analysis of PNN- and ESRP1-regulated alternative pre-mRNA splicing in human corneal epithelial cells.

Joo Jeong-Hoon JH   Correia Greg P GP   Li Jian-Liang JL   Lopez Maria-Cecilia MC   Baker Henry V HV   Sugrue Stephen P SP  

Investigative ophthalmology & visual science 20130123 1


We investigated the impact of PININ (PNN) and epithelial splicing regulatory protein 1 (ESRP1) on alternative pre-mRNA splicing in the corneal epithelial context.Isoform-specific RT-PCR assays were performed on wild-type and Pnn knockout mouse cornea. Protein interactions were examined by deconvolution microscopy and co-immunoprecipitation. For genome-wide alternative splicing study, immortalized human corneal epithelial cells (HCET) harboring doxycycline-inducible shRNA against PNN or ESRP1 wer  ...[more]

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