Exon expression profiling reveals stimulus-mediated exon use in neural cells

McKee, Adrienne E.; Neretti, Nicola; Carvalho, Luís; Meyer, Clifford A.; Fox, Edward A.; Brodsky, Alexander S.; Silver, Pamela A.

doi:10.1186/gb-2007-8-8-r159

Cited by 37 publications

(34 citation statements)

References 64 publications

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“…29 We propose that some of the events may be explained by the mechanism we uncovered. Interestingly, manipulations of RNAPII elongation rate globally have generated mixed results of alternative splicing pattern changes.…”

Section: Discussionmentioning

confidence: 99%

Histone hyperacetylation and exon skipping: a calcium-mediated dynamic regulation in cardiomyocytes

Sharma

Nguyen

Cai

et al. 2015

Nucleus

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Section: Discussionmentioning

confidence: 99%

Histone hyperacetylation and exon skipping: a calcium-mediated dynamic regulation in cardiomyocytes

Sharma

Nguyen

Cai

et al. 2015

Nucleus

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“…Depolarization-associated gene lists were curated from two publications (McKee et al [45] and Kim et al [46]). The ASD susceptibility genes were curated from the SFARI gene database [47].…”

Section: Gene Set Over-representation Analysismentioning

confidence: 99%

Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome

et al. 2014

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Background: Common genetic variation and rare mutations in genes encoding calcium channel subunits have pleiotropic effects on risk for multiple neuropsychiatric disorders, including autism spectrum disorder (ASD) and schizophrenia. To gain further mechanistic insights by extending previous gene expression data, we constructed co-expression networks in Timothy syndrome (TS), a monogenic condition with high penetrance for ASD, caused by mutations in the L-type calcium channel, Ca v 1.2. Methods: To identify patient-specific alterations in transcriptome organization, we conducted a genome-wide weighted co-expression network analysis (WGCNA) on neural progenitors and neurons from multiple lines of induced pluripotent stem cells (iPSC) derived from normal and TS (G406R in CACNA1C) individuals. We employed transcription factor binding site enrichment analysis to assess whether TS associated co-expression changes reflect calcium-dependent co-regulation.

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“…While this exon-tiling design has generated considerable enthusiasm (Gardina et al 2006;Clark et al 2007;Kwan et al 2007;McKee et al 2007;Yeo et al 2007;Hung et al 2008), it is in fact challenging to detect differential alternative splicing events. It is unclear whether the exon-tiling probes alone are sufficient for reliable analysis of splicing, without the inverse correlation between probes for exon skipping and inclusion obtained from the splice junction design (Srinivasan et al 2005).…”

Section: Introductionmentioning

confidence: 99%

MADS: A new and improved method for analysis of differential alternative splicing by exon-tiling microarrays

Xing¹,

Stoilov²,

Kapur³

et al. 2008

RNA

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We describe a method, microarray analysis of differential splicing (MADS), for discovery of differential alternative splicing from exon-tiling microarray data. MADS incorporates a series of low-level analysis algorithms motivated by the ''probe-rich'' design of exon arrays, including background correction, iterative probe selection, and removal of sequence-specific cross-hybridization to off-target transcripts. We used MADS to analyze Affymetrix Exon 1.0 array data on a mouse neuroblastoma cell line after shRNA-mediated knockdown of the splicing factor polypyrimidine tract binding protein (PTB). From a list of exons with predetermined inclusion/exclusion profiles in response to PTB depletion, MADS recognized all exons known to have large changes in transcript inclusion levels and offered improvement over Affymetrix's analysis procedure. We also identified numerous novel PTB-dependent splicing events. Thirty novel events were tested by RT-PCR and 27 were confirmed. This work demonstrates that the exon-tiling microarray design is an efficient and powerful approach for global, unbiased analysis of pre-mRNA splicing.

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Exon expression profiling reveals stimulus-mediated exon use in neural cells

Cited by 37 publications

References 64 publications

Histone hyperacetylation and exon skipping: a calcium-mediated dynamic regulation in cardiomyocytes

Histone hyperacetylation and exon skipping: a calcium-mediated dynamic regulation in cardiomyocytes

Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome

MADS: A new and improved method for analysis of differential alternative splicing by exon-tiling microarrays

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