Abstract
BackgroundThe developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models.ResultsTo address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs.ConclusionThe resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events.
Highlights
The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level
Transcriptional profiling of the developing kidney using microarrays coupled with RNA in situ hybridizations (ISH) have provided a detailed view of gene expression networks driving developmental processes
Given the consequences of transcriptional complexity, understanding the complete repertoire of transcripts is crucial for accurate modelling of kidney organogenesis
Summary
The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening These studies, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on “gene-centric” models. Transcriptional profiling of the developing kidney using microarrays coupled with RNA in situ hybridizations (ISH) have provided a detailed view of gene expression networks driving developmental processes [3,4,5,6] Despite these advances, microarrays cannot capture the entire transcriptional output from mammalian genes (reviewed in [7,8]) as they require a priori assumptions about the portion of the genome that is expressed, limiting the ability to use this technology for uncharacterized gene or transcript discovery [8]. Given the consequences of transcriptional complexity (alternate domain content, differential transcription factor binding sites and microRNA binding sites from alternative promoter and 3’UTR usage, respectively), understanding the complete repertoire of transcripts is crucial for accurate modelling of kidney organogenesis
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