Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

BMC Genomics

Research Article

Bree A Rumballe¹  Tim R Mercer¹  Nicole Cloonan¹  Brooke B Gardiner¹  Dave Tang¹  Gabriel Kolle¹  John S Mattick¹  Melissa H Little¹  Sean M Grimmond¹  Keerthana Krishnan¹  Ehsan Nourbakhsh¹  Han S Chiu¹  Rathi D Thiagarajan¹  Shivangi Wani¹  Kylie M Georgas¹  Jason A Steen¹ 

[1] Institute for Molecular Bioscience, The University of Queensland, 4072, St. Lucia QLD, Australia;

关键词: RNA-Seq;    kidney development;    microarray;    Six2, Wt1;    sense-antisense transcripts;    alternative splicing;    mesenchymal-epithelial transition;    miR-214, microRNA;   

DOI  :  10.1186/1471-2164-12-441

 received in 2011-03-24, accepted in 2011-09-05,  发布年份 2011

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Thiagarajan et al; licensee BioMed Central Ltd. 2011