Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts.
BACKGROUND
Accurate and comprehensive de novo transcriptome profiling in heart is a central issue to better understand cardiac physiology and diseases. Although significant progress has been made in genome-wide profiling for quantitative changes in cardiac gene expression, current knowledge offers limited insights to the total complexity in cardiac transcriptome at individual exon level.


OBJECTIVE
To develop more robust bioinformatic approaches to analyze high-throughput RNA sequencing (RNA-Seq) data, with the focus on the investigation of transcriptome complexity at individual exon and transcript levels.


RESULTS
In addition to overall gene expression analysis, the methods developed in this study were used to analyze RNA-Seq data with respect to individual transcript isoforms, novel spliced exons, novel alternative terminal exons, novel transcript clusters (ie, novel genes), and long noncoding RNA genes. We applied these approaches to RNA-Seq data obtained from mouse hearts after pressure-overload-induced by transaortic constriction. Based on experimental validations, analyses of the features of the identified exons/transcripts, and expression analyses including previously published RNA-Seq data, we demonstrate that the methods are highly effective in detecting and quantifying individual exons and transcripts. Novel insights inferred from the examined aspects of the cardiac transcriptome open ways to further experimental investigations.


CONCLUSIONS
Our work provided a comprehensive set of methods to analyze mouse cardiac transcriptome complexity at individual exon and transcript levels. Applications of the methods may infer important new insights to gene regulation in normal and disease hearts in terms of exon utilization and potential involvement of novel components of cardiac transcriptome.
Integrative Biology and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
Jae-Hyung
JH
Lee
Chen
C
Gao
Guangdun
G
Peng
Christopher
C
Greer
Shuxun
S
Ren
Yibin
Y
Wang
Xinshu
X
Xiao
D000818:Animals; D004195:Disease Models, Animal; D005091:Exons / Q000235:genetics / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology; D006321:Heart / Q000502:physiology*; D006333:Heart Failure / Q000235:genetics* / Q000503:physiopathology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA / Q000379:methods*; D014158:Transcription, Genetic / Q000235:genetics / Q000502:physiology