TY - JOUR
T1 - 5'RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy
AU - Christodoulou, Danos C.
AU - Wakimoto, Hiroko
AU - Onoue, Kenji
AU - Eminaga, Seda
AU - Gorham, Joshua M.
AU - DePalma, Steve R.
AU - Herman, Daniel S.
AU - Teekakirikul, Polakit
AU - Conner, David A.
AU - McKean, David M.
AU - Domenighetti, Andrea A.
AU - Aboukhalil, Anton
AU - Chang, Stephen
AU - Srivastava, Gyan
AU - McDonough, Barbara
AU - De Jager, Philip L.
AU - Chen, Ju
AU - Bulyk, Martha L.
AU - Muehlschlegel, Jochen D.
AU - Seidman, Christine E.
AU - Seidman, J. G.
PY - 2014/3/3
Y1 - 2014/3/3
N2 - The transcriptome is subject to multiple changes during pathogenesis, including the use of alternate 5' startsites that can affect transcription levels and output. Current RNA sequencing techniques can assess mRNA levels, but do not robustly detect changes in 5' start-site use. Here, we developed a transcriptome sequencing strategy that detects genome-wide changes in start-site usage (5'RNA-Seq) and applied this methodology to identify regulatory events that occur in hypertrophic cardiomyopathy (HCM). Compared with transcripts from WT mice, 92 genes had altered start-site usage in a mouse model of HCM, including four-and-a-half LIM domains protein 1 (Fhl1). HCM-induced altered transcriptional regulation of Fhl1 resulted in robust myocyte expression of a distinct protein isoform, a response that was conserved in humans with genetic or acquired cardiomyopathies. Genetic ablation of Fhl1 in HCM mice was deleterious, which suggests that Fhl1 transcriptional changes provide salutary effects on stressed myocytes in this disease. Because Fhl1 is a chromosome X-encoded gene, stress-induced changes in its transcription may contribute to gender differences in the clinical severity of HCM. Our findings indicate that 5'RNA-Seq has the potential to identify genomewide changes in 5' start-site usage that are associated with pathogenic phenotypes.
AB - The transcriptome is subject to multiple changes during pathogenesis, including the use of alternate 5' startsites that can affect transcription levels and output. Current RNA sequencing techniques can assess mRNA levels, but do not robustly detect changes in 5' start-site use. Here, we developed a transcriptome sequencing strategy that detects genome-wide changes in start-site usage (5'RNA-Seq) and applied this methodology to identify regulatory events that occur in hypertrophic cardiomyopathy (HCM). Compared with transcripts from WT mice, 92 genes had altered start-site usage in a mouse model of HCM, including four-and-a-half LIM domains protein 1 (Fhl1). HCM-induced altered transcriptional regulation of Fhl1 resulted in robust myocyte expression of a distinct protein isoform, a response that was conserved in humans with genetic or acquired cardiomyopathies. Genetic ablation of Fhl1 in HCM mice was deleterious, which suggests that Fhl1 transcriptional changes provide salutary effects on stressed myocytes in this disease. Because Fhl1 is a chromosome X-encoded gene, stress-induced changes in its transcription may contribute to gender differences in the clinical severity of HCM. Our findings indicate that 5'RNA-Seq has the potential to identify genomewide changes in 5' start-site usage that are associated with pathogenic phenotypes.
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U2 - 10.1172/JCI70108
DO - 10.1172/JCI70108
M3 - Article
C2 - 24509080
AN - SCOPUS:84896785073
SN - 0021-9738
VL - 124
SP - 1364
EP - 1370
JO - Journal of Clinical Investigation
JF - Journal of Clinical Investigation
IS - 3
ER -