5′RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy

Abstract

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.

Molecular genetics and pathogenesis of cardiomyopathy

“…116 It has recently been reported from the analysis of transcriptome in mice with the MYH7 Arg403Asn mutation that a four-and-a-half LIM domain protein 1 gene (FHL1) has a key role in modifying the cardiac phenotype. 117 It has also been speculated that FHL1 might be a genetic factor to determine the gender difference in the cardiac phenotype of HCM observed in this model mice. 117 In addition, systematic search for genetic loci involved in the strain-specific cardiac phenotypes in calsequestrin gene (CSQ) overexpressing transgenic mice showing DCM phenotype has identified at least seven different quantitative trait loci, 118-120 among which only one locus was clarified as cardiac troponin I-interacting kinase gene (TNNI3K) at the gene level.…”

Cardiac myosin binding protein C regulates postnatal myocyte cytokinesis

“…Hearts from mice were rapidly isolated, placed in room temperature PBS to evacuate blood, and then immersed in RNALater (Qiagen) at room temperature. We used 2 μg of total ventricular RNA to construct RNAseq sequencing libraries (48). At least 20 million 50-bp paired-end DNA reads were obtained from each library using the Illumina HiSeq2500.…”

“…At least 20 million 50-bp paired-end DNA reads were obtained from each library using the Illumina HiSeq2500. Data were processed as previously described (48).…”

Identification of hub genes and their SNP analysis in West Nile virus infection for designing therapeutic methodologies using RNA-Seq data

“…RNA-Seq is presently suggested as cost-effective new tool, which can be applied for deciphering the genetic basis of diseases, and traits that could not be detected based on previous conventional gene-discovery methods (Bamshad et al 2011). RNA-Seq has been employed to investigate biological phenomena in diverse areas such as viral infections (Jones et al 2014), cancer (Young et al 2014) and cardiomyopathy (Christodoulou et al 2014). Recently, we have also used RNA-Seq analysis to explore the role of glycogenes in skeletal muscle development in MYOG kd cells ) and also used precomputed expression values from mouse RNA-Seq data to understand the role glycogenes in various biological processes that are involved in the development of brain, muscle, and liver tissues (Firoz et al 2014).…”