Yan et al. 2021 (PRJNA655955)

General Details

Title The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes [Ribo-seq]
Organism
Number of Samples 4
Release Date 2020/08/07 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP276711
ENA SRP276711
GEO
BioProject PRJNA655955

Publication

Title
Authors Yan Y,Tang R,Li B,Cheng L,Ye S,Yang T,Han YC,Liu C,Dong Y,Qu LH,Lui KO,Yang JH,Huang ZP
Journal Molecular therapy : the journal of the American Society of Gene Therapy
Publication Date 2021 Jul 7
Abstract Hypertrophic growth of cardiomyocytes is one of the major compensatory responses in the heart after physiological or pathological stimulation. Protein synthesis enhancement, which is mediated by the translation of messenger RNAs, is one of the main features of cardiomyocyte hypertrophy. Although the transcriptome shift caused by cardiac hypertrophy induced by different stimuli has been extensively investigated, translatome dynamics in this cellular process has been less studied. Here, we generated a nucleotide-resolution translatome as well as transcriptome data from isolated primary cardiomyocytes undergoing hypertrophy. More than 10,000 open reading frames (ORFs) were detected from the deep sequencing of ribosome-protected fragments (Ribo-seq), which orchestrated the shift of the translatome in hypertrophied cardiomyocytes. Our data suggest that rather than increase the translational rate of ribosomes, the increased efficiency of protein synthesis in cardiomyocyte hypertrophy was attributable to an increased quantity of ribosomes. In addition, more than 100 uncharacterized short ORFs (sORFs) were detected in long noncoding RNA genes from Ribo-seq with potential of micropeptide coding. In a random test of 15 candidates, the coding potential of 11 sORFs was experimentally supported. Three micropeptides were identified to regulate cardiomyocyte hypertrophy by modulating the activities of oxidative phosphorylation, the calcium signaling pathway, and the mitogen-activated protein kinase (MAPK) pathway. Our study provides a genome-wide overview of the translational controls behind cardiomyocyte hypertrophy and demonstrates an unrecognized role of micropeptides in cardiomyocyte biology. Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.
PMC PMC8261087
PMID 33677093
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR12414240 PRJNA655955 Rattus norvegicus ventricular cardiomyocytes Ribo-Seq
SRR12414241 PRJNA655955 Rattus norvegicus ventricular cardiomyocytes Ribo-Seq
SRR12414242 PRJNA655955 Rattus norvegicus ventricular cardiomyocytes Ribo-Seq untreated
SRR12414243 PRJNA655955 Rattus norvegicus ventricular cardiomyocytes Ribo-Seq untreated
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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