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SRX20541242: GSM7433520: Sham_Ribo_2; Mus musculus; OTHER
1 ILLUMINA (NextSeq 500) run: 100.6M spots, 7.5G bases, 2.2Gb downloads

External Id: GSM7433520_r1
Submitted by: Department of Cardiology, School of Medicine, Southeast University
Study: Nat10 is involved in myocardial remodeling through ac4C-mediated transcriptomic regulation
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Background: Heart failure (HF), characterized by cardiac remodeling, is associated with abnormal epigenetic processes and aberrant gene expression. Here, we aimed to elucidate the effects and mechanisms of N-acetyltransferase 10 (NAT10)-mediated N4?acetylcytidine (ac4C) acetylation during cardiac remodeling. Methods: NAT10 and ac4C expression were detected in both human and mouse subjects with cardiac remodeling through multiple assays. Subsequently, acetylated RNA immunoprecipitation and sequencing (acRIP-seq), thiol (SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq), and ribosome sequencing (Ribo-seq) were employed to elucidate the role of ac4C-modified post-transcriptional regulation in cardiac remodeling. Additionally, functional experiments involving the overexpression or knockdown of NAT10 were conducted in mice models challenged with Ang II and transverse aortic constriction (TAC). Results: NAT10 expression and RNA ac4C levels were increased in in vitro and in vivo cardiac remodeling models, as well as in patients with cardiac hypertrophy. Silencing and inhibiting NAT10 attenuated Ang II-induced cardiomyocyte hypertrophy and cardio-fibroblast activation. Next-generation sequencing revealed ac4C changes in both mice and humans with cardiac hypertrophy were associated with changes in global mRNA abundance, stability and translation efficiency. Mechanistically, NAT10 could enhance the stability and translation efficiency of CD47 and ROCK2 transcripts by upregulating their mRNA ac4C modification, thereby resulting in an increase in their protein expression during cardiac remodeling. Furthermore, the administration of Remodelin, a NAT10 inhibitor, has been shown to prevent cardiac functional impairments in mice subjected to TAC by suppressing cardiac fibrosis, hypertrophy, and inflammatory responses, while also regulating the expression levels of CD47 and ROCK2. Conclusions: Therefore, our data suggest that modulating epitranscriptomic processes, such as ac4C acetylation through NAT10, may be a promising therapeutic target against cardiac remodeling. Overall design: We performed ac4C-seq from human heart samples (six participants per group) and four mice groups (AAV9:CONi, AAV9:NAT10i, Ang II, and Ang II +AAV9:NAT10i, with three biological repeats per group) in Model 2 by Epibiotek (Guangzhou, China). SLAM-seq was performed to measure the effect of NAT10 on mRNA half-life transcriptome-wide in NMCMs and NMCFs (two biological repeats per group) with Epi? SLAM-seq Library Prep Kit (R202208-2, Epibiotek, China) by Epibiotek (Guangzhou, China) according to the manufacturer?s instructions. Ribo-seq was performed from three mice groups (AAV9:CONi, Ang II, and Ang II +AAV9:NAT10i, with three biological repeats per group) by Epibiotek (Guangzhou, China). RNA-seq was performed from human heart samples (six biological repeats per group) and four mice groups (AAV9:Coni, AAV9:NAT10i, Ang II, And Ang II +AAV9:NAT10i, With Three Biological Repeats Per Group) in Model 2 by Epibiotek (Guangzhou, China).
Sample: Sham_Ribo_2
SAMN35531791 • SRS17848403 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM7433520
Instrument: NextSeq 500
Strategy: OTHER
Source: TRANSCRIPTOMIC
Selection: other
Layout: SINGLE
Construction protocol: For acRIP-seq: Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2. Subsequently, the purified RNA was incubated with anti-ac4c polyclonal antibody for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The ac4c-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106). The RNA-seq library was prepared by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, E7775). For Ribo-seq:tissue were pulverized manually under liquid nitrogen and treated by ice-cold PBS containing 100 μg/mL cycloheximide. Ribosome profiling was performed using Epi™ Ribosome Profiling Kit (Epibiotek, R1814). Subsquently, RPFs (ribosome-protected RNA fragments) was extracted using RNA clean&ConcentratorTM-5 kit (ZYMO, R1016). EpiTM RiboRNA Depletion Kit (Epibiotek, R1805) was used for rRNA depletion. Sequencing libraries were constructed using QIAseq miRNA Library kit (QIAGEN, 1103679). RNA libraries were prepared for sequencing using standard Illumina protocols acRIP-seq; Ribo-seq; RNA-seq
Runs: 1 run, 100.6M spots, 7.5G bases, 2.2Gb
Run# of Spots# of BasesSizePublished
SRR24765956100,646,9287.5G2.2Gb2023-10-31

ID:
27965301

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