NAT10 depletion suppresses fatty acid metabolism in MCF7 breast cancer cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA863634 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20711421_1.fastq.gz | Fastqsanger.gz | |||
| SRR20711421_2.fastq.gz | Fastqsanger.gz | |||
| SRR20711422_1.fastq.gz | Fastqsanger.gz | |||
| SRR20711422_2.fastq.gz | Fastqsanger.gz | |||
| SRR20711423_1.fastq.gz | Fastqsanger.gz |
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Project description:NAT10 is an RNA cytidine transferase known to add acetyl group on RNA transcripts thereby promoting translational efficiency. It was reported that NAT10 regulates epithelial to mesenchymal transition (EMT), DNA damage, and cell proliferation in cancers. However, weather NAT10 regulates other crucial pathways is unknown. In our study we conducted gene expression profiling analysis using data obtained from RNA-seq of MCF7 NAT10 KO and scramble control. High throughput sequencing revealed fatty acid metabolism as the top enriched pathway with fatty acid metabolic genes such ELOVL6, ACSL1, ACSL3, ACSL4, ACADSB, and ACAT1 were found to be differentially down-regulated. Overall our results revealed NAT10 depletion suppresses fatty acid metabolism in MCF7.
2022-08-03 | GSE210086 | GEO
Project description:We show that non-toxic exogenous palmitate uptake in MCF7 cells promotes NAT10 expression and NAT10-dependent ac4C RNA modification. It was previously reported that NAT10 modulates the addition of ac4C on RNA transcripts in normal and cancer conditions. However, no study report the impact of NAT10 in palmitate driven cells. Here we performed RNA immunoprecipitation sequencing (RIP-seq) in palmitate loaded MCF7 knockdown with NAT10 siRNA. Based on the pathways and enrichment landscape identified. We found that ac4C peaks of fatty acid metabolic genes including ELOVL6, ACSL1, ACSL3, ACSL4, ACADSB and ACAT1 were significantly decreased upon knockdown with NAT10 siRNA. Overall, our results revealed the impact of NAT10 as a regulator of fatty acid metabolism in ac4C-dependent manner
2022-08-03 | GSE210017 | GEO
Project description:NAT10 modulates fatty acid metabolism of palmitate driven MCF7 in ac4C dependent manner
| PRJNA863318 | ENA
Project description:NAT10 (N-acetyltransferase-like protein) regulates N4-acetylcytidine formation in RNA. However, the biological function and mechanisms of NAT10 were poorly defined. To understand the molecular mechanism by which NAT10 affect GC progression, we performed RNA sequencing (RNA-seq) in AGS cells with NAT10 knockout and in BGC823 cells with shNAT10, with independent biological replicates.
2024-06-30 | GSE180422 | GEO
Project description:RNA-seq analysis of mRNA expression profiles upon NAT10 depletion
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Project description:In this experiment, we aim to examine the role of NAT10 inhibition in Hutchinson-Gilford progeria syndrome (HGPS), a rare but devastating premature ageing syndrome caused by a mutation in the LMNA gene. NAT10 inhibition improves HGPS cellular phenotypes by releasing Transportin-1 (TNPO1) from the cytoplasm, restoring the TNPO1 pathway and allowing hnRNPA1 and NUP153 nuclear import, TPR anchorage at the nuclear pore complexes and RanGTP gradient re-balancing. We have promoted NAT10 inhibition by two ways in normal or patient derived primary skin fibroblasts; the NAT10 inhibitor Remodelin, and an siRNA directly targeting NAT10 (siNAT10). In addition, we have also used an siRNA against TNPO1 and a combined siTNPO1 and siNAT10 treatment. This is a 2-factor design, with treatment (Remodelin vs untreated, or siNAT10 vs siCT) and condition (HGPS vs normal fibroblasts) as the two conditions. Transcriptional profiling was performed using HumanHT-12 v4 Expression BeadChip microarrays, and all conditions were run in triplicate.
2018-06-25 | E-MTAB-6651 | biostudies-arrayexpress
Project description:Spatiotemporal regulation of chromatin replication (replication timing, RT） in eukaryotes is critical to maintain the genomic integrity. Here we focused on epigenetic mechanisms in rewiring genomic 3D conformation and replication timing. The results show that the novel lysine β-hydroxybutyrylation (Kbhb) modifications accelerates chromatin replication without inducing replication defects. This effect was mediated by the NAT10, a novel b-hydroxybutyryl-transferase, through regulating the association of NAT10 and CTCF with chromatin. Depletion of NAT10 and NAT10-mediated Kbhb dramatically reduce chromatin-bound NAT10 and CTCF, resulting in reorganization of genomic 3D conformation with enhanced trans- and cis-interaction in Hi-C matrix, with elevated proportion of A compartments, and with reorganized TADs boundaries. Moreover, reorganization of genomic 3D conformation contributes to rewire replication timing. These results support models in which NAT10-mediated β-hydroxybutyrylation coordinates genomic 3D conformation reorganization with replication timing alteration, and emphatically address the concept that epigenetic mechanisms reconcile genomic 3D conformation with replication timing.
2021-09-08 | GSE175731 | GEO
Project description:The diverse RNA modifications play essential functions in gene expression regulation. Aberrant RNA modifications are frequently associated with cancers, while the underlying mechanisms and clinical significance remain poorly understood. Here we revealed that the ac4C RNA acetyltransferase NAT10 is significantly upregulated in esophageal cancers (ESCA) and associated with poor ESCA prognosis. In addition, using cancer cell lines, xenograft tumor models, Nat10 conditional knockin and conditional knockout mice, in vivo ESCA tumorigenesis model and chemical inhibition approaches, we uncovered the critical physiological functions of NAT10 in promoting esophageal cancer tumorigenesis and progression in vitro and in vivo. Mechanistically, NAT10 depletion reduced the abundance of ac4C-modified tRNAs and significantly decreased the translation efficiencies of mRNAs enriched for ac4C-modified-tRNA decoded codons. We further identified EGFR as a key downstream target that facilitates NAT10’s oncogenic functions in promoting esophageal cancer progression. In terms of clinical significance, we demonstrated that NAT10 promotes esophageal cancer resistance to EGFR inhibitor gefitinib, and combination of NAT10 depletion and gefitinib treatment synergistically inhibits esophageal cancer progression in vitro and in vivo. Our data uncovered novel molecular mechanisms underlying esophageal cancer progression at the layer of mRNA translation control and provided molecular insights for development of effective cancer therapeutic strategies.
2023-02-16 | GSE225131 | GEO
Project description:Spatiotemporal regulation of chromatin replication (replication timing, RT） in eukaryotes is critical to maintain the genomic integrity. Here we focused on epigenetic mechanisms in rewiring genomic 3D conformation and replication timing. The results show that the novel lysine β-hydroxybutyrylation (Kbhb) modifications accelerates chromatin replication without inducing replication defects. This effect was mediated by the NAT10, a novel b-hydroxybutyryl-transferase, through regulating the association of NAT10 and CTCF with chromatin. Depletion of NAT10 and NAT10-mediated Kbhb dramatically reduce chromatin-bound NAT10 and CTCF, resulting in reorganization of genomic 3D conformation with enhanced trans- and cis-interaction in Hi-C matrix, with elevated proportion of A compartments, and with reorganized TADs boundaries. Moreover, reorganization of genomic 3D conformation contributes to rewire replication timing. These results support models in which NAT10-mediated β-hydroxybutyrylation coordinates genomic 3D conformation reorganization with replication timing alteration, and emphatically address the concept that epigenetic mechanisms reconcile genomic 3D conformation with replication timing.
2024-07-04 | GSE179410 | GEO
Project description:Spatiotemporal regulation of chromatin replication (replication timing, RT) in eukaryotes is critical to maintain the genomic integrity. Here we focused on epigenetic mechanisms in rewiring genomic 3D conformation and replication timing. The results show that the novel lysine β-hydroxybutyrylation (Kbhb) modifications accelerates chromatin replication without inducing replication defects. This effect was mediated by the NAT10, a novel b-hydroxybutyryl-transferase, through regulating the association of NAT10 and CTCF with chromatin. Depletion of NAT10 and NAT10-mediated Kbhb dramatically reduce chromatin-bound NAT10 and CTCF, resulting in reorganization of genomic 3D conformation with enhanced trans- and cis-interaction in Hi-C matrix, with elevated proportion of A compartments, and with reorganized TADs boundaries. Moreover, reorganization of genomic 3D conformation contributes to rewire replication timing. These results support models in which NAT10-mediated β-hydroxybutyrylation coordinates genomic 3D conformation reorganization with replication timing alteration, and emphatically address the concept that epigenetic mechanisms reconcile genomic 3D conformation with replication timing.
2021-09-08 | GSE176359 | GEO