Biology subjects

Saglam, B.

Publications and source records attributed to Saglam, B..

4 recordsLinked to original sources

bioRxiv2023

Expression patterns of m6A RNA methylation regulators under apoptotic conditions in various human cancer cell lines

The emerging evidence suggests that epitranscriptomics changes play a crucial role in the pathogenesis of cancer. However, expression patterns of m6A RNA modifiers under apoptotic conditions are unknown. We measured the transcript abundance of m6A RNA modifiers under cisplatin- and tumor necrosis factor alpha (TNF-)-induced apoptotic conditions. In general, the abundance of m6A modifiers is increased upon cisplatin treatment whereas TNF- treatment has led to a reduction in their expression. Specifically, cisplatin-induced apoptosis, but not TNF- mediated apoptosis, lowered the abundance of METTL14 and FTO transcripts. Additionally, cisplatin treatment plummeted the abundance of IGF2BP2 and IGF2BP3 readers following cisplatin treatment. These results suggest that differential response of cancer cells to apoptotic inducers could be partially due to m6A RNA modifiers.

cancer biology↗

bioRxiv2023

Epitranscriptomics m6A analyses reveal distinct m6A marks under tumor necrosis α (TNF-α)-induced apoptotic conditions in HeLa cells

TNF- is a ligand that induces both intrinsic and extrinsic apoptotic pathways in HeLa cells by modulating complex gene regulatory mechanisms. However, the full spectrum of TNF--modulated epitranscriptomic m6A marks is unknown. We employed a genomewide approach to examine the extent of m6A RNA modifications under TNF--modulated apoptotic conditions in HeLa cells. miCLIP-seq analyses revealed a plethora of m6A marks on 632 target mRNAs with an enrichment on 99 mRNAs associated with apoptosis. Interestingly, the m6A RNA modification patterns were quite different under cisplatin- and TNF--mediated apoptotic conditions. We then examined the abundance and translational efficiencies of several mRNAs under METTL3 knockdown and/or TNF- treatment conditions. Our analyses showed changes in the translational efficiency of TP53INP1 mRNA based on the polysome profile analyses. Additionally, TP53INP1 protein amount was modulated by METTL3 knockdown upon TNF- treatment but not CP treatment, suggesting the existence of a pathway-specific METTL3-TP53INP1 axis. Congruently, METLL3 knockdown sensitized HeLa cells to TNF--mediated apoptosis, which was also validated in a zebrafish larval xenograft model. These results suggest that apoptotic pathway-specific m6A methylation marks exist in cells and TNF--METTL3-TP53INP1 axis modulates TNF--mediated apoptosis in HeLa cells.

cell biology↗

bioRxiv2022

Genomewide m6A mapping uncovers dynamic changes in the m6A epitranscriptome of cisplatin-treated apoptotic HeLa cells

Cisplatin, which is a traditional cancer therapeutic drug, induces apoptosis by modulating a diverse array of gene regulatory mechanisms. However, cisplatin-mediated changes in the m6A methylome is unknown. We employed m6A miCLIP-seq to investigate the effect of m6A methylation events under cisplatin-mediated apoptotic conditions in HeLa cells. Our high-resolution approach revealed numerous m6A marks on 972 target mRNAs with an enrichment on 132 apoptotic mRNAs. Following validation of site-specific m6A events on candidate RNAs, we tracked the fate of candidate mRNAs under METTL3 knockdown and cisplatin treatment conditions. We detected perturbations in the translational efficiency of PMAIP1 and PHLDA1 transcripts based on the polysome profile analyses. Congruently, PMAIP1 and p53 amounts were dependent on METTL3. Additionally, cisplatin-mediated apoptosis was sensitized by METTL3 knockdown. These results suggest that apoptotic pathways are modulated by m6A methylation events and METTL3-p53-PMAIP1 axis modulates cisplatin-mediated apoptosis in HeLa cells.

cell biology↗

bioRxiv2020

Knockout of zebrafish desmin genes does not cause skeletal muscle degeneration but alters calcium flux

Desmin is a muscle-specific intermediate filament protein that has fundamental role in muscle structure and force transmission. Whereas human desmin protein is encoded by a single gene, two desmin paralogs (desma and desmb) exist in zebrafish. Desma and desmb show differential spatiotemporal expression during zebrafish embryonic and larval development, being similarly expressed in skeletal muscle until hatching, after which expression of desmb shifts to gut smooth muscle. We generated knockout (KO) mutant lines carrying loss-of-function mutations for each gene by using CRISPR/Cas9. Mutants are viable and fertile, and lack obvious skeletal muscle, heart or intestinal defects. In contrast to morphants, knockout of each gene did not cause any overt muscular phenotype, but did alter calcium flux in myofibres. These results point to a possible compensation mechanism in these mutant lines generated by targeting nonsense mutations to the first coding exon.

developmental biology↗