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Disome profiling of rocaglamide A treatment in HEK293FT cells

ABSTRACT: Disome profiling of rocaglamide A treatment in HEK293FT cells

PROVIDER: PRJNA831100 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18901163.fastq.gz	Fastqsanger.gz
	SRR18901164.fastq.gz	Fastqsanger.gz
	SRR18901165.fastq.gz	Fastqsanger.gz

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Disome profiling of rocaglamide A treatment in HEK293FT cells

Project description:For the past decade, extensive studies of translation have produced a vast amount of ribosome profiling data, an insightful resource for mining of critical details about the dynamics of translation regulation under various biological contexts. Previously, Rocaglamide A (RocA), an anti-tumor heterotricyclic natural compound, has been shown to selectively inhibit translation initiation of a large group of mRNA species by clamping eukaryotic translation initiation factor 4A (eIF4A) onto poly-purine motifs in the 5’ un-translational regions (5’UTRs). However, re-analysis of the previous ribosome profiling datasets revealed an unexpected shift of the ribosome occupancy pattern during early translation elongation upon RocA treatment in various types of cells, for a specific group of mRNA transcripts without poly-purine motifs over-presented in their 5’UTRs. Such perturbation of the translation elongation dynamics can be attributed to the blockage of translating ribosomes due to the binding of eIF4A to the poly-purine sequence in coding sequences. This new mode of action of RocA, which is complementary to the canonical function inhibiting translation initiation, selectively interfere with the translation of the genes involved in fundamental processes such as ATP synthase, mitochondrial respiratory chain complex, et al. In summary, re-analyses of previous ribosome profiling data has revealed the complete dual modes of RocA in blocking translation and thus underlying the potent anti-tumor effect

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Effect of homoharringtonine and Rocaglamide A on synchronized AC16 cells

Project description:Transcriptomic analysis of synchonized AC16 cells treated with homoharringtonine 1 µM or Rocaglamide A 100 nM for 4h (20h after synchronization) We used microarrays to detail the global programme of gene expression

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Whole transcriptomes analyses of HEK293FT cell line treated with ISLR secreted supernatant or empty vector control supernatant

Project description:Purpose: To explore the molecular mechanisms of ISLR protein, RNA sequencing was performed to analyze the geome-wide change of ISLR secreted supernatant treated HEK293FT cells compared to those of control supernatant treated cells. Methods: Total mRNA was extracted from HEK293FT cells in triplicate respectively. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: We mapped about 60 million sequence reads per sample to the human genome and identified about 58,000 transcripts in HEK293FT cells. Many transcripts showed different expression between ISLR secreted supernatant and control treated HEK293FT cells, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly positive enrichment of Hippo target genes. Conclusion: Our study present the datiled transcripts analysis of HEK293FT cells, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of ISLR regulating multiple pathways related to tissue repair.

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Project description:Purpose: We aimed to identify the targets of the RNA binding protein TruB1 in HEK293FT cells. Methods: Total RNA from endogenous-Flag KI cells were treated with UV light to crosslink RNA and proteins, then RNA-protein complexes were pulled down with anti-Flag. RNA was extracted and used to make cDNS libraries that were then sequenced by MiSeq 150bp single-end read (Sample1). Results: Reads were trimmed to remove any adaptor sequence and barcodes before mapping reads to genome hg38 using Bowtie2. Conclusions: We identified TruB1 binding sites in tRNAs and noncodingRNAs.

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