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Transcriptional readthrough and splicing upon chemotherapy treatment [long-read, nascent RNA]

ABSTRACT: The Neugebauer lab has previously shown that splicing occurs co-transcriptionally and is coupled to 3’end cleavage. It is known that stress, such as hyperosmotic shock, affects RNA processing. The cellular stress response is an important component of cancer cell response to chemotherapy that can determine cell survival. Herein, we study how the coupling of the RNA processes in leukemia cells is affected in response to stress and therapeutic agents. We used short- and long-read sequencing to follow RNA processing upon treatment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE283849 | GEO | 2026/02/15

REPOSITORIES: GEO

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Transcriptional readthrough and splicing upon chemotherapy treatment

Project description:The Neugebauer lab has previously shown that splicing occurs co-transcriptionally and is coupled to 3’end cleavage. It is known that stress, such as hyperosmotic shock, affects RNA processing. The cellular stress response is an important component of cancer cell response to chemotherapy that can determine cell survival. Herein, we study how the coupling of the RNA processes in leukemia cells is affected in response to stress and therapeutic agents. We used short- and long-read sequencing to follow RNA processing upon treatment.

2026-02-15 | GSE283813 | GEO

Improved co-transcriptional splicing of readthrough transcripts during chemotherapy treatment [CML_RNA-seq]

Project description:The cellular stress response is an important component of cancer cell response to chemotherapy that can determine cell survival. Herein, we study how the coupling of the RNA processes in leukemia cells is affected in response to stress and therapeutic agents. We used short- and long-read sequencing to follow RNA processing upon treatment.

2026-02-15 | GSE310243 | GEO

Short-read nascent RNA sequencing from S. pombe

Project description:Short-read sequencing of nascent RNA from exponentially growing S. pombe cells was employed to quantify co-transcriptional splicing and expression levels. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010). Single-end Illumina sequencing data were generated from chromatin-associated, non-polyadenylated RNA (nascent RNA) and cytoplasmic mRNA for reference. In an experiment to test for splicing-associated gene expression changes cells were treated with 10mM Caffeine for 15minutes and nascent and mRNA-seq data were generated subsequently.

2018-05-18 | GSE104680 | GEO

Long-read nascent RNA sequencing from S. pombe

Project description:Long-read SMRT cDNA sequencing of nascent RNA from exponentially growing S. pombe cells was employed to obtain transcription elongation and splicing information from single transcripts. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010). The nascent 3’ end was labeled with a 3’ DNA adaptor through ligation. The adaptor sequence served as template for full-length reverse transcription and double-stranded cDNA was obtained in a transcriptome-wide PCR. SMRT DNA sequencing libraries were prepared subsequently.

2018-05-18 | GSE104679 | GEO

Long read sequencing of nascent RNA from S. cerevisiae and S. pombe

Project description:Long read SMRT cDNA sequencing of nascent RNA from exponentially growing S. cerevisiae and S. pombe cells was employed to obtain transcription elongation and splicing information from single transcripts. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010). The nascent 3â?? end was labeled with a 3â?? DNA adaptor through ligation. The adaptor sequence served as template for full-length reverse transcription and double-stranded cDNA was obtained in a PCR (gene-specific or transcriptome-wide). SMRT DNA sequencing libraries were prepared subsequently. Nascent RNA profiles for mainly intron-containing genes were generated with long-read SMRT cDNA sequencing.

2016-03-24 | E-GEOD-70906 | biostudies-arrayexpress

Long read sequencing of nascent RNA from S. cerevisiae and S. pombe

Project description:Long read SMRT cDNA sequencing of nascent RNA from exponentially growing S. cerevisiae and S. pombe cells was employed to obtain transcription elongation and splicing information from single transcripts. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010). The nascent 3’ end was labeled with a 3’ DNA adaptor through ligation. The adaptor sequence served as template for full-length reverse transcription and double-stranded cDNA was obtained in a PCR (gene-specific or transcriptome-wide). SMRT DNA sequencing libraries were prepared subsequently.

2016-03-24 | GSE70906 | GEO

Transcriptional readthrough and splicing upon chemotherapy treatment [long-read, nascent RNA]

Project description:Transcriptional readthrough and splicing upon chemotherapy treatment [long-read, nascent RNA]

| PRJNA1195901 | ENA

ChIP-chip of RNAP in E. coli strains exposed to 0.5M NaCl

Project description:We have analysed the genome-wide distribution of RNA polymerase in mechanosenstive deletion strains of E.coli upon hyperosmotic stress. We have used ChIP-chip of the ß subunit of RNA polymerase and we have assessed changes in RNA polymerase distribution in Frag1 MJF612 and MJF641 strains that are deleted for incresing numbers of mechanosensitive channels in response to hyperosmotic stress .

2012-03-30 | E-MTAB-592 | biostudies-arrayexpress

sRNA participates in hyperosmotic stress response regulation in Sphingomonas melonis TY

Project description:Drought and salinity are most ubiquitous environmental factors that causing hyperosmotic threats to Sphingomonas and impairs their efficiency of performing environmental functions. However, bacteria have developed various responses and regulation systems to coping with these abiotic challenges. Among which post-transcriptional regulation plays vital roles in regulating gene expression and cellular homeostasis, as hyperosmotic stress conditions could lead to induction of specific small RNA (sRNA) that participates in stress response regulation. Here, we report a candidate functional sRNAs landscape of S. melonis which could help for comprehensive analyses of sRNA regulation in Sphingomonas species. WGCNA analysis revealed a 263 nt sRNA SNC251 which transcribed from its own promoter and shew the most dramatic correlation coefficient with hyperosmotic factors was characterized. An in vivo translation-reporter system constructed in this study revealed positive regulation and feedback mechanisms between the SNC251 and nicotine degradation genes. Deletion of snc251 affected multiple cellular processes and nicotine degradation capacity of S. melonis TY, while overexpression of SNC251 facilitated the biofilm formation capability of TY under hyperosmotic stress. Two genes of TonB system were further verified could be activated by SNC251, which also means SNC251 is a trans-acting small RNA. Briefly, this research reported a summary of sRNAs which participate in hyperosmotic stress response in S. melonis TY and revealed a novel sRNA SNC251 which is necessary for hyperosmotic stress response.

2023-02-07 | GSE224545 | GEO

Transcriptome profiling of Arabidopsis seedlings upon hyperosmotic stress

Project description:We examined the possible effect of hyperosmotic stress on Arabidopsis transcriptome using mRNA-seq. We found that the transcriptome is reprogrammed in response to hyperosmotic stress, in a DCP5-dependent.

2022-10-01 | GSE214366 | GEO

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