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Detection of APOBEC3B-mediated RNA editing sites in T-47D cells [RNA-seq]

ABSTRACT: Detection of APOBEC3B-mediated RNA editing sites in T-47D cells [RNA-seq]

PROVIDER: PRJNA1029590 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26422314_1.fastq.gz	Fastqsanger.gz
	SRR26422314_2.fastq.gz	Fastqsanger.gz
	SRR26422315_1.fastq.gz	Fastqsanger.gz
	SRR26422315_2.fastq.gz	Fastqsanger.gz
	SRR26422316_1.fastq.gz	Fastqsanger.gz

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Detection of APOBEC3B-mediated RNA editing sites in T-47D cells [RNA-seq]

Project description:RNA editing is a crucial post-transcriptional process that diversifies proteomic outcomes and influences gene expression. Particularly, the APOBEC3 family has emerged as a significant player in this mechanism, with APOBEC3A (A3A) showing notable roles in immune response and stress conditions. APOBEC3B (A3B), another family member, has garnered attention for its potential role in breast cancer genomic mutations. In this study, we employ an inducible expression cell model and a novel methodology for identifying differential variants in RNA (DVRs) to map A3B-mediated RNA editing sites in a breast cancer cell model. Our findings indicate that A3B engages in selective RNA editing and targets NEAT1 and MALAT1 long non-coding RNAs. Notably, the binding of these RNAs sequesters A3B’s catalytic activity, and thereby affects A3A’s activity through a feedback loop.

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RNA-seq of T-47D cells treated with 17-beta-estradiol and/or APOBEC3B-targeting siRNA

Project description:Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3B, A3B) is a key molecular driver inducing mutations in multiple human cancer. A3B belongs to the APOBEC3 enzyme family, which consists seven closely related DNA deaminases that catalyse cytosine-to-uracil (C>U) editing of single-stranded DNA (ssDNA). Here, we used RNA-seq technology to study the effect of A3B knockdown on the effect of estradiol induction in T-47D cells.

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Whole genome sequencing of T-47D cell colonies overexpressed with APOBEC3B and hUGI

Project description:Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3B, A3B) is a key molecular driver inducing mutations in multiple human cancer. A3B belongs to the APOBEC3 enzyme family, which consists seven closely related DNA deaminases that catalyse cytosine-to-uracil (C>U) editing of single-stranded DNA (ssDNA). Here, we used a lentiviral inducible system to overexpress A3B and hUGI in T-47D cells. This system will allow augmented genomic editing by A3B, while preserving the C>U editing sites from DNA repair by inhibiting base excision repair mechanism.

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Strand-specific DNA:RNA immunoprecipitation sequencing on T-47D breast cancer cells.

Project description:Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3B) is a key molecular driver inducing mutations in multiple human cancer. A3B is a member of the APOBEC3 enzyme family, which consists seven closely related DNA deaminases that catalyse cytosine-to-uracil (C>U) editing of single-stranded DNA (ssDNA). Using a cell model that lacks base excision repair function, we sampled A3B editing sites in bulk. Analyses conducted on these A3B editing sites point to a function of A3B in editing DNA:RNA hybrid structure known as R-loops. In order to verify this result, we conducted strand-specific DNA:RNA immunoprecipitation sequencing (ssDRIP-seq; S9.6, KeraFAST, ENH001) on T-47D breast cancer cells.

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Detection of APOBEC3B's RNA binding sites in T-47D cells using eCLIP-seq

Project description:RNA editing is a crucial post-transcriptional process that diversifies proteomic outcomes and influences gene expression. Particularly, the APOBEC3 family has emerged as a significant player in this mechanism, with APOBEC3A (A3A) showing notable roles in immune response and stress conditions. APOBEC3B (A3B), another family member, has garnered attention for its potential role in breast cancer genomic mutations. In this study, we employ an inducible expression cell model and eCLIP-seq to detect the RNA binding sites for A3B a breast cancer cell model. Our findings indicate that A3B engages in selective RNA editing and targets NEAT1 and MALAT1 long non-coding RNAs. Notably, the binding of these RNAs sequesters A3B’s catalytic activity, and thereby affects A3A’s activity through a feedback loop.

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Project description:Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3B) is a key molecular driver inducing mutations in multiple human cancer. A3B belongs to the APOBEC3 enzyme family, which consists seven closely related DNA deaminases that catalyse cytosine-to-uracil (C>U) editing of single-stranded DNA (ssDNA). Using a cell model that lacks base excision repair function, we sampled A3B editing sites in bulk. Analyses conducted on these A3B editing sites point to a function of A3B in editing DNA:RNA hybrid structure known as R-loops. In order to verify this result, we conducted strand-specific DNA:RNA immunoprecipitation sequencing (ssDRIP-seq; S9.6, KeraFAST, ENH001) on T-47D breast cancer cells.

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Project description:Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3B, A3B) is a key molecular driver inducing mutations in multiple human cancer. A3B belongs to the APOBEC3 enzyme family, which consists seven closely related DNA deaminases that catalyse cytosine-to-uracil (C>U) editing of single-stranded DNA (ssDNA). Here, we used DSBCapture-seq to study the formation of DNA double-strand breaks (DSB) by estrogen receptor activation upon 17-estradiol (E2) induction. The effect of A3B-depletion on DSB formation was investigated using RNA interference.

2025-01-06 | GSE193230 | GEO

Mapping the genomic occupancy by flag-tagged APOBEC3B protein

Project description:Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3B) is a key molecular driver inducing mutations in multiple human cancers. APOBEC3B belongs to the APOBEC3 enzyme family, which consists seven closely related DNA deaminases that catalyse cytosine-to-uracil (C>U) editing of single-stranded DNA (ssDNA). In order to investigate the genomic binding sites of APOBEC3B, high through-put sequencing experiments were conducted using DNA samples acquired by standard chromatin immunoprecipitation (ChIP) and ssDNA protein immunoprecipitation (SPI) samples. Substrate preference by APOBEC3B were characterised by comparing these results.

2025-01-06 | GSE193227 | GEO

RNA-seq of T-47D cells treated with 17-beta-estradiol and/or APOBEC3B-targeting siRNA

Project description:RNA-seq of T-47D cells treated with 17-beta-estradiol and/or APOBEC3B-targeting siRNA

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Detection of APOBEC3B's RNA binding sites in T-47D cells using eCLIP-seq

Project description:Detection of APOBEC3B's RNA binding sites in T-47D cells using eCLIP-seq

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