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RNA sequencing (RNA-SEQ) of BUD31 knockout by cre-loxp in the mouse reproductive system

ABSTRACT: RNA sequencing (RNA-SEQ) of BUD31 knockout by cre-loxp in the mouse reproductive system

PROVIDER: PRJNA784266 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17055287_1.fastq.gz	Fastqsanger.gz
	SRR17055287_2.fastq.gz	Fastqsanger.gz
	SRR17055288_1.fastq.gz	Fastqsanger.gz
	SRR17055288_2.fastq.gz	Fastqsanger.gz
	SRR17055289_1.fastq.gz	Fastqsanger.gz

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RNA sequencing (RNA-SEQ) of BUD31 knockout by cre-loxp in the mouse reproductive system

Project description:The testis is the organ with the most transcriptome diversity and alternative splicing (AS) is considered to be the most important source. However, the physiological role of AS in spermatogenesis is poorly understood. Here, we report that spliceosome component BUD31 is a prominent AS regulator in early stage of spermatogenesis in mice. Bud31 expression in the testis is initiated soon after birth. Conditional knock out of Bud31 in germ cells in Vasa-Cre mice led to loss of spermatogonial stem cells (SSCs) and to infertility. We further demonstrate that BUD31was required for both SSC pool maintenance and initiation of spermatogenesis. Mechanistically, BUD31 regulates the alternative splicing of multiple genes involved in cell cycle checkpoint and cell differentiation. In particular, we identified CDK2 as a direct splicing target of BUD31 through integrative analysis of SMART-seq and RIP-seq data. Knockout of BUD31 results in the intron retention as well as exon skipping of CDK2, which led to decrease in CDK2 expression. Our findings highlight the significance of BUD31 and its regulated AS in SSC self-renewal and differentiation.

2022-11-04 | GSE189714 | GEO

RNA Immunoprecipitation(RIP)-seq of BUD31 in the mouse reproductive system

2022-11-04 | GSE189715 | GEO

RNA Sequencing of mouse E15.5 Six2-Cre Irx3/5(loxP/loxP) whole kidneys

Project description:RNA Sequencing of mouse E15.5 Six2-Cre Irx3/5(loxP/loxP) whole kidneys

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Study on the genomic changes in ColIa2 Cre x RBP-Jkappa loxp/loxp mice

Project description:Skin tumor formed in the ColIa2 Cre x RBP-Jkappa loxp/loxp mice was analyzed for genomic changes by comparing with normal tissues from the same mice.

2012-05-01 | GSE36464 | GEO

RNA Immunoprecipitation(RIP)-seq of BUD31 in the mouse reproductive system

Project description:RNA Immunoprecipitation(RIP)-seq of BUD31 in the mouse reproductive system

| PRJNA784265 | ENA

Engineering spacer specificity of the Cre/loxP system

Project description:Translational research on the Cre/loxP recombination system focuses on enhancing its specificity by modifying Cre/DNA interactions. Despite extensive efforts, the exact mechanisms governing how Cre distinguishes between substrates remains elusive. Cre recognizes 13 bp inverted repeats, initiating recombination in the 8 bp spacer region. While literature suggests that efficient recombination proceeds between lox sites with non-loxP spacer sequences when both lox sites have matching spacers, experimental validation for this assumption is lacking. To fill this gap, we investigated target site variations of identical pairs of the loxP 8 bp spacer region, screening 6,000 unique loxP-like sequences. Approximately 84% of these sites exhibited efficient recombination, affirming the flexibility of spacer sequences for catalysis. However, certain spacers negatively impacted recombination, emphasizing sequence dependence. Directed evolution of Cre on inefficiently recombined spacers not only yielded recombinases with enhanced activity but also mutants with reprogrammed selective activity. Mutations altering spacer specificity were identified, and molecular modelling and dynamics simulations elucidated the mechanism behind this specificity switch. These findings highlight the potential to fine-tune site-specific recombinases for spacer sequence specificity, offering a novel concept to enhance the applied properties of designer-recombinases for genome engineering applications.

2024-07-25 | GSE254392 | GEO

Cre-loxP-induced Ewsr1-Atf1 translocation tumors

Project description:Cre-loxP-induced Ewsr1-Atf1 translocation tumors

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Study on the genomic changes in ColIa2 Cre x RBP-Jkappa loxp/loxp mice

Project description:Skin tumor formed in the ColIa2 Cre x RBP-Jkappa loxp/loxp mice was analyzed for genomic changes by comparing with normal tissues from the same mice. Genomic DNA were isolated from each individual tumor and compared with the DNA extracted from the brain tissue in the same mouse.

2012-04-30 | E-GEOD-36464 | biostudies-arrayexpress

Engineering spacer specificity of the Cre/loxP system

Project description:Engineering spacer specificity of the Cre/loxP system

| PRJNA1070297 | ENA

RNA immunoprecipitation sequencing (RIP-seq) of BUD31 in ovarian cancer cells

Project description:Mis-regulation of splicing factors are thought to activate cancer specific splicing programs that contribute to cancer development and progression. However, it remains a major challenge to identify the key splicing variants caused by aberrant expression of splicing factors in cancer. Here we report that splicing factor BUD31 is commonly overexpressed in high-grade serous ovarian carcinoma (HGSOC) and high level of BUD31 is associated with poor prognosis. RNA-seq analysis reveals that BUD31 inhibition predominantly results in alternation of exon skipping and intron retention. RNA immunoprecipitation sequencing (RIP-seq) was used to analysis the interaction between BUD31 and the target RNA. Our data indicate that BUD31 is a critical oncogenic splicing factor in ovarian cancer and might act as a potential therapeutic target.

2022-09-19 | GSE183450 | GEO

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