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Genome-wide R-loops dynamics and its alteration by Nkapl knockout in mouse testes with ssDRIP-seq

ABSTRACT: Genome-wide R-loops dynamics and its alteration by Nkapl knockout in mouse testes with ssDRIP-seq

PROVIDER: PRJNA971954 | ENA |

REPOSITORIES: ENA

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			Action	DRS
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	SRR24530322_1.fastq.gz	Fastqsanger.gz
	SRR24530322_2.fastq.gz	Fastqsanger.gz
	SRR24530323_1.fastq.gz	Fastqsanger.gz
	SRR24530323_2.fastq.gz	Fastqsanger.gz

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Genome-wide R-loops dynamics and its alteration by Nkapl knockout in mouse testes with ssDRIP-seq

Project description:To investigate genome-wide R-loops during meiosis exit and R-loop profiles changes with Nkapl knockout, we employed ssDRIP-seq (single-strand DNA ligation-based library preparation after DNA:RNA hybrid immunoprecipitation by S9.6 and sequencing) in wild-type and Nkapl-KO testes at P21.

2024-12-12 | GSE232417 | GEO

Genome-wide maps of R-loops in Arabidopsis

Project description:Inspired by the important roles of the special chromatin structure R-loops, here we report a new method, ssDRIP-seq, for genome-wide identification of R-loops, and demonstrate its high efficiency, low bias, and strand-specificity when profiling the R-loops in Arabidopsis. Using this single-strand DNA ligation based library construction technique, we find that Arabidopsis R-loops are formed in both the sense and antisense orientations of genes, and prefer both AT and GC skews. R-loops are prevalent in regions with multiple chromatin modifications, and are negatively correlated with CG DNA hypermethylation. R-loops are strongly enriched in gene promoters and gene bodies, highly associated with noncoding RNA and repetitive genomic regions, and correlated with activated and repressed gene loci. In summary, our analysis reveals that R-loop is a common feature of the Arabidopsis genome, and suggests diverse roles for R-loops in genome organization and gene regulation, thereby providing novel insights into plant nuclear genome formation and function.

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Project description:We performed single cell RNA-sequencing (scRNA-Seq) of testes from bovine fetuses derived from either CRISPR/Cas9 NANOS3 knockout (KO; NANOS3 -/-) or wildtype control (NANOS3 +/+) embryos. The scRNA-Seq analysis showed a complete loss of primordial germ cells (PGCs) and gonocytes in NANOS3 KO fetal testes, while maintaining the development of somatic support cells.

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RBM46 in mouse testes.

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Expression data from testes of CG3875 knockout and wildtype flies

Project description:CG3875 is a young duplicate gene of kep1 family originated recently in Drosophila melanogaster (D. melanogaster) species complex (including D. melanogaster, D. simulans, D. mauritiana and D. sechellia) after it split from D. yakuba. It encodes an RNA-binding protein containing a single maxi-KH domain. Characterization of loss-of-function phenotypes of CG3875 mutants generated by gene targeting demonstrated that CG3875 null males display a seriously reduced fertility compared with wildtype males and most of the null males are completely sterile. Further cytological identification of CG3875 null males suggested that CG3875 plays an important role in spermiogenesis processes including sperm individualization and sperm coiling. In addition, CG3875 is also essential for the formation of outer dynein arm of sperm axoneme. In order to identify the molecular mechanism responsible for the involvement of CG3875 in spermiogenesis and structural integrity of sperm axoneme, we performed microarray analysis to identify transcripts whose levels are altered in the testes of CG3875 null males. We compared gene expression profiles between testes of 0-2 day CG3875 null mutants and wildtype flies, respectively. For the sake of an identical genetic background between knockout flies and wildtype flies, the wildtype stock used here is wildtype recombinant line created during gene targeting. Seminal vesicles were removed from the testes during dissection. Two independent RNA extractions and hybridizations were conducted for each sample.

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Project description:Abcg8 knockout mice, fed chow, are infertile. These mice also are susceptible to absorption and retention of xenosterols contained in the diet. Ezetimibe, a blocker of dieary sterol entry, can reverse the fertility in Abcg8 knockout mice. In order to identify if the xenosterols resulted in disruption of a specific set of genes in the testes, we compared wild-type testes, Abcg8 knockout testes, or testes from Abcg8 knockout mice fed chow supplemented with 0.005% ezetimibe. To identify genes of interest, we reasoned that any causative gene expression changes seen in Abcg8 knockout mice fed chow, resulting in xenosterol exposure and accumulation, leading to infertilty, would be reveresed back to a pattern seen in the wild-type mice, when Abcg8 knockout mice are raised on chow containing ezetimibe (which prevents xenosterol absorption in the intestine). The target of this drug, Npc1l1, is not expressed in the testes.

2012-08-02 | GSE39813 | GEO

R-loops induce repressive chromatin marks over mammalian gene terminators

Project description:The formation of R-loops is a natural consequence of the transcription process, caused by invasion of the DNA duplex by nascent transcripts. These structures have been considered rare transcriptional by-products with potential harmful effects on genome integrity, due to the fragility of the displaced DNA coding strand. However R-loops may also possess beneficial effects as their widespread formation has been detected over CpG island promoters in human genes. Furthermore we have previously shown that R-loops are particularly enriched over G-rich terminator elements. These facilitate RNA polymerase II (Pol II) pausing prior to efficient termination. Here we reveal an unanticipated link between R-loops and RNA interference (RNAi)-dependent H3K9me2 formation over pause site termination regions of mammalian protein coding genes. We show that R-loops induce antisense transcription over these pause elements which in turn lead to the generation of double-strand RNA (dsRNA) and recruitment of Dicer, Ago1, Ago2, and G9a histone lysine methyltransferase (HKMT). Consequently an H3K9me2 repressive mark is formed and Heterochromatin Protein 1γ (HP1γ) is recruited, that reinforces Pol II pausing prior to efficient transcriptional termination. We predict that R-loops promote a chromatin architecture that defines the termination region for a substantial subset of mammalian genes. PolIIS2ph ChIP-seq and input in untreated condition and treated with BIX and RNaseH1 overexpression in HeLa cells. The 4 samples have been multiplexed, pooled and sequenced on 3 lanes of Illumina HiSeq2000.

2014-09-29 | E-GEOD-59878 | biostudies-arrayexpress

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