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De novo deletions and duplications at recombination hotspots in mouse germlines

ABSTRACT: De novo deletions and duplications at recombination hotspots in mouse germlines

PROVIDER: PRJNA755308 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15483418_1.fastq.gz	Fastqsanger.gz
	SRR15483418_2.fastq.gz	Fastqsanger.gz
	SRR15483419_1.fastq.gz	Fastqsanger.gz
	SRR15483419_2.fastq.gz	Fastqsanger.gz
	SRR15483420_1.fastq.gz	Fastqsanger.gz

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De novo deletions and duplications at recombination hotspots in mouse germlines

Project description:Numerous DNA double-strand breaks (DSBs) arise during meiosis to initiate homologous recombination. These DSBs are usually repaired faithfully, but here we uncover a new type of mutational event in which deletions form via joining of ends from two closely-spaced DSBs (double cuts) within a single hotspot or at adjacent hotspots on the same or different chromatids. Deletions occur in normal meiosis but are much more frequent when DSB formation is dysregulated in the absence of the ATM kinase. Events between chromosome homologs point to multi-chromatid damage and aborted gap repair. Some deletions contain DNA from other hotspots, indicating that double cutting at distant sites creates substrates for insertional mutagenesis. End joining at double cuts can also yield tandem duplications or extrachromosomal circles. Our findings highlight the importance of DSB regulation and reveal a previously hidden potential for meiotic mutagenesis that is likely to affect human health and genome evolution.

2021-10-01 | GSE182210 | GEO

De novo deletions and duplications at recombination hotspots in mouse germlines.

Project description:Numerous DNA double-strand breaks (DSBs) arise during meiosis to initiate homologous recombination. These DSBs are usually repaired faithfully, but here, we uncover a distinct type of mutational event in which deletions form via joining of ends from two closely spaced DSBs (double cuts) within a single hotspot or at adjacent hotspots on the same or different chromatids. Deletions occur in normal meiosis but are much more frequent when DSB formation is dysregulated in the absence of the ATM kinase. Events between chromosome homologs point to multi-chromatid damage and aborted gap repair. Some deletions contain DNA from other hotspots, indicating that double cutting at distant sites creates substrates for insertional mutagenesis. End joining at double cuts can also yield tandem duplications or extrachromosomal circles. Our findings highlight the importance of DSB regulation and reveal a previously hidden potential for meiotic mutagenesis that is likely to affect human health and genome evolution.

| S-EPMC8616837 | biostudies-literature

Gene duplications and deletion in the Poeciliidae

Project description:Gene duplications and deletions in the Poeciliidae

| PRJEB49340 | ENA

Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing

Project description:Deletions and duplications in mitochondrial DNA (mtDNA) cause mitochondrial disease and accumulate in conditions such as cancer and age-related disorders, but validated high-throughput methodology that can readily detect and discriminate between these two types of events is lacking. Here we present MitoSAlt, a computational method for accurate identification, quantification and visualization of mtDNA deletions and duplications from whole genome, whole exome or transcriptome sequencing data. MitoSAlt was tested on simulated sequencing reads and human patient samples with single deletions and duplications to verify its accuracy. Application to mouse models of mtDNA maintenance disease further demonstrated the ability to detect deletions and duplications even at low levels of heteroplasmy. MitoSAlt paves the way for simple and reliable determination of mtDNA deletions and duplications across a wide range of relevant conditions and available sequencing datasets. Ã¢Â€Âƒ

| EGAS00001004380 | EGA

The meiotic recombination activator PRDM9 trimethylates both H3K4 and H3K36 at recombination hotspots in vivo

Project description:Mammalian genetic recombination is concentrated at hotspots, specialized 1-2 Kb sites separated by long stretches of DNA lacking recombination. Mammalian hotspot locations depend on PRDM9, a zinc finger protein that binds at hotspots and uses its SET domain to locally trimethylate histone H3K4. Here we find that PRDM9 also locally trimethylates H3K36 at hotspots. Using ChIP-seq and immunoprecipitation data for H3K36me3 in murine spermatocytes, we show that H3K4me3 and H3K36me3 coincide only at hotspots in germ cells, and that this H3K4me3/H3K36me3-double-positive signature is almost entirely dependent on PRDM9. We performed ChIP-seq with an antibody against H3K36me3, using chromatin extracted from murine spermatocytes, and compared it to previously generated ChIP-seq data for H3K4me3 in the same cell type. ---------------------------------- This dataset represents the H3K36 component only

2016-06-30 | E-GEOD-76416 | biostudies-arrayexpress

Mutational and Transcriptional Landscape of Spontaneous Gene Duplications and Deletions in Caenorhabditis elegans

Project description:Mutational and Transcriptional Landscape of Spontaneous Gene Duplications and Deletions in Caenorhabditis elegans

| PRJNA449086 | ENA

The meiotic recombination activator PRDM9 trimethylates both H3K4 and H3K36 at recombination hotspots in vivo

2016-06-30 | GSE76416 | GEO

Histone H3 lysine9 acetylation, rather than lysine4 trimethylation, marks meiotic recombination hotspots and promotes recombination initiation in fission yeast

Project description:Histone modifications are associated with meiotic recombination hotspots, discrete sites with augmented recombination frequency. For example, trimethylation of histone H3 lysine4 (H3K4me3) marks most hotspots in budding yeast and mouse. Modified histones are known to regulate meiotic recombination partly by promoting DNA double strand break (DSB) formation, but the role and precise landscape of histone modifications at hotspots remain unclear. Here, we studied hotspot-associated modifications in fission yeast and found general features: acetylation of H3 lysine9 (H3K9ac) is strikingly elevated, and H3K4me3 is not significantly enriched. Remarkably, elimination of H3K9ac reduced binding of the DSB-inducing enzyme Rec12 and DSB at hotspots. We also found that the H3K4 metyltransferase Set1 promotes DSB formation at some loci, but it restricts Rec12 binding to hotspots. These results suggest that H3K9ac rather than H3K4me3 is a hotspot-associated mark involved in meiotic DSB formation in fission yeast. S.pombe cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested one hour after the induction. ChIP were performed using anti-H3Cter, H3K9ac, -H3K14ac and -H3K4me3 antibodies. pat1-114 rad50S rec12+-FLAG cells in a wild type, H3K9A or set1+ deletion background were induced to enter meiosis by the haploid meiosis system, and harvested five hours after the induction. ChIP were performed using anti-FLAG antibodies.

2013-03-07 | E-GEOD-31648 | biostudies-arrayexpress

RNA-seq transcriptome profiling of 1) C. elegans male germlines vs. oogenic germlines, and 2) male germlines, sperm, and F1 offspring germlines when offspring inherited sperm chromatin lacking H3K27me3.

Project description:Paternal contributions to epigenetic inheritance are not well understood. We report that in C. elegans sperm, the genome is packaged in nucleosomes and carries a histone-based epigenetic memory of gene expressions during spermatogenesis. In mature sperm, genes with spermatogenesis-specific expression are marked with both active and represseive histone modifications and genes with oogenesis-enriched expression are marked with active histone modifications. We showed that genes with oogenesis-enriched expression are in fact transcribed in spermatogenic germlines. We tested if sperm chromatin marking is necessary for germ cell development in offspring that inherit both sperm and oocyte chromosomes, using male parents that either can or cannot generate H3K27me3. Males homozygous for a mutation in mes-3, which encodes a member of the worm PRC2 complex, were mated with feminized mes-3/+ heterozygous worms to produce offspring that inherited sperm chromosomes lacking H3K27me3. We call these offspring M+P- or MpPm (Maternal chromosomes are + or plus for H3K27me3, Paternal chromosomes are - or minus for H3K27me3). Most of the resulting mes-3 homozygous M+P- offspring developed into sterile adults in this sensitized genetic background. In contrast, genetically identical control offspring that received appropriate H3K27me3-marked sperm chromosomes (M+P+ or MpPp) displayed low sterility. We compared genes mis-regulated in mes-3 male germlines versus control him-8 male germlines, mature sperm from those germlines, and germlines of mes-3 mutant F1 offspring that inherited sperm chromatin lacking H3K27me3 (M+P-) versus inherited sperm chromatin with H3K27me3 (M+P+), based on RNA-seq.

2018-07-23 | GSE115708 | GEO

Histone H3 lysine9 acetylation, rather than lysine4 trimethylation, marks meiotic recombination hotspots and promotes recombination initiation in fission yeast

2013-03-07 | GSE31648 | GEO