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Susceptibility to cancer is heritable, but much of this heritability remains unexplained. Some 'missing' heritability may be mediated by epigenetic changes in the parental germ line that do not involve transmission of genetic variants from parent to offspring. We report that deletion of the chromatin regulator Kdm6a (Utx) in the paternal germ line results in elevated tumor incidence in genetically wild type mice. This effect increases following passage through two successive generations of Kdm6a male germline deletion, but is lost following passage through a wild type germ line. The H3K27me3 mark is redistributed in sperm of Kdm6a mutants, and we define approximately 200 H3K27me3-marked regions that exhibit increased DNA methylation, both in sperm of Kdm6a mutants and in somatic tissue of progeny. Hypermethylated regions in enhancers may alter regulation of genes involved in cancer initiation or progression. Epigenetic changes in male gametes may therefore impact cancer susceptibility in adult offspring.
Pubmed ID: 30963999 RIS Download
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Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
View all literature mentionsA commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis.
View all literature mentionsEpigenDx is a genomic and epigenomic research company specializing in disease biomarker discovery and molecular diagnosis. The company provides products related to DNA methylation analysis research. Currently available products include DNA methylation controls and validated DNA methylation assays for human, mouse, and rat. EpigenDx also provides products and laboratory services for scientific researchers from academic, government and industrial communities. Our commitment to quality comes from our desire and dedication to provide the best products and services to our customers. EpigenDx has knowledge and expertise in Pyrosequencing and its many applications. CpG methylation and allele quantification analysis are conducted using Qiagen-Pyrosequencing PSQ MD system, while short-read sequence analysis is carried out using Qiagen-Pyrosequencing PSQ ID system.
View all literature mentionsA commercial antibody supplier which supplies primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits.
View all literature mentionsAn Antibody supplier; Dako was purchased by Agilent in 2012 and several years later the websites began to reflect the Dako products as part of the Agilent catalog.
View all literature mentionsMus musculus with name C57BL/6J from IMSR.
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View all literature mentionsMus musculus with name B6;129S4-Kdm6atm1c(EUCOMM)Jae/J from IMSR.
View all literature mentionsAllele Detail: Targeted This is a legacy resource.
View all literature mentionsSuite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.
View all literature mentionsSoftware R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables.
View all literature mentionsAn R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.
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View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsSoftware tool to map bisulfite converted sequence reads and determine cytosine methylation states. Flexible aligner and methylation caller for Bisulfite-Seq applications. Used to map bisulfite treated sequencing reads to genome of interest and perform methylation calls in single step.
View all literature mentionsUltrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.
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View all literature mentionsSoftware tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
View all literature mentionsSoftware environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
View all literature mentionsSoftware Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
View all literature mentionsSoftware Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
View all literature mentionsSoftware R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables.
View all literature mentionsAn R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.
View all literature mentionsSoftware tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads.
View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsSoftware tool to map bisulfite converted sequence reads and determine cytosine methylation states. Flexible aligner and methylation caller for Bisulfite-Seq applications. Used to map bisulfite treated sequencing reads to genome of interest and perform methylation calls in single step.
View all literature mentionsSoftware tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.
View all literature mentionsUltrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.
View all literature mentionsSoftware ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
View all literature mentionsSoftware Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
View all literature mentionsSoftware Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
View all literature mentionsSoftware tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
View all literature mentionsSoftware environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
View all literature mentionsThis polyclonal targets CD3
View all literature mentionsThis monoclonal targets ERG antibody [EPR3864(2)]
View all literature mentionsThis monoclonal targets VEGF antibody [EP1176Y] - Carboxyterminal end
View all literature mentionsThis monoclonal targets RAT ANTI MOUSE F4/80
View all literature mentionsThis monoclonal targets GAPDH (6C5)
View all literature mentionsThis polyclonal targets H3K27ac
View all literature mentionsThis polyclonal targets GLUL
View all literature mentionsThis polyclonal targets H3K4me1
View all literature mentionsThis polyclonal targets Histone H3, trimethyl (Lys27)
View all literature mentionsThis monoclonal targets Histone H3 (tri methyl K27) antibody [mAbcam 6002] - ChIP Grade
View all literature mentionsMus musculus with name B6;129S4-Kdm6atm1c(EUCOMM)Jae/J from IMSR.
View all literature mentionsAllele Detail: Targeted This is a legacy resource.
View all literature mentionsMus musculus with name B6;129S4-Kdm6atm1c(EUCOMM)Jae/J from IMSR.
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