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Impact of Mobile Element Insertions on Human Transcriptome Variation

ABSTRACT: Impact of Mobile Element Insertions on Human Transcriptome Variation

PROVIDER: PRJNA632951 | ENA |

REPOSITORIES: ENA

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Impact of Mobile Element Insertions on Human Transcriptome Variation

Project description:Impact of Mobile Element Insertions on Human Transcriptome Variation

| PRJNA632952 | ENA

A map of mobile DNA insertions in the NCI-60 human cancer cell panel

Project description:The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the NCI-60 have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy. To approach a functional understanding of these sequences in transformed cells, we used transposon insertion profiling (TIP) to map Long INterspersed Element-1 (LINE-1, L1) and Alu Short INterspersed Element (SINE) insertions in cancer genes in NCI-60 cells. As expected, this identified known insertions, polymorphisms shared in unrelated tumor cell lines, as well as unique, potentially tumor-specific insertions. Here, we report a map of these insertion sites and conduct association analyses relating individual insertions to a variety of cellular phenotypes.

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Detection of mobile-genetic-element variation between colonizing and infecting hospital-associated methicillin-resistant Staphylococcus aureus isolates.

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Primate genome architecture linked with formation mechanisms and functional consequences of structural variation

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Dog_CGH_Array on 54 breed and village dogs and one wolf

Project description:Comprehensive view of structural variation across dog genomes including mobile elements and nuclear mitochondrial insertions

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Primate genome architecture linked with formation mechanisms and functional consequences of structural variation

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Mechanisms of insertions at a double strand break

Project description:Insertions and deletions (indels) are common sources of structural variation, and insertions originating from spontaneous DNA lesions are frequent in cancer. We developed a highly sensitive assay (Indel-Seq) to monitor rearrangements in human cells at the TRIM37 acceptor locus that reports indels stemming from experimentallyinduced and spontaneous genome instability. Templated insertions, which derive from sequences genome-wide, require contact between donor and acceptor loci, homologous recombination, and are stimulated by DNA end-processing. Insertions are facilitated by transcription and involve a DNA/RNA hybrid intermediate. Indel-Seq reveals that insertions are generated via multiple pathways. The broken acceptor site anneals with a resected DNA break or invades the displaced strand of a transcription bubble or R-loop followed by DNA synthesis, displacement and then ligation by nonhomologous end-joining. Our studies identify transcription-coupled insertions as a critical source of spontaneous genome instability that are distinct from cut-and-paste events

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Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions.

Project description: Not available

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Mobile Technology to Identify Mechanisms Linking Genetic Variation and Depression

Project description:Mobile Technology to Identify Mechanisms Linking Genetic Variation and Depression

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