Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1146948_1.fastq.gz | Fastqsanger.gz | |||
| ERR1146948_2.fastq.gz | Fastqsanger.gz | |||
| ERR1146949_1.fastq.gz | Fastqsanger.gz | |||
| ERR1146949_2.fastq.gz | Fastqsanger.gz | |||
| ERR1163949_1.fastq.gz | Fastqsanger.gz |
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Project description:RNA helicase MOV10 participates in RNA-induced gene silencing, nonsense-mediated decay and suppression of retrotransposition in cultured cells. We describe a critical role for MOV10 in early postnatal brain, where there is an ~40 fold increase in MOV10 protein levels along with a nucleo-cytoplasmic localization pattern. The isolation of MOV10-associated RNAs from this stage showed a preponderance of retrotransposon encoded RNAs along with messenger RNAs. Furthermore, reduced MOV10 expression led to an increase in genomic L1 levels in P2 brain. We show that MOV10 likely suppresses retrotransposition by binding to the LINE1 reverse transcriptase and blocking cDNA synthesis. MOV10 also binds cytoskeletal mRNAs and is required for normal neurite outgrowth in both Neuro2A and cultured hippocampal neurons. Finally, standard MOV10 levels in brain are required for normal mouse behavior. We provide the first evidence of a role for MOV10 in retrotransposon control in brain and in neuronal development and function.
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Project description:Germline retrotransposition revealed by mouse retrotransposon capture sequencing (mRC-seq)
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Project description:L1 retrotransposons are active elements in the genome, capable of mobilization in neuronal progenitor cells. Previously, we showed that chromatin remodeling during neuronal differentiation allows for a transient stimulation of L1 transcription. The activity of L1 retrotransposons during brain development can impact gene expression and neuronal function. Here we show that L1 neuronal retrotransposition in rodents is increased in the absence of MeCP2, a protein involved in global methylation and human neurodevelopmental diseases. Using neuronal progenitor cells derived from human induced pluripotent stem cells and human tissues, we revealed that Rett syndrome patients, with MeCP2 mutations, have increased susceptibility for L1 retrotransposition. Our data demonstrate that disease-related genetic mutations can influence the frequency of neuronal L1 retrotransposition, thereby increasing brain-specific genetic mosaicism. Genetic reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells, or iPSCs) by over-expression of specific genes has been accomplished for fibroblasts derived from controls and Rett syndrome patients. Different clones from each were compared to respective original fibroblasts and a human embryonic stem cell line. Gene expression profiles measured using human genome Affymetrix Gene Chip arrays were grouped by hierarchical clustering, and correlation coefficients were computed for all pair-wise comparisons.
2010-11-11 | E-GEOD-21037 | biostudies-arrayexpress
Project description:Somatic L1 retrotransposition events have been shown to occur in epithelial cancers1-8. Here, we attempted to determine how early somatic L1 insertions occurred during the development of gastrointestinal (GI) cancers. Using L1-targeted resequencing (L1-seq), we studied different stages of four colorectal cancers arising from colonic polyps, seven pancreatic carcinomas, as well as seven gastric cancers. Surprisingly, we found somatic L1 insertions not only in all cancer types and metastases, but also in colonic adenomas, well-known cancer precursors. Some insertions were also present in low quantities in normal GI tissues, occasionally caught in the act of being clonally fixed in the adjacent tumors. Insertions in adenomas and cancers numbered in the hundreds and many were present in multiple tumor sections implying clonal distribution. Our results demonstrate that extensive somatic insertional mutagenesis occurs very early during the development of GI tumors, probably before dysplastic growth. Here we show Human SNP 6.0 Array experiments on DNAs from four colorectal cancer patients (1BV, 2BV, 3BV, and 4BV) with polyps and metastases. Here we characterize the samples for CNVs and compare the samples' CNV status to their respective somatic L1 retrotransposition profile.
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Project description:We used ATLAS-seq-neo to map the sites of integration of an engineered LINE-1 (L1) retrotransposon into the genome of HeLa S3 cells. In brief, we transfected cells with a plasmid-borne L1.3 element carrying a neomycin-resistance-based retrotransposition cassette, as well as a hygromycin-resistance cassette on the plasmid backbone. For this set of experiments, cells were only selected for transfection (hygromycin) but not for retrotransposition (neomycin). Then we prepared ATLAS-seq-neo libraries. Each sample corresponds to an independent transfection and pool of hygromycin-resistant cells. ATLAS-seq-neo relies on the random mechanical fragmentation of the genomic DNA to ensure high-coverage, ligation of adapter sequences, suppression PCR-amplification of the 3' end L1 junction with its flanking genomic sequence, and Ion Torrent sequencing using single-end 400 bp read chemistry. The primer used for suppression PCR specifically targets the engineered element and not endogenous copies as in the original ATLAS-seq protocol (Philippe et al. eLife 2016). For some libraries, the linker-ligated genomic DNA was digested with BamHI, which cuts downstream of L1 polyA site in the plasmid backbone, to limit amplification from the plasmid and enrich for retrotransposition-mediated insertion events into the genomic DNA.
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Project description:Single Neuron Sequencing Quantifies L1 Retrotransposition and Somatic Mutation in the Human Brain
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