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L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force

ABSTRACT: L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force

PROVIDER: PRJNA638973 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12000244_1.fastq.gz	Fastqsanger.gz
	SRR12000244_2.fastq.gz	Fastqsanger.gz
	SRR12000245_1.fastq.gz	Fastqsanger.gz
	SRR12000245_2.fastq.gz	Fastqsanger.gz
	SRR12000246_1.fastq.gz	Fastqsanger.gz

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L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force

Project description:To investigate the m6A profiles of full-length L1 RNA, we use MeRIP-seq in HeLa cells expressing reporter L1. We find that L1 RNA contains functional m6A sites, predominantly in 5'UTR.

2021-01-09 | GSE152328 | GEO

L1 retrotransposons exploit RNA m<sup>6</sup>A modification as an evolutionary driving force.

Project description:L1 retrotransposons can pose a threat to genome integrity. The host has evolved to restrict L1 replication. However, mechanisms underlying L1 propagation out of the host surveillance remains unclear. Here, we propose an evolutionary survival strategy of L1, which exploits RNA m6A modification. We discover that m6A 'writer' METTL3 facilitates L1 retrotransposition, whereas m6A 'eraser' ALKBH5 suppresses it. The essential m6A cluster that is located on L1 5' UTR serves as a docking site for eukaryotic initiation factor 3 (eIF3), enhances translational efficiency and promotes the formation of L1 ribonucleoprotein. Furthermore, through the comparative analysis of human- and primate-specific L1 lineages, we find that the most functional m6A motif-containing L1s have been positively selected and became a distinctive feature of evolutionarily young L1s. Thus, our findings demonstrate that L1 retrotransposons hijack the RNA m6A modification system for their successful replication.

| S-EPMC7873242 | biostudies-literature

L1 chimeric transcripts are expressed in healthy brain and their deregulation in glioma follows that of their host locus.

Project description:Background: Besides the consequences of retrotransposition, long interspersed element 1 (L1) retrotransposons can affect the host genome though their antisense promoter. In addition to the sense promoter, the evolutionarily recent L1 retrotransposons, which are present in several thousand copies, also possess an anti-sense promoter that can produce L1 chimeric transcripts (LCT) composed of the L1 5’ UTR followed by the adjacent genomic sequence. The full extent to which LCT expression occurs in a given tissue and whether disruption of the defense mechanisms that normally control L1 retrotransposons affect their expression and function in cancer cells, remain to be established. Results: By using CLIFinder, a dedicated bioinformatics tool, we found that LCT expression was widespread in normal brain and aggressive glioma samples, and that approximately 17% of recent L1 retrotransposons, from the L1PA1 to L1PA7 subfamilies, were involved in their production. Importantly, the transcriptional activities of the L1 antisense promoters and of their host loci were coupled. Accordingly, we detected LCT-producing L1 retrotransposons mainly in transcriptionally active genes and genomic loci. Moreover, changes in the host genomic locus expression level in glioma was associated with a similar change in LCT expression level, regardless of the L1 promoter methylation status. Conclusions: Our findings support a model in which the host genomic locus transcriptional activity is the main driving force of LCT expression. We hypothesize that this model is more applicable when host gene and LCT are transcribed from the same strand.

2022-03-24 | GSE180209 | GEO

L1 retrotransposition in neurons is mediated by MeCP2

2010-11-11 | GSE21037 | GEO

L1 retrotransposition in neurons is mediated by MeCP2

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

Docosahexaenoic acid (DHA) a driving force regulating gene expression in bluefin tuna (Thunnus thynnus) larvae development.

Project description:Docosahexaenoic acid (DHA) a driving force regulating gene expression in bluefin tuna (Thunnus thynnus) larvae development.

| PRJNA1097605 | ENA

Suppression of HSF1 activity by wildtype p53 creates a driving force for p53 loss-of-heterozygosity

Project description:Suppression of HSF1 activity by wildtype p53 creates a driving force for p53 loss-of-heterozygosity

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Asymmetric distribution of H3K9me3 at replicating DNA strands silences L1 retrotransposons during S phase

Project description:Asymmetric distribution of H3K9me3 at replicating DNA strands silences L1 retrotransposons during S phase

| PRJNA869455 | ENA

Effect of Anesthesia on Force Application During Colonoscopy

Project description:The aim of the study is to determine if more force is used during colonoscopy when patients receive monitored anesthesia with propofol versus conscious sedation. Force measurements will be performed using the colonoscopy force monitor (CFM). This device measures the magnitude and direction of force applied to the insertion tube of a standard colonoscope during colonoscopy.

| 2163741 | ecrin-mdr-crc

Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites

Project description:CRISPR/Cas9-based genome editing has revolutionized experimental molecular biology and entered the clinical world for targeted gene therapy. Identifying DNA modifications occurring at CRISPR/Cas9 target sites is critical to determine efficiency and safety of editing tools. Here we show that insertions of LINE-1 (L1) retrotransposons can occur frequently at CRISPR/Cas9 editing sites. Together with PolyA-seq and an improved amplicon sequencing, we characterize more than 2,500 de novo L1 insertions at multiple CRISPR/Cas9 editing sites in HEK293T, HeLa and U2OS cells. These L1 retrotransposition events exploit CRISPR/Cas9-induced DSB formation and require L1 RT activity. Importantly, de novo L1 insertions are rare during genome editing by prime editors (PE), cytidine or adenine base editors (CBE or ABE), consistent with their reduced DSB formation. These data demonstrate that insertions of retrotransposons might be a potential outcome of CRISPR/Cas9 genome editing and provide further evidence on the safety of different CRISPR-based editing tools.

2022-06-07 | GSE178440 | GEO

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