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63 results for “LINE1”
Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae
<p>The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. Results The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. Conclusions The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.</p>
Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae
Open the record for dataset details and reuse information.
Two-factor authentication underpins the precision of piRNA-directed LINE1 DNA methylation
<p>Source data for figures 3 and Extended figure 3.</p>
DAXX governs the silencing of LINE1 during spermatogenesis in mice [BiSulfite-seq]
GEO Series GSE315864. Mus musculus. 4 samples. Type: Methylation profiling by high throughput sequencing.
LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic cells [small RNA-seq]
GEO Series GSE203288. Homo sapiens. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic cells [RNA-seq]
GEO Series GSE203287. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
FTO mediates LINE1 m6A demethylation and chromatin regulation in mESCs and mouse tissues
GEO Series GSE151704. Mus musculus. 104 samples. Type: Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Nuclear exosome targeting complex core factor Zcchc8 regulates the degradation of LINE1 RNA in early embryos and embryonic stem cells
GEO Series GSE127790. Mus musculus. 59 samples. Type: Expression profiling by high throughput sequencing.
RNAseq analysis of Hep3B cells upon overexpression of LINE1 retrotransposon encoded protein L1orf1p
GEO Series GSE194251. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-Seq_RSeT_H9_L1KD]
GEO Series GSE232937. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-seq_primed,RSeT,RSeT+DT_hESCs]
GEO Series GSE275237. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-seq_PXGL H9_L1KD]
GEO Series GSE263287. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
The Rhox gene cluster suppresses germline LINE1 transposition
GEO Series GSE160600. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-Seq_Primed_H9_L1KD]
GEO Series GSE232930. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic cells [ChIP-seq]
GEO Series GSE203285. Homo sapiens. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Subfamily-Selective PCR primers for the Human LINE1 L1PA Lineage
GEO Series GSE301759. Homo sapiens. 6 samples. Type: Other.
DAXX governs the silencing of LINE1 during spermatogenesis in mice [RNA-seq]
GEO Series GSE315982. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Two-factor authentication underpins the precision of piRNA-directed LINE1 DNA methylation
GEO Series GSE228294. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Effect of LINE1 intervention on vascular calcification （RNA-seq）
GEO Series GSE279148. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [scRNA-seq]
GEO Series GSE232938. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
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