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Locus-specific chromatin profiling of evolutionarily young transposable elements [Hi-C]

ABSTRACT: Locus-specific chromatin profiling of evolutionarily young transposable elements [Hi-C]

PROVIDER: PRJNA755723 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15503419_1.fastq.gz	Fastqsanger.gz
	SRR15503419_2.fastq.gz	Fastqsanger.gz
	SRR15503420_1.fastq.gz	Fastqsanger.gz
	SRR15503420_2.fastq.gz	Fastqsanger.gz
	SRR15503421_1.fastq.gz	Fastqsanger.gz

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Locus-specific chromatin profiling of evolutionarily young transposable elements [Hi-C]

Project description:Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of Hi-ChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we show that young TEs display locus- and tissue-specific chromatin profiles in both mice and humans. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.

2021-08-19 | GSE182305 | GEO

Locus-specific chromatin profiling of evolutionarily young transposable elements

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Locus-specific chromatin profiling of evolutionarily young transposable elements [HiChIP]

Project description:Locus-specific chromatin profiling of evolutionarily young transposable elements [HiChIP]

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Locus-specific chromatin profiling of evolutionarily young transposable elements.

Project description:Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of HiChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we reveal previously unappreciated variation in the epigenetic profiles of young TE loci in mouse and human cells. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.

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Locus-specific chromatin profiling of evolutionarily young transposable elements

Project description:This SuperSeries is composed of the SubSeries listed below.

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Circular RNA repertoires are associated with evolutionarily young transposable elements.

Project description:Circular RNAs (circRNAs) are found across eukaryotes and can function in post-transcriptional gene regulation. Their biogenesis through a circle-forming backsplicing reaction is facilitated by reverse-complementary repetitive sequences promoting pre-mRNA folding. Orthologous genes from which circRNAs arise, overall contain more strongly conserved splice sites and exons than other genes, yet it remains unclear to what extent this conservation reflects purifying selection acting on the circRNAs themselves. Our analyses of circRNA repertoires from five species representing three mammalian lineages (marsupials, eutherians: rodents, primates) reveal that surprisingly few circRNAs arise from orthologous exonic loci across all species. Even the circRNAs from orthologous loci are associated with young, recently active and species-specific transposable elements, rather than with common, ancient transposon integration events. These observations suggest that many circRNAs emerged convergently during evolution - as a byproduct of splicing in orthologs prone to transposon insertion. Overall, our findings argue against widespread functional circRNA conservation.

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