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LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation

ABSTRACT: LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation

PROVIDER: PRJNA448528 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6929780_1.fastq.gz	Fastqsanger.gz
	SRR6929780_2.fastq.gz	Fastqsanger.gz
	SRR6929781_1.fastq.gz	Fastqsanger.gz
	SRR6929781_2.fastq.gz	Fastqsanger.gz
	SRR6929782_1.fastq.gz	Fastqsanger.gz

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LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation

Project description:De novo DNA methylation (DNAme) occurs coincident with transcription during mouse oogenesis. As many oocyte transcripts originate in Long Terminal Repeats (LTRs), which are divergent across species, we examined whether polymorphic LTR-initiated transcription units (LITs) shape the oocyte methylome. We identified thousands of syntenic regions in mouse, rat and human, including CpG islands (CGIs), that show divergent DNAme associated with polymorphic LITs. Notably, many CGI promoters methylated exclusively in mouse and/or rat are embedded within rodent-specific LITs, and show persistent maternal methylation in the blastocyst. Polymorphic LITs are also responsible for divergent methylation of CGI promoters in distantly related mouse strains, revealing that LITs also promote intra-species diversification of promoter DNAme.

2018-07-06 | GSE112622 | GEO

LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation.

Project description:De novo DNA methylation (DNAme) during mouse oogenesis occurs within transcribed regions enriched for H3K36me3. As many oocyte transcripts originate in long terminal repeats (LTRs), which are heterogeneous even between closely related mammals, we examined whether species-specific LTR-initiated transcription units (LITs) shape the oocyte methylome. Here we identify thousands of syntenic regions in mouse, rat, and human that show divergent DNAme associated with private LITs, many of which initiate in lineage-specific LTR retrotransposons. Furthermore, CpG island (CGI) promoters methylated in mouse and/or rat, but not human oocytes, are embedded within rodent-specific LITs and vice versa. Notably, at a subset of such CGI promoters, DNAme persists on the maternal genome in fertilized and parthenogenetic mouse blastocysts or in human placenta, indicative of species-specific epigenetic inheritance. Polymorphic LITs are also responsible for disparate DNAme at promoter CGIs in distantly related mouse strains, revealing that LITs also promote intra-species divergence in CGI DNAme.

| S-EPMC6102241 | biostudies-literature

Long noncoding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function [RNA-Seq]

Project description:LTR retrotransposons are repetitive DNA elements comprising ~10% of the human genome. However, Whether or how the LTR lncRNAs serve biological functions is largely unknown. Here we show that in primary human erythroblasts, lncRNAs transcribed from the LTR retrotransposons of ERV-9 human endogenous retrovirus regulated transcription of key erythroid genes. Global knock-down of ERV-LTR lncRNAs was performed in the in vitro erythropoiesis system of human CD34 cells, and genome wide RNA-seq was carried out to detect the effect on transcription.

2017-01-07 | GSE93280 | GEO

Long noncoding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function [ChIRP-Seq]

Project description:LTR retrotransposons are repetitive DNA elements comprising ~10% of the human genome.However, Whether or how the LTR lncRNAs serve biological functions is largely unknown. Here we show that in primary human erythroblasts, lncRNAs transcribed from the LTR retrotransposons of ERV-9 human endogenous retrovirus regulated transcription of key erythroid genes. Genome wide ChIRP-Seq was carried out to detect the association of ERV-9 lncRNAs with the genomic DNA in the Day 13 erythroid cells from in vitro culture and phenylhydrazine treated Day 5 spleen cells from transgenic mice in vivo.

2017-01-07 | GSE93281 | GEO

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

Project description:Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome. Examination of small RNA populations in the sugarcane leaves that show matches against sugarcane LTR-RTs.

2012-04-16 | E-GEOD-35143 | biostudies-arrayexpress

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

2012-04-16 | GSE35143 | GEO

Long noncoding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function

Project description:Long noncoding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function

| PRJNA360458 | ENA

Modulation of LTR-retrotransposons expression in septic shock patients: a pilot study [MIP]

Project description:Modulation of LTR-retrotransposons expression in septic shock patients: a pilot study [MIP]

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Long noncoding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function [ChIRP-Seq]

Project description:Long noncoding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function [ChIRP-Seq]

| PRJNA360462 | ENA

Evidence of developmental escape from transcriptional-gene-silencing in MESSI retrotransposons

Project description:The intent of the experiment was to infer, from tissue-specific PCR-free whole DNA sequencing analysis, the putative increase in DNA copy number of active LTR retrotransposons in shoot apical meristems of tomato (Solanum lycopersicum). For this, we performed two lanes of Illumina pair-end DNA-seq in meristems and leaves of M82 tomato line.

2019-06-14 | E-MTAB-7823 | biostudies-arrayexpress

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