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Pervasive transcription and endosiRNAs restrain transposons during global demethylation in embryonic stem cells [RNA-Seq 2]

ABSTRACT: DNA methylation and other repressive epigenetic marks are erased in the mammalian germline and transposable elements (TEs) acquire the potential to be transcribed. This is a critical phase for genome defense and complementary TE silencing pathways are required to limit their activity. We find overlapping sense/antisense transcription in TEs in mouse embryonic stem cells, with an increase of sense transcription induced by acute deletion of Dnmt1, leading to increased abundance of small RNAs. These small RNAs are loaded into ARGONAUTE2 (AGO2) suggesting an endosiRNA based silencing mechanism. Reduction of Dicer and Ago2 levels reveals that small RNAs are involved in an immediate response to transposon activation by demethylation, while the deposition of repressive histone marks represents an ensuing chronic response. Dicer dependent endosiRNAs which map to TEs are also found in vivo during primordial germ cell development. Our results suggest that TE antisense transcription acts as a trap that restrains acute transposon activity through small RNAs during epigenetic reprogramming in the germline.

ORGANISM(S): Mus musculus

PROVIDER: GSE102446 | GEO | 2017/11/01

SECONDARY ACCESSION(S): PRJNA397756

REPOSITORIES: GEO

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Pervasive transcription and endosiRNAs restrain transposons during global demethylation in embryonic stem cells [ChIP-Seq 2]

Project description:DNA methylation and other repressive epigenetic marks are erased in the mammalian germline and transposable elements (TEs) acquire the potential to be transcribed. This is a critical phase for genome defense and complementary TE silencing pathways are required to limit their activity. We find overlapping sense/antisense transcription in TEs in mouse embryonic stem cells, with an increase of sense transcription induced by acute deletion of Dnmt1, leading to increased abundance of small RNAs. These small RNAs are loaded into ARGONAUTE2 (AGO2) suggesting an endosiRNA based silencing mechanism. Reduction of Dicer and Ago2 levels reveals that small RNAs are involved in an immediate response to transposon activation by demethylation, while the deposition of repressive histone marks represents an ensuing chronic response. Dicer dependent endosiRNAs which map to TEs are also found in vivo during primordial germ cell development. Our results suggest that TE antisense transcription acts as a trap that restrains acute transposon activity through small RNAs during epigenetic reprogramming in the germline.

2017-11-01 | GSE102445 | GEO

Pervasive transcription and endosiRNAs restrain transposons during global demethylation in embryonic stem cells [smallRNA-Seq 2]

2017-11-01 | GSE102447 | GEO

A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [smallRNA-Seq]

Project description:DNA methylation and other repressive epigenetic marks are erased genome-wide in mammalian primordial germ cells (PGCs), the early embryo and in naïve embryonic stem cells (ESCs). This is a critical phase for transposon element (TE) defense since presumably alternative pathways need to be employed to limit their activity. It has been reported that pervasive transcription is enriched for TEs in ESCs in comparison to somatic cells. Here we test the hypothesis that pervasive transcription overlapping TEs forms a sensor for loss of their transcriptional repression. Overlapping sense and antisense transcription is found in TEs, and the increase of sense transcription induced by acute deletion of DNMT1 leads to the emergence of small RNAs. These small RNAs are loaded into ARGONAUTE 2 suggesting an endosiRNA mechanism for transposon silencing. Indeed, deletion of DICER reveals this mechanism to be important for silencing of certain transposon classes, while others are additionally repressed by deposition of repressive histone marks. Our observations suggest that pervasive transcription overlapping with TEs resulting in endosiRNAs is a transposon sensor that restrains their activity during epigenetic reprogramming in the germline.

2017-11-01 | GSE89696 | GEO

A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [RNA-Seq]

2017-11-01 | GSE89695 | GEO

A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [ChIP-Seq]

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A transposon sensor during epigenetic reprogramming consists of pervasive transcription and endosiRNAs in mouse ES cells [BS-Seq]

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Antisense transcription of retro transposable elements in Drosophila: The origin of endogenous small interfering RNA precursors

Project description:Unrestricted movement of mobile genetic elements could cause pre-mature lethality in Drosophila melanogaster. Specifically, retro transposons can disrupt genomic integrity through insertions, deletions and chromosomal rearrangements. Therefore, eukaryotes have developed defense mechanisms to silence these elements. In Drosophila, endogenous small interfering (endo-siRNAs) repress retro transposon mobility in somatic cells. The generation of endo-siRNAs requires Dicer-2 processing of double-stranded RNA precursors, yet the origins of this precursor are unknown. Here we show that retro transposons in Dmel-2 cells produce sense and antisense transcripts and identify bonafide transcription start sites for these RNAs. We determine that retro transposon antisense transcripts are less polyadenylated than sense transcripts. RNA-seq and small RNA-seq upon Dicer-2 depletion showed global decrease in endo-siRNAs mapping to retro transposons and increased expression of both S and AS retro transposon transcripts. These data support a model in which double-stranded RNA precursors are derived from convergent transcription and retained in the nucleus. Dicer-2 processes these precursors into endo-siRNAs that silence both sense and antisense retro transposon transcripts. Reduction of sense retro transposon transcripts potentially lowers element specific protein levels required for movement. This mechanism preserves genomic integrity and is especially important for Drosophila fitness because mobile genetic elements are highly active.

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TE-Array-- A high throughput tool to study transposon transcription

Project description:TE-Array is a custom Agilent microarray that probes for transposable elements in both sense and antisense orientations in humans and mice. TE-Array was used to study expression levels of transposable elements (TE) in a panel of normal mouse tissues. TE-Array comprises of 4 different custom Agilent 4X44K designs. These 4 different designs have probes for human sense orientation, human antisense orientation, mouse sense orientation and mouse antisense orientation transposable elements. These array designs were used to study the transposon abundance profile in 7 different mouse tissue samples, 2 mouse cell lines and 1 transposon transfected versus untransfected human cell line.

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Drosophila endogenous small RNAs bind to Argonaute2 in somatic cells

Project description:RNA silencing is a conserved mechanism in which small RNAs trigger various forms of sequence specific gene silencing by guiding Argonaute complexes to target RNAs via base-pairing. RNA silencing is thought to have evolved as a form of nucleic-acid-based immunity to inactivate viruses and transposable elements (TEs). Although the activity of TEs in animals has been thought to be largely restricted to the germline, recent studies have shown that they may also actively transpose in somatic cells, creating somatic mosaicism in animals3. In the Drosophila germline, piRNAs arise from repetitive intergenic elements including retrotransposons by a Dicer-independent pathway and function through the PIWI subfamily of Argonautes to ensure silencing of retrotransposons. Here we show that in Drosophila cultured S2 cells, Argonaute2 (AGO2), an AGO subfamily member of Argonautes, associates with endogenous small RNAs of 20-22 nucleotides in length, which we have collectively named esiRNAs (endogenous siRNAs). esiRNAs can be divided into two groups: one that mainly corresponds to a subset of retrotransposons, and the other that arises from stem-loop structures. esiRNAs are produced in a Dicer-2-dependent manner from distinctive genomic loci, are modified at their 3’ ends and can direct AGO2 to cleave target RNAs. Depletion of Dicer2 or AGO2 in S2 cells coincided with higher levels of retrotransposon transcripts. Together, our findings indicate that in Drosophila, different types of small RNAs and Argonautes are utilized to repress retrotransposons in germline and somatic cells. Keywords: AGO2, small RNA 454 sequencing - high throughput

2008-05-08 | GSE10277 | GEO

Euchromatic transposon insertions trigger production of novel pi- and endo-siRNAs at the target sites in the Drosophila germline

Project description:The control of transposable element (TE) activity in germ cells provides genome integrity over generations. A distinct small RNA-mediated pathway utilizing Piwi-interacting RNAs (piRNAs) suppresses TE expression in gonads of metazoans. In the fly, primary piRNAs derive from so-called piRNA clusters, which are enriched in damaged repeated sequences. These piRNAs launch a cycle of TE and piRNA cluster transcript cleavages resulting in the amplification of piRNA and TE silencing. Using genome-wide comparison of TE insertions and ovarian small RNA libraries from two Drosophila strains, we found that individual TEs inserted into euchromatic loci form novel dual-stranded piRNA clusters. Formation of the piRNA-generating loci by active individual TEs provides a more potent silencing response to the TE expansion. Like all piRNA clusters, individual TEs are also capable of triggering the production of endogenous small interfering (endo-si) RNAs. Small RNA production by individual TEs spreads into the flanking genomic regions including coding cellular genes. We show that formation of TE-associated small RNA clusters can down-regulate expression of nearby genes in ovaries. Integration of TEs into the 3' untranslated region of actively transcribed genes induces piRNA production towards the 3'-end of transcripts, causing the appearance of genic piRNA clusters, a phenomenon that has been reported in different organisms. These data suggest a significant role of TE-associated small RNAs in the evolution of regulatory networks in the germline. The fractions of small RNAs (19-29 nt) from ovaries of y[1]; cn[1] bw[1] sp[1] line of Drosophila melanogaster were sequenced using Illumina HiSeq 2000.

2014-02-07 | E-GEOD-46105 | biostudies-arrayexpress

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