Project description:Background: The small RNAs that Transposable Elements generate are vastly different when they are transcriptionally silenced compared to when they are transcriptionally activated. We performed the deep sequencing of small RNAs in a number of small RNA biogenesis mutants in both Transposable Element-silenced and Transposable Element-active epigenome backgrounds. Results: We found that Transposable Elements generate large amounts of 21-22nt siRNAs only when they are transcriptionally active. These 21-22nt siRNAs are incorporated into the AGO6 protein. Conclusion: Ago6 is the key protein that bridges the post-transcriptional degradation of Transposable Element mRNAs and the establishment of DNA methylation. Examination of flower bud small RNAs from wild type and 5 single or double mutant combinations, many of which have biological replicates. In addition, IP purification of the AGO6 protein (and mock no-antigen controls) followed by sequencing of the incorporated small RNAs. Replicate A for Col and ddm1 are submitted in GSE41755

2014-11-14 | E-GEOD-57191 | biostudies-arrayexpress

DNA virus infections shape transposable element activity in vitro and in vivo

Project description:DUX4 is known to be crucial for TEs induction during zygotic genome activation in early embryonic development. In adults, DUX4 is usually silenced and we previously showed that DUX4 expression is induced by infection with various DNA viruses. We demonstrate binding of DUX4 to TEs upon herpesviral infection and analysis of genes adjacent to TEs shows pathways that are known to be crucial for tumor development. Overexpression of DUX4 significantly induced TEs expression, while its knockout (KO) diminished TEs expression upon HSV-1 infection, underscoring the essential role of DUX4 in TEs activation.

2025-01-01 | GSE253543 | GEO

Small RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes

2014-11-14 | GSE57191 | GEO

DNA virus infections shape transposable element activity in vitro and in vivo [HFF]

Project description:We show strong activation of TEs in the context of DNA virus infection and investigate the molecular mechanisms of how TEs are induced. We demonstrate that herpesvirus infection leads to a robust expression of the MLT and THE1-class of LTR containing retrotransposons as well as a subset of long-interspersed nuclear elements-1 (LINEs), Alu-elements and some HERVs. Mechanistically we demonstrate that this TEs upregulation is induced by two pathways that act synergistically: de-repression of KAP1/TRIM28 mediated by phosphorylation and expression of the pioneer factor double-homeobox 4 (DUX4).

2025-01-01 | GSE256111 | GEO

Incorporation of transposable element small RNAs into the Arabidopsis AGO1 protein

Project description:Background: Transposable element 24 nucleotide small RNAs are not efficiently incorporated into the AGO1 protein, which is involved in endogenous RNAi and gene regulation through the microRNA and tasiRNA pathways. Results: The AGO1 protein incorporates large quantities of transposable element siRNAs when transposable elements are epigenetically activated and transcribed. The incorporation of transposable element siRNAs is at the expense of the most abundant microRNAs. These transposable element siRNAs can act as tasiRNAs, regulating genes that they have partial complementarity to. Conclusion: Transposable element small RNAs are more dynamic than previously thought. They can be incorporated into AGO1 and regulate genes. Three biological replicates of small RNA sequencing from two genotypes

2014-04-07 | E-GEOD-45990 | biostudies-arrayexpress

DNA virus infections shape transposable element activity in vitro and in vivo (DUX4 knockout)

2025-01-27 | GSE287622 | GEO

DNA virus infections shape transposable element activity in vitro and in vivo (HCMV,KSHV,DUX4)

2025-01-01 | GSE280380 | GEO