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

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

PROVIDER: PRJNA1078282 | ENA |

REPOSITORIES: ENA

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

Project description:DNA virus infections shape transposable element activity in vitro and in vivo

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

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

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

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

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

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

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

2014-11-14 | GSE57191 | 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 [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

Epigenomic conservation of transposable element silencing

Project description:Epigenomic conservation of transposable element silencing

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Incorporation of transposable element small RNAs into the Arabidopsis AGO1 protein

2014-04-07 | GSE45990 | GEO

Gene expression in Arabidopsis ddm1 mutants with high levels of Transposable Element activity

Project description:Background: Transposable elements are known to influence the regulation of some genes. We aimed to determine which genes show altered gene expression when transposable elements are epigenetically activated. Results: We find over 2000 genes with altered steady-state expression levels in ddm1 mutants. Some of these genes are influenced by neighboring transposable element fragments, while other genes are targeted by transposable element derived 21 nucleotide siRNAs. Conclusion: The regulation of the genic portion of the Arabidopsis genome is heavily influenced by the epigenetic regulation of transposable elements. The regulation of genes by transposable elements can occur through multiple mechanisms. Three biological replicates for two genotypes

2014-04-07 | E-GEOD-46050 | biostudies-arrayexpress

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