Cross-Regulation between Transposable Elements and Host DNA Replication

Zaratiegui, Mikel

doi:10.3390/v9030057

Cited by 13 publications

(9 citation statements)

References 117 publications

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“…Also for Arabidopsis , we and others have seen that RBR1 is involved in DNA repair at the site of the lesion [34,35], partially co-localizing with RAD51, a major player in HR [34]. It is known that TEs use and modify the cellular machinery of the host at several levels to promote their own survival [104,105]. Thus, RBR1 might provide a link to the recombination/repair machinery required for stable MITE transposition in the host genome.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators

et al. 2018

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Retinoblastoma (pRb) is a multifunctional regulator, which was likely present in the last common ancestor of all eukaryotes. The Arabidopsis pRb homolog RETINOBLASTOMA RELATED 1 (RBR1), similar to its animal counterparts, controls not only cell proliferation but is also implicated in developmental decisions, stress responses and maintenance of genome integrity. Although most functions of pRb-type proteins involve chromatin association, a genome-wide understanding of RBR1 binding sites in Arabidopsis is still missing. Here, we present a plant chromatin immunoprecipitation protocol optimized for genome-wide studies of indirectly DNA-bound proteins like RBR1. Our analysis revealed binding of Arabidopsis RBR1 to approximately 1000 genes and roughly 500 transposable elements, preferentially MITES. The RBR1-decorated genes broadly overlap with previously identified targets of two major transcription factors controlling the cell cycle, i.e. E2F and MYB3R3 and represent a robust inventory of RBR1-targets in dividing cells. Consistently, enriched motifs in the RBR1-marked domains include sequences related to the E2F consensus site and the MSA-core element bound by MYB3R transcription factors. Following up a key role of RBR1 in DNA damage response, we performed a meta-analysis combining the information about the RBR1-binding sites with genome-wide expression studies under DNA stress. As a result, we present the identification and mutant characterization of three novel genes required for growth upon genotoxic stress.

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators

et al. 2018

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“…For example, tRF production could be a consequence of low H3K9me3 levels and tRNA metabolism [65]. Of course it is ideal for transposons to replicate in highly proliferating cells: high levels of tRNAs for translation of viral proteins and RT priming, abundant replication forks, and breakdown of the nuclear membrane for genome integration all play in favor of transposition [59, 66, 67]. Transposition rates can be limited by host tRNA expression [68] and oncogenic LTR-retroviruses like RSV and MuLV are known to induce expression of their primer tRNA [69].…”

Section: Trf Biogenesis - the Who? What? When? Where? Why?mentioning

confidence: 99%

Tie-Break: Host and Retrotransposons Play tRNA

Schorn

Martienssen

2018

Trends in Cell Biology

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tRNA fragments (tRFs) are a class of small, regulatory RNAs with diverse functions. 3'-Derived tRFs perfectly match long terminal repeat (LTR)-retroelements which use the 3'-end of tRNAs to prime reverse transcription. Recent work has shown that tRFs target LTR-retroviruses and -transposons for the RNA interference (RNAi) pathway and also inhibit mobility by blocking reverse transcription. The highly conserved tRNA primer binding site (PBS) in LTR-retroelements is a unique target for 3'-tRFs to recognize and block abundant but diverse LTR-retrotransposons that become transcriptionally active during epigenetic reprogramming in development and disease. 3'-tRFs are processed from full-length tRNAs under so far unknown conditions and potentially protect many cell types. tRFs appear to be an ancient link between RNAi, transposons, and genome stability.

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“…DNA transposons are mobilized during DNA replication, and LTR retrotransposons are preferentially inserted at sites of replication fork arrest (67). In that regard, fork arrest and slower S-phase completion caused by replication stress and checkpoint activation is likely to favor TE mobilization.…”

Section: Discussionmentioning

confidence: 99%

DNA polymerase epsilon is a central coordinator of heterochromatin structure and function in Arabidopsis

Bourguet

López-González

Gómez-Zambrano

et al. 2020

Preprint

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BackgroundChromatin organizes the DNA molecule and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications must be faithfully passed on to daughter strands. There is evidence that DNA polymerases play a role in transcriptional silencing, but the extent of their contribution and how it relates to heterochromatin maintenance is unclear.ResultsWe isolate a strong hypomorphic Arabidopsis thaliana mutant of the POL2A catalytic subunit of DNA polymerase epsilon and show that POL2A is required to stabilize heterochromatin silencing genome wide, likely by preventing replicative stress. We reveal that POL2A inhibits DNA methylation and histone H3 lysine 9 methylation. Hence, release of heterochromatin silencing in POL2A deficient mutants paradoxically occurs in a chromatin context of increased level of these two repressive epigenetic marks. At the nuclear level, POL2A defect is associated with fragmentation of heterochromatin.ConclusionThese results indicate that POL2A is critical to secure both heterochromatin structure and function. We also reveal that unhindered replisome progression is required for the faithful propagation of DNA methylation through the cell cycle.

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Cross-Regulation between Transposable Elements and Host DNA Replication

Cited by 13 publications

References 117 publications

Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators

Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators

Tie-Break: Host and Retrotransposons Play tRNA

DNA polymerase epsilon is a central coordinator of heterochromatin structure and function in Arabidopsis

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