The First Rule of Plant Transposable Element Silencing: Location, Location, Location

Sigman, Meredith J.; Slotkin, R. Keith

doi:10.1105/tpc.15.00869

Cited by 170 publications

(190 citation statements)

References 78 publications

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“…In Arabidopsis, TEs are separated into two classes based on their locations (Sigman and Slotkin, 2016). One class is present in large constitutive heterochromatic regions, and their CHH methylation is maintained by chromomethylase2; the other class is located near genes where CHH methylation is constantly targeted by RNA-directed DNA methylation.…”

Section: Discussionmentioning

confidence: 99%

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

2017

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Long terminal repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. The identification of LTR-RTs is critical for achieving high-quality gene annotation. Based on the well-conserved structure, multiple programs were developed for the de novo identification of LTR-RTs; however, these programs are associated with low specificity and high false discovery rates. Here, we report LTR_retriever, a multithreading-empowered Perl program that identifies LTR-RTs and generates high-quality LTR libraries from genomic sequences. LTR_retriever demonstrated significant improvements by achieving high levels of sensitivity (91%), specificity (97%), accuracy (96%), and precision (90%) in rice (Oryza sativa). LTR_retriever is also compatible with long sequencing reads. With 40k self-corrected PacBio reads equivalent to 4.53 genome coverage in Arabidopsis (Arabidopsis thaliana), the constructed LTR library showed excellent sensitivity and specificity. In addition to canonical LTRRTs with 59-TG.CA-39 termini, LTR_retriever also identifies noncanonical LTR-RTs (non-TGCA), which have been largely ignored in genome-wide studies. We identified seven types of noncanonical LTRs from 42 out of 50 plant genomes. The majority of noncanonical LTRs are Copia elements, with which the LTR is four times shorter than that of other Copia elements, which may be a result of their target specificity. Strikingly, non-TGCA Copia elements are often located in genic regions and preferentially insert nearby or within genes, indicating their impact on the evolution of genes and their potential as mutagenesis tools.

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Section: Discussionmentioning

confidence: 99%

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

2017

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“…CHH methylation over TE bodies is mediated by two partially overlapping pathways: RNA-directed DNA methylation (RdDM) and RdDM-independent (Zemach et al 2013;Stroud et al 2014). However, it is not clear how these two pathways branch to target different TEs (for review, see Sigman and Slotkin 2016). DOMAINS REARRANGED METHYLASE 1 (DRM1) and DRM2 are responsible for CHH methylation in the RdDM pathway, whereas CHROMOMETHYLASE 2 (CMT2) is required for the RdDM-independent pathway (Cao et al 2003;Stroud et al 2013;Zemach et al 2013).…”

Section: Positioning Of Tes At the Nuclear Periphery Correlates Withmentioning

confidence: 99%

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Cheng

et al. 2017

Genome Res.

106

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The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonrandom positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants. Here, using a strategy using restriction enzyme-mediated chromatin immunoprecipitation, we present genome-wide identification of nonrandom domain organization of chromatin at the peripheral zone of Arabidopsis thaliana nuclei. We show that in various tissues, 10%-20% of the regions on the chromosome arms are anchored at the nuclear periphery, and these regions largely overlap between different tissues. Unlike LADs in animals, the identified domains in plants are not gene-poor or A/T-rich. These domains are enriched with silenced protein-coding genes, transposable element genes, and heterochromatic marks, which collectively define a repressed environment. In addition, these domains strongly correlate with our genome-wide chromatin interaction data set (Hi-C) by largely explaining the patterns of chromatin compartments, revealed on Hi-C maps. Moreover, our results reveal a spatial compartment of different DNA methylation pathways that regulate silencing of transposable elements, where the CHH methylation of transposable elements located at the nuclear periphery and in the interior are preferentially mediated by CMT2 and DRM methyltransferases, respectively. Taken together, the results demonstrate functional partitioning of the Arabidopsis genome in the nuclear space.

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“…As the copy number of any given element increases, it would seem increasingly likely that that this TE will be recognized and heritably silenced, either due to increases in intrinsically produced triggers (Marí-Ordóñez et al, 2013) or due to the production of a single variant that triggers silencing of all of the active elements (Slotkin et al, 2005). Once silenced, it is hypothesized that these elements are maintained in that state via heritably propagated DNA methylation and histone modifications, as well as tissue-specific reinforcement via transacting small RNAs (Slotkin et al, 2009;Creasey et al, 2014;Kim and Zilberman, 2014;Sigman and Slotkin, 2016).…”

Section: Arresting Te Activitymentioning

confidence: 99%

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Springer

Lisch

2016

Plant Cell

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ORCID IDs: 0000-0002-7301-4759 (N.M.S.); 0000-0003-3232-9479 (Q.L.)Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that the current structure of a genome is the result of various TE bursts and WGDs and it is likely that the silencing mechanisms and the chromatin structure of a genome have been shaped by these events. This suggests that the specific mechanisms targeting chromatin modifications and epigenomic patterns may vary among different species. Many crop species have likely evolved chromatin-based mechanisms to tolerate silenced TEs near actively expressed genes. These interactions of heterochromatin and euchromatin are likely to have important roles in modulating gene expression and variability within species.

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The First Rule of Plant Transposable Element Silencing: Location, Location, Location

Cited by 170 publications

References 78 publications

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

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