The Evolutionary Origin and Genomic Organization of SINEs in Arabidopsis thaliana

Lenoir, Alain; Lavie, Laurence; Prieto, José-Luis; Goubely, Chantal; Côté, Jean-Charles; Pélissier, Thierry; Deragon, Jean-Marc

doi:10.1093/oxfordjournals.molbev.a003778

Cited by 53 publications

(47 citation statements)

References 40 publications

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“…In such genomes, including those of many common crops, mobile sRNAs may be an important mechanism of genome defense. The TE superfamilies targeted by mobile sRNAs are enriched in euchromatic regions, typically within c. 500 nt of the nearest gene (48,49). TEs inserted near genes can have dramatic effects on gene expression (15,49).…”

Section: Discussionmentioning

confidence: 99%

Mobile small RNAs regulate genome-wide DNA methylation

Lewsey

Hardcastle

Melnyk

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

206

167

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RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous gene expression, controls invading transposable elements (TEs), and protects the cell against viruses. Key components of the mechanism are small RNAs (sRNAs) of 21–24 nt that guide the silencing machinery to their nucleic acid targets in a nucleotide sequence-specific manner. Transcriptional gene silencing is associated with 24-nt sRNAs and RNA-directed DNA methylation (RdDM) at cytosine residues in three DNA sequence contexts (CG, CHG, and CHH). We previously demonstrated that 24-nt sRNAs are mobile from shoot to root in Arabidopsis thaliana and confirmed that they mediate DNA methylation at three sites in recipient cells. In this study, we extend this finding by demonstrating that RdDM of thousands of loci in root tissues is dependent upon mobile sRNAs from the shoot and that mobile sRNA-dependent DNA methylation occurs predominantly in non-CG contexts. Mobile sRNA-dependent non-CG methylation is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) RdDM pathway but is independent of the CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. Specific superfamilies of TEs, including those typically found in gene-rich euchromatic regions, lose DNA methylation in a mutant lacking 22- to 24-nt sRNAs (dicer-like 2, 3, 4 triple mutant). Transcriptome analyses identified a small number of genes whose expression in roots is associated with mobile sRNAs and connected to DNA methylation directly or indirectly. Finally, we demonstrate that sRNAs from shoots of one accession move across a graft union and target DNA methylation de novo at normally unmethylated sites in the genomes of root cells from a different accession.

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Section: Discussionmentioning

confidence: 99%

Mobile small RNAs regulate genome-wide DNA methylation

Lewsey

Hardcastle

Melnyk

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

206

167

View full text Add to dashboard Cite

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“…example, CACTA TEs are active in methylation-deficient mutants of A. thaliana (48), some families of Ac-like elements show evidence of recent activity (47,49), and both SINE-like and Gypsy-like elements have been inferred to be active within A. thaliana's recent past (35,50). In addition, SINE, Ac-like, CACTA, and MITE TEs are presumed to have been active recently because they contain ORFs (19) or vary in location among A. thaliana ecotypes (51).…”

Section: Discussionmentioning

confidence: 99%

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

Lockton

Ross‐Ibarra

Gaut

2008

Proc. Natl. Acad. Sci. U.S.A.

104

128

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Transposable elements (TEs) are the major component of most plant genomes, and characterizing their population dynamics is key to understanding plant genome complexity. Yet there have been few studies of TE population genetics in plant systems. To study the roles of selection, transposition, and demography in shaping TE population diversity, we generated a polymorphism dataset for six TE families in four populations of the flowering plant Arabidopsis lyrata. The TE data indicated significant differentiation among populations, and maximum likelihood procedures suggested weak selection. For strongly bottlenecked populations, the observed TE band-frequency spectra fit data simulated under neutral demographic models constructed from nucleotide polymorphism data. Overall, we propose that TEs are subjected to weak selection, the efficacy of which varies as a function of demographic factors. Thus, demographic effects could be a major factor driving distributions of TEs among plant lineages.bottleneck ͉ genetics ͉ TE-display

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“…Among the 105 p-SINE1 members identified in the Nipponbare genome, 3 members were present in the coding frames of hypothetical proteins, 32 members in the putative introns and 18 members were located within a 0.5-kb region adjacent to the putative coding frames. This suggests that p-SINE1 tends to be inserted within or near genes like Arabidopsis SINEs (Lenoir et al 2001). Presently, it remains to be determined whether the p-SINE1 members affect the expression of these genes.…”

Section: Mapping Of P-sine1 Members On Rice Chromosomesmentioning

confidence: 99%

Rice Retroposon p-SINE1 and Origin of Cultivated Rice

et al. 2004

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The wild rice species Oryza rufipogon displays wide intraspecific variations. It is considered to be the progenitor of the cultivated rice species Oryza sativa with two ecotypes, japonica and indica. p-SINE1 is the first plant retroposon SINE identified in O. sativa and is present in strains of Oryza species with the AA genome in multiple copies. Some p-SINE1 members show interspecific insertion polymorphism among the rice strains and are thus assumed to be suitable markers for classifying the strains and to infer their relationships based on the presence or absence of the members at the corresponding loci. Subfamily members of p-SINE1 show insertion polymorphism in the O. sativa -O. rufipogon population. To determine the origin of cultivated rice, we used these p-SINE1 members to bar-code each of 101 cultivated and wild rice strains based on the insertion polymorphism at the respective loci. A phylogenetic tree constructed using the bar codes given to all the rice strains showed that O. sativa strains could be divided into two groups corresponding to japonica and indica, whereas O. rufipogon strains were divided into four groups, of which, one group consisted of annual O. rufipogon strains, while the other three of the perennial O. rufipogon strains. Japonica strains were closely related to the O. rufipogon perennial strains of one group, and the indica strains to the O. rufipogon annual strains, indicating that O. sativa had been derived polyphyletically from O. rufipogon. Furthermore, we identified new p-SINE1 members showing interspecific insertion polymorphism from representative strains of four wild rice species with the AA genome, O. barthii, O. glumaepatula, O. longistaminata and O. meridionalis. A phylogenetic tree constructed using the polymorphic p-SINE1 members showed that O. longistaminata and O. meridionalis had diverged early, whereas the other species including O. rufipogon diverged relatively recently in an evolutionary time. We also presented the results of mapping of all p-SINE1 members identified from databases of rice genome sequences, and showed that they were present in all the chromosomes, but not distributed in the regions near the centromere in each chromosome, unlike other retroelements.

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The Evolutionary Origin and Genomic Organization of SINEs in Arabidopsis thaliana

Cited by 53 publications

References 40 publications

Mobile small RNAs regulate genome-wide DNA methylation

Mobile small RNAs regulate genome-wide DNA methylation

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

Rice Retroposon p-SINE1 and Origin of Cultivated Rice

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