Regulatory mechanism of a heat-activated retrotransposon by DDR complex in Arabidopsis thaliana

Abstract

The RNA-directed DNA methylation (RdDM) pathway plays an essential role in the transposon silencing mechanism; the DDR complex, consisting of DRD1, DMS3, and RDM1, is an essential component of the RdDM pathway. ONSEN, identified in Arabidopsis, is a retrotransposon activated by heat stress at 37°C; however, studies on the regulation of ONSEN are limited. In this study, we analyzed the regulation of ONSEN activity by the DDR complex in Arabidopsis. We elucidated that loss of any component of the DDR complex increased ONSEN transcript levels. Transgenerational transposition of ONSEN was observed in the DDR-complex mutants treated with heat stress for 48 h. Furthermore, the DDR complex components DRD1, DMS3, and RDM1 played independent roles in suppressing ONSEN transcription and transposition. Moreover, we found that the duration of heat stress affects ONSEN activity. Therefore, the results of this study provide new insights into the retrotransposon regulatory mechanisms of the DDR complex in the RdDM pathway.

Regulatory mechanism of heat-active retrotransposons by the SET domain protein SUVH2

“…The CHH hypermethylation of ONSEN in suvh9 may be responsible for the inability of ONSEN to be transcribed at a high level. Heat stress did not change the DNA methylation levels of the ONSEN region in suvh2 ( Supplementary Figure 1 ), which is consistent with our previous findings ( Niu et al., 2022b ). In addition, the DNA methylation pattern of ONSEN in suvh2 was nearly identical to that of nrpd1 ( Figure 3 ), indicating that DNA hypomethylation released transcriptional silencing of ONSEN but did not affect transposition.…”

“…ONSEN is an LTR retrotransposon defined in A. thaliana and is usually activated by heat stress ( Ito et al., 2011 ). Previous studies have shown that some RdDM pathway mutants subjected to heat stress show transcriptional activation of ONSEN ( Hayashi et al., 2020 ; Niu et al., 2022b ). siRNAs are involved in transcriptional repression processes, especially in TEs ( Moses et al., 2010 ).…”

PTGS is dispensable for the initiation of epigenetic silencing of an active transposon inArabidopsis

“…Recruitment of RdDM to EVD-LTRs independently of RDR6-RdDM, together with the absence of EVD TGS in either nrpd1 or nrpe1 backgrounds, indicates that PolIV-RdDM is essential for de novo EVD silencing during its genome colonization. Although absence of RdDM has little impact in the reactivation of silenced TEs in the Arabidopsis genome (He et al , 2021; 2022), a role for RdDM in controlling TE propagation has been previously shown for the heat-responsive LTR-retrotransposon (LTR-RTE) ONSEN , for which proliferation and copy number following induction is increased in NRPD1 mutants (Ito et al , 2011; Matsunaga et al , 2012; Hayashi et al , 2020; Niu et al , 2022). Furthermore, genetic variation in the RdDM components RDR2 and NRPE1 has been associated with variation in TE content within Arabidopsis natural populations (Baduel et al , 2021; Sasaki et al , 2022; Jiang et al , 2023).…”

“…ONSEN, for which proliferation and copy number following induction is increased in NRPD1 mutants (Ito et al, 2011;Matsunaga et al, 2012;Hayashi et al, 2020;Niu et al, 2022). Furthermore, genetic variation in the RdDM components RDR2 and NRPE1…”

DOMESTICATION IS THE PROPRIETARY CASE OF EVOLUTION: ABOUT THE UNIVERSALITY OF PRINCIPLES AND ELEMENTS (review)

“…ERV -важные факторы видовой изменчивости, характеризуются большим разнообразием структуры, размеров и механизмов транспозиций, что делает их важными участниками эволюции геномов (66). Кроме того, ERV влияют на паттерн экспрессии соседних генов, вовлекаясь в формирование малой интерферирующей РНК (siRNA) и РНКнаправленное метилирование ДНК (RdDM) (67).…”