Exogenous Transposable Elements Circumvent Identity-Based Silencing, Permitting the Dissection of...

Area of Science:

• Epigenetics and Gene Regulation
• Plant Molecular Biology
• Genomics

Background:

• Initiation of epigenetic silencing for new genetic elements is poorly understood.
• Overlapping silencing mechanisms complicate investigation.
• Two distinct initiation mechanisms, identity-based and expression-dependent silencing, are proposed.

Purpose of the Study:

• To elucidate the mechanisms initiating epigenetic silencing.
• To isolate and investigate expression-dependent silencing.
• To understand the role of genotype in establishing transgenerational silencing.

Main Methods:

• Transformation of exogenous transposable elements (TEs) into *Arabidopsis thaliana*.
• Analysis of small interfering RNA (siRNA) generation and RNA-directed DNA methylation (RdDM).
• Comparison of silencing in wild-type versus mutant genotypes and subsequent introgression.

Main Results:

• Identity-based silencing is mediated by 21-24 nt siRNAs from silenced regions.
• Expression-dependent silencing triggers de novo RdDM via RNA Polymerase V.
• Full-length TEs achieve heterochromatin formation, while fragments stall at RdDM.
• Plant genotype at insertion/transformation is critical for transgenerational silencing extent.

Conclusions:

• Two independent pathways initiate epigenetic silencing: identity-based and expression-dependent.
• Expression-dependent silencing is a key de novo RdDM pathway.
• The plant's genetic background during initial insertion dictates long-term epigenetic stability.