Establishment of Heterochromatin: Transposons and Trans-Generational Silencing by Dr. R. Keith Slokin, Associate Professor in the Department of Molecular Genetics and director of the Arabidopsis Biological Resource Center (ABRC), Ohio State University.
The epigenetic control mechanisms of TE have always been a really complicated diagram of multiple interconnected pathways, tons of what binds what and then recruit what details of molecular interactions. I know there are players including DNA methylation, RNA cleavage, small RNA generation and silencing, but can hardly speak all the names or piece everything together without staring at that diagram, and struggling. Today’s talk seemed to cure my fear for that diagram. ^_^
So how does a cell keep TEs quiet? When a new TE (the cell never had it or saw it before) is getting active and PolII transcribed, the cell first need to make the decision whether it is a regular gene transcript or a parasite. This decision making is based on the present of repeats in TE structure, not the length. Once the parasite is recognized, the cell activate the PTGS/RNAi (post-transcriptional gene silencing) pathway to cleave TE transcript into 21-22nt fragments, reverse transcribed to form double stranded siRNA, feed back to assist the cleavage of TE transcripts. This is the called Expression dependent silencing, which serves as the initation of TE silencing cascade.
After initiation, some leftover 21-22nt siRNAs act as molecular memories to remind the cell of this type of TE. So the same type of this TE, even not expressed, will be recognized and de novo methylated. Next, PolIV transcribe the TE to generate 24nt siRNA to reinforce DNA methylation. This is the Identity based silencing, to further establish the TE control.
The last step is trans-generational Maintenance of DNA methylation (CG and CHG), stable and inheritable.
Because expression and identity based silencing are often coupled in cell, the beauty of molecular genetic experiments is to dissect their effects by designing TE introduction that triggers only one of the mechanisms.
Another cool story I learned from the talk is about TE control in pollen grain. As the two sperm cells are highly compacted into heterochromatin, the nucleus of vegetative cell is apparantly larger and relaxed letting TEs go viral! The expressed TEs triggered PTGS to form abundant 21-22nt sRNAs, which are then sent over to sperm cells to ensure high level of TE silencning!
One of the questions from audience is that Considering all layers of TE control mechanisms, why can some TE still escape silencing control some time?
It is also a fun mental practice to imagine what happed to genomic shock introduced by hybridization or polyploidization. A ding in the maintenance system to let unmethylated TE be transcribed? Or breaking the identity based system, not enough surveilance 24nt siRNA to cause the cell Amnesia, no longer recognizing TEs. The initiation step ought to happen later to fix the problem though.
Slotkin lab website is https://molgen.osu.edu/people/slotkin.2