Examples of Epigenetics

Transcription

1 Examples of Computational EvoDevo, University of Leipzig WS 2016/17

2 How do plants know that winter is over? external input: light, photoperiodic external input: temperature receptive tissue: meristem, found at the growing tips of roots and shoots consisting of actively dividing cells Vernalization is the induction of a plant s flowering process by exposure to the prolonged cold of winter, or by an artificial equivalent.

3 Vernalization: the observation observation long cold exposure fast flowering short cold exposure slow flowering no cold exposure no flowering explanation FLC (flowering locus C) high levels of FLC flowering is repressed low levels of FLC flowering can occur The longer the cold exposure the lower the level of FLC.

4 How is FLC expression level changed by cold? Four phases of FLC expression 1. setting FLC expression before exposure to cold 2. cold-induced silencing of FLC 3. epigenetic silencing of FLC after the return to warm temperature 4. reactivation of FLC expression Arabidopsis thaliana Thale cress, Ackerschmalwand Family: Brassicaceae a plant model organism small 20-25cm small genome of 135Mb annual plant (einjährig)

5 The FLC Gene Locus Genomic features FLC gene: transcriptional repressor of flowering genes COOLAIR spliced, antisense non-coding transcripts COLDAIR unspliced sense transcript nucleation region ( regulatory element )

6 Setting FLC expression before exposure to cold Antagonistic action: activation RNA polymerase II Paf1C RNA polymerase-associated factor 1 complex required for transcriptional elongation FRI FRIGIDA is a strong upregulator of FLC expression and recruits ATWDR5a ATWDR5a recruits histone metyltransferase: ATXR7 Set1-type metyltransferase ATX1, ATX2 Trithorax-type metyltransferase they write H3K4me3 marks EFS early flowering in short days writes H3K36me2 and H3K36me3

7 Setting FLC expression before exposure to cold Antagonistic action: repression autonomous pathway leading to H3K4 demethylation PRC2 polycomb repressive complex is loosely associated with much of the locus, but hardly active Resulting state enhanced expression of FLC very low expression of COOLAIR no expression of COLDAIR

8 Cold-induced silencing of FLC FLC expression decreases rapidly in the cold step 1: upregulation of COOLAIR expression on the antisense strand COOLAIR enhances down-regulation of FLC expression step 2: COLDAIR is expressed from the sense strand COLDAIR interacts with PRC2 step 3: PHD proteins (plant homeodomain proteins) associate with PRC2 one of them, VAL1, has sequence specificity for the nucleation region PHD-PRC2 sets silencing marks (H3K27me3) at nucleation region progressive accumulation of H3K27me3 only at the nucleation region

9 Epigenetic silencing of FLC after the return to warm temperature transfer to warm conditions epigenetic silencing by (H3K27me3 marks) and PHD-PRC2 complexes spreading across the whole FLC locus H3K27me3 marks responsible for stable repression increasing levels of H3K27me3 with increasing length of cold decreasing level of FLC expression dividing meristem cells inherit the silencing marks Important! Cells in the meristem autonomously switches to the silent state (or not).

10 Epigenetic Switch The epigenetic switch is cell-autonomous. The quantitative nature of the vernalization response is the result of an increasing number of cells switching to a silenced state after increasing cold exposure.

11 Reactivation of FLC expression Reprogramming the germ line in reporductive tissue ELF6 a histone demethylase removes H3K27me3 FLC expression is reactivated flowering is repressed winter can come... Only two genes, i.e. Soc1 and FLU, need to be knocked-out to turn an annual (einjährige) into a perennial (mehrjährige) plant. Song et al. (2012) Vernalization - a cold-induced epigenetic switch. Crevillén et al. (2014) Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state.

12 Erratum concerning Cold-induced silencing of FLC on page 8:... transcription can be blocked by H2A.Z at TSS Ca 2+ channels open on cold exposure Ca 2+ concentration increases H2A.Z is displaced transcription... was incorrect! In the nucleus, warming decreases H2A.Z histone occupancy at HSP (heat shock protein) promoters. by Mittler Mittler et al. (2012) How do plants feel the heat?