1. Lecture 19 – Epigenomics – Plants
BIOL 5190/6190 Cellular & Molecular Singal Transduction
Prepared by Bob Locy
Last modified -13F

2. Epigenetics – Stable, but expression-related changes in gene function
Methylation of DNA & Histones is involved in epigenetic transcriptional regulation
Correlation between DNA methylation and histone modification
Correlation between gene expression changes and DNA Methylation
Transposable elements are regulated by DNA Methylation
Correlation between DNA Methylation and TE transposition
How is DNA methylation mediated?
Enzymology known
Transposable elements part of repeat-associated/heterochromatic DNA in the genome
Repeat associated DNA methylation controls “transposase” function that mediates transposition, and thus, epigenetic “inheritance”

3. Plant Biotic and Abiotic Stress Responses
Old time work
Epigenetic stuff
State of the Art

4. Epigenetic Regulation of Transcription and Transposition
Figure 1. Example of distinct regulation of two endogenous LTR retrotransposons in Arabidopsis thaliana. We illustrate the differences in epigenetic control of transcription and transposition using the two LTR retrotransposons EVADE (left side) and ONSEN (right side). Loss of CG methylation triggers transcriptional activity of EVADE whereas heat shock activates ONSEN transcription. Transposition could not be detected in both cases in the first generation of plants but heritable neo-insertions were detected upon inbreeding (EVADE) or in a mutant background unable to synthesize 24nt-siRNAs (EVADE and ONSEN). Legend as follows: red lollipops, CG methylation; blue lollipops, non-CG methylation; blue boxes, LTRs; orange boxes, ORFs.
Bucher et al., (2012) Current Opinion in Plant Biology 15 (5):

5. Stress Regulated Epigenenic Gene Regulation
A schematic representation of the events taking place in a plant cell during environmental stress imposition. Exogenous genome (such as viral genome) is also subjected to viral DNA methylation by plant epigenetic factors. CMT3 Chromomethylase, DRM domain rearrangement methyltransferase, MET1 methyltransferase
Cell Signalling Biology - Michael J. Berridge

6. Proposed model for Epigenetic Control of TE-host coevolution
Proposed model for the roles of epigenetic control in TE-host coevolution.
The main steps occurring during TE invasion of the host
genome (blue arrows), the interplay between the host’s epigenetic
machinery and the TE (red, experimentally supported, pink, proposed
regulation) and the influence of the environment (green arrows) are
represented. TEs enter the genome via an unknown mechanism possibly
through horizontal transfer or genomic hybridization. During co-evolution
within a host genome, TEs can be transcriptionally active, some even
exhibiting transposition bursts within a species, and become silenced
again. Eventually some TEs can be eliminated from the genome through
deletion and/or recombination. While host regulation can exert
epigenetic control through TGS and PTGS mechanisms, TE regulation
can be co-opted to affect host gene expression by attracting epigenetic
marks to nearby genes. Some of these regulatory steps are incompletely
understood and specific questions are highlighted as follows: (1) How is
a new TE recognized by the epigenetic machinery upon its entry into a
naive genome? (2) How are siRNAs involved in controlling the TE burst?
(3) Did TEs evolve anti-silencing functions? (4) Is TE silencing reversible?
(5) Is TE deletion epigenetically controlled? (6) Does stress directly have
an impact on the efficiency of the host epigenetic machinery?.
Bucher et al., (2012) Current Opinion in Plant Biology 15 (5):

7. Transducers Second Messengers I
J.R., and Pikaard, C.S  Nature Reviews Molecular Cell Biology 12:483–492.

8. CSB Fig 02:01 Cell signalling pathways
J.R., and Pikaard, C.S  Nature Reviews Molecular Cell Biology 12:483–492.
Figure 1: Model for the RNA-directed DNA methylation pathway in Arabidopsis thaliana.
Polymerase IV (Pol IV) initiates the RNA-directed DNA methylation (RdDM) pathway (1), generating transcripts that are then copied into double-stranded RNA (dsRNA) by RNA-DEPENDENT POLYMERASE 2 (RDR2) (2). The putative chromatin remodeler and/or helicase CLSY1 assists in one or more of these steps. DICER-LIKE 3 (DCL3) cleaves the dsRNA into 24-nucleotide small interfering RNA (siRNA) duplexes (3) that are methylated by HEN1 (4). A single strand of the siRNA duplex associates with AGO4 to form an RNA-induced silencing complex (RISC) (5).
Independent of siRNA biogenesis, Pol V transcription is assisted by the DDR complex (DRD1, DMS3, and RDM1) and DMS4 (6). AGO4 binds Pol V transcripts via base-pairing with the siRNA and is stabilized by AGO4 interaction with the NRPE1 carboxyl-terminal domain (CTD) and KTF1, which also binds RNA (7). IDN2 may stabilize Pol V transcript–siRNA pairing (8). The RDM1 protein of the DDR complex binds AGO4 and the de novo cytosine methyltransferase DRM2, bringing them to Pol V–transcribed regions (9). Histone modifications resulting from the RdDM pathway include the removal of activating marks (acetylation) and the establishment of repressive marks (deacetylation), facilitating transcriptional silencing (10).
J.R., and Pikaard, C.S  Nature Reviews Molecular Cell Biology 12:483–492.