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

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”

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

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): 503-510

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 - www.cellsignallingbiology.org - 2012

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): 503-510

Transducers Second Messengers I J.R., and Pikaard, C.S. 2011. Nature Reviews Molecular Cell Biology 12:483–492.

CSB Fig 02:01 Cell signalling pathways J.R., and Pikaard, C.S. 2011. 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. 2011. Nature Reviews Molecular Cell Biology 12:483–492.