Epigenetics - Index Page

Meagher Laboratory's Research on the Epigenetic Control of Multicellular Development & Chromatin Remodeling (epigenetics is defined at the bottom of this page) -Over the last several years our laboratory has explored the epigenetic control (see definition below) of gene expression and multicellular development. We have made significant headway dissecting the roles of several nuclear actin-related proteins (ARPs) in chromatin remodeling and epigenetic control. We have just begun to study the nuclear activities of conventional cytoplasmic cytoskeletal proteins like actin, actin depolymerizing factor (ADF/cofilin), and profilin. Defects in the nuclear ARPs and these associated proteins in the model plant Arabidopsis have resulted in dramatic alterations in the development of all tissues and organs. -Chromatin remodeling is necessary to over come the basal repression that affects all genes due to DNA compaction. However, chromatin restructuring at loci for some high level transcription factors and signalling proteins appears to be essential for normal multicellular development. Our working hypothesis has been that besides their roles in relieving the basel repression that affects all genes "numerous isoforms of nuclear ARP- and actin-containing chromatin remodeling complexes potentiate the activities of master regulators of multicellular development." These activities are at the heart of epigenetic control.
Figure 1: Nuclear ARPs control cell size and the cell cycle, and thus, regulate leaf morphology (see Meagher et al., 2007, Trends in Cell Biology). ARP4 (a, e, ARP4-Ri) andARP7(b, f, ARP7-Ri) RNA interference (RNAi) lines develop small leaves composed of small cells as compared to wildtype (WT). ARP6 null mutants (arp6-1) make small leaves (c) composed of fewer cells, but of relatively normal cell sizes. d, e, f. Scanning electron micrographs compare the epidermis of WT to ARP deficient lines. The perimeters of example cells are indicated with dotted lines. For ARP7-Ri a small cell and a moderately sized cell are marked.  Images were prepared from the largest rosette leaves from 3-week-old plants.  g. Leaf development requires the integration of diverse cues that control the cell cycle and the endocycle. Points at which these cycles are likely controlled indirectly by E2Fs and other transcription factors  and directly by cyclins, cyclin dependent kinases, and other factors are shown with small green arrows. These proteins regulate important control points that affect leaf cell proliferation, expansion, and organ development (green arrows), including G2/M phase transition, initiation of mitosis, G1 entry and DNA synthesis (S), and entry into the endocycle from the cell cycle. h. Model for roles of ARP4, ARP6, and ARP7-chromatin remodeling complexes in regulating the cell cycle and cell proliferation. Among large numbers of genes whose expression is potentiated by the activities of ARP-containing chromatin remodeling complexes, a small subset are essential transcriptional regulatory factors (E2Fs, DPs, MADS Box).  The target genes of these factors are cell cycle regulators including cyclins and cyclin dependent kinases. These latter regulatory proteins exert direct control over the cell cycle, the endocycle, and leaf development (see Figure 1G). Feedback arrows between leaf differentiation and chromatin remodeling were positioned to suggest the reiterative restructuring of chromatin as the leaf expands and matures.	Overview of the nuclear actin-related proteins (nuclear ARPs) Summary of the multicellular phenotypes of plants deficient in ARP4, 6, & 7 Nuclear localization of ARP7 as an example Tissue specific expression of ARP7 as an example ARPs in flowering time control ARP6-SWR1-like activity controlling histone variant H2AZ deposition Model for ARP-containing complexes potentiating gene expression   Figure 3. Delayed floral organ senescence and abscission in Arabidopsis defective in ARP4 or ARP7 expression (see Meagher et al., 2007, Trends in Cell Biology). ARP4-Ri and ARP7-Ri knockdown lines retain petals and sepals after fertilization and even after the fruits are fully developed, unlike wild type (WT). a. Retention of floral organs in a strong ARP7-Ri line as compared to WT. b. WT retains sepals and petals on only 4 to 5 flowers.  c.  A moderate ARP7-Ri line retains turgid floral organs at the base of most developing fruits. d and e. Close up examination of developing fruits reveals retention of sepals and petals for a longer period in a moderate ARP4-Ri line compared to WT (numbers indicate sequence from terminal fully-opened flower). f. Model for the activities of ARP4 and ARP7 in sepal and petal abscission.  ARP7-dependent chromatin remodeling complexes appear to act downstream or independent of ethylene perception, while the site(s) of ARP4 activities are less clear. Possible target genes that promote abscission, whose expression could be potentiated by the action of both ARP4 or ARP7, include CTR1,EIN2, EIN3, ERF1, DAB1, HAESA, and IDA genes. ARP4 might act upstream of ethylene by activating ARF2. Conversely, ARP-dependent chromatin remodeling might potentiate the repression of factors repressing abscission like AGL15. Abscission would be delayed when ARP4 or ARP7 deficiencies resulted in these genes being insufficiently activated or repressed.

Definitions of epigenetics and epigenetic control: Literially epigenetics as derived from its Latin root means "outside genetics". Epigenetics has had several definitions dating to the 18th century. The broadest definition in current use describes epigenetic controls or epigenetic differences as those inherited from cell to cell that are not due to changes in the classical DNA base sequence (GATC). This definition was first suggested by David L. Nanney (1958, Epigenetic Control Systems, Proc. Natl. Acad. Sci. USA, 44: 271-717; 1958, Epigenetic factors affecting mating type expression in certain ciliates, Cold Spring Harbor Symp. Quant. Biol. 23: 327:335). Thus, chromatin remodeling activities that cause temporary changes in gene expression such as changes in nucleosome spacing and histone modifications within nucleosomes that often cause phenotypic differences among daughter cells are within epigenetics. In plants and animals epigenetic defects are often manifested as alterations in multicellular organ development. One benefit of this definition is that it broadly encompases chromatin level control in all eukaryotic cells. An older definition that is also in current use was put forth by Charles H. Waddington in the 1940s and 50s. It describes epigenetics as morphogenic gradients present during multicellular organ development that determine organ structure (1957, The strateg of the genes, Published London, Ruskin House, George Allen and Unwin, LTD). It use is limited to describing processes in multicellular development and hence is most commonly used to describe organ development in plants and animals. A greater part of this type of epigenetic control appears to be directed by changes in chromatin structure and thus Waddington's definition may be encompased by Nanney's. A good reference that furthers this discussion of the meaning of epigenetics is D. Haig's article (2004, The dual origin of epigenetics, Cold Spring Harb Symp Quant Biol, 69: 67:70).