class="head no_bottom_margin" id="sec1title">IntroductionA defining feature of multicellular animals is their capacity to generate multiple specialized cell types through temporally and spatially regulated developmental programs. These programs of individual cell differentiation involve the generation of cell-specific transcriptional profiles. Recent genomic analyses, however, have shown that the unicellular ancestor of Metazoa already had a complex gene repertoire involved in multicellular functions, including specific differentiation programs (, , , , , ).Since the origin of animals was not solely dependent on the appearance of new genes, it is likely that animal evolution involved a shift in the genome regulatory capabilities required to generate cell-type-specific transcriptional profiles during animal development. In animals, these profiles are established and maintained by a complex combination of chromatin regulatory dynamics, distal cis-regulatory elements, and transcription factor networks (, , , , , ). Interestingly, a recent analysis of an early branching and morphologically simple animal, the cnidarian Nematostella vectensis, has shown that cnidarians and bilaterians share a conserved gene regulatory landscape (). However, it is unclear whether these ancient genome regulatory features are animal innovations or whether they were already present in the unicellular ancestor of Metazoa.To determine the timing and importance of regulatory changes in the origin of Metazoa, we need to unravel the genomic regulation of the extant animal relatives. Among the closest extant unicellular relatives of Metazoa, the amoeboid filasterean Capsaspora owczarzaki (herein Capsaspora), has the richest repertoire of transcription factors described to date (). These include genes, such as Brachyury, Myc, and Runx, that are essential for animal development. Moreover, Capsaspora is known to differentiate into three temporal life stages that are transcriptionally tightly regulated (). These temporal cell types include (1) a filopodiated amoeba, which corresponds to the proliferative trophic stage, (2) an aggregative multicellular stage, in which the cells produces an extracellular matrix, and (3) a cystic resistance form without filopodia (see an schematic representation of the life cycle in href="/pmc/articles/PMC4877666/figure/fig3/" target="figure" class="fig-table-link figpopup" rid-figpopup="fig3" rid-ob="ob-fig3" co-legend-rid="lgnd_fig3">Figure 3). Its key phylogenetic position as the sister group of animals and choanoflagellates, its rich gene repertoire, and the observed regulatory capabilities of Capsaspora, therefore, make it an ideal candidate to explore the origin of animal genome regulation.href="/pmc/articles/PMC4877666/figure/fig3/" target="figure" rid-figpopup="fig3" rid-ob="ob-fig3">class="inline_block ts_canvas" href="/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=4877666_gr3.jpg" target="tileshopwindow">target="object" href="/pmc/articles/PMC4877666/figure/fig3/?report=objectonly">Open in a separate windowclass="figpopup" href="/pmc/articles/PMC4877666/figure/fig3/" target="figure" rid-figpopup="fig3" rid-ob="ob-fig3">Figure 3Dynamic Chromatin Modifications(A) Boxplots showing hPTMs coverage levels in differentially expressed genes between stages, as indicated above each boxplot. The p value is indicated for the Wilcoxon signed-rank test.(B) Illustrative examples of dynamic chromatin modifications in Capsaspora. Different genomic windows show normalized coverage for different chromatin features and their dynamic association with gene expression. For each feature, the top track corresponds to the filopodial stage, the middle track to the aggregative stage, and the bottom track to the cystic stage.(C) Histone deacetylase inhibition experiments. Pictures of Capsaspora cells at different time points of incubation with DMSO (negative control) and TSA 3 μM. Transition from cystic to filopodial stage is blocked in the TSA-treated cells. Scale bar, 10 μm.(D) Western blot against total H3 and H3K27ac on histone extracts from control cells (DMSO) and cells treated with 0.5 and 3 μM TSA. White line indicates a lane was removed.(E) Gene expression distributions from biological replicates of control (DMSO, gray colors) and TSA-treated (red colors) cells. Notice the decrease in the fraction of non-expressed genes and the general shift in the distribution of TSA-treated cells.See also href="/pmc/articles/PMC4877666/figure/figs2/" target="figure" class="fig-table-link figpopup" rid-figpopup="figs2" rid-ob="ob-figs2" co-legend-rid="lgnd_figs2">Figures S2 and href="/pmc/articles/PMC4877666/figure/figs3/" target="figure" class="fig-table-link figpopup" rid-figpopup="figs3" rid-ob="ob-figs3" co-legend-rid="lgnd_figs3">andS3S3.
展开▼
