Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response

Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits global identification of the binding sites for transcription factors using chromatin immunoprecipitation and deep sequencing. We describe and validate this strategy, and apply it to the transcription factor PHA-4, which plays critical roles in organ development and other cellular processes. We identified thousands of binding sites for PHA-4 during formation of the embryonic pharynx, and also found a role for this factor during the starvation response. Many binding sites were found to shift dramatically between embryos and starved larvae, from developmentally regulated genes to genes involved in metabolism. These results indicate distinct roles for this regulator in two different biological processes and demonstrate the versatility of transcription factors in mediating diverse biological roles.Molecular and Cellular Biolog

Quantitative Differences in Nuclear β-catenin and TCF Pattern Embryonic Cells in <i>C</i>. <i>elegans</i>

<div><p>The Wnt signaling pathway plays a conserved role during animal development in transcriptional regulation of distinct targets in different developmental contexts but it remains unclear whether quantitative differences in the nuclear localization of effector proteins TCF and β-catenin contribute to context-specific regulation. We investigated this question in <i>Caenorhabditis elegans</i> embryos by quantifying nuclear localization of fluorescently tagged SYS-1/β-catenin and POP-1/TCF and expression of Wnt ligands at cellular resolution by time-lapse microscopy and automated lineage tracing. We identified reproducible, quantitative differences that generate a subset of Wnt-signaled cells with a significantly higher nuclear concentration of the TCF/β-catenin activating complex. Specifically, β-catenin and TCF are preferentially enriched in nuclei of daughter cells whose parents also had high nuclear levels of that protein, a pattern that could influence developmental gene expression. Consistent with this, we found that expression of synthetic reporters of POP-1-dependent activation is biased towards cells that had high nuclear SYS-1 in consecutive divisions. We identified new genes whose embryonic expression patterns depend on <i>pop-1</i>. Most of these require POP-1 for either transcriptional activation or repression, and targets requiring POP-1 for activation are more likely to be expressed in the cells with high nuclear SYS-1 in consecutive divisions than those requiring POP-1 for repression. Taken together, these results indicate that SYS-1 and POP-1 levels are influenced by the parent cell’s SYS-1/POP-1 levels and this may provide an additional mechanism by which POP-1 regulates distinct targets in different developmental contexts.</p></div

Updated model for TCF-mediated lineage diversification.

<p>A) Examples of wild-type expression patterns for genes that require TCF primarily for repression or activation. Repressed genes have exclusive (<i>ceh-27</i>) or equal (<i>tbx-11</i>) expression in SYS-1 Low-High lineages (yellow arrows), while activated genes have exclusive (<i>nhr-67</i>) or stronger (<i>ceh-13</i>) expression in SYS-1 High-High lineages (white arrows). B) Expression in SYS-1 High-High lineages for all genes and synthetic enhancers assayed. SYS-1 High-High score is the fraction of expressing lineages that are SYS-1 High-High. Expression is significantly more limited to SYS-1 High-High lineages for genes that require POP-1 for activation (green) than repression (purple) (p = 0.004, Wilcoxon rank sum test), as predicted by our model. C) A proposed model of TCF-mediated lineage patterning in <i>C</i>. <i>elegans</i> embryos. POP-1 and β-catenin concentrations vary depending on previous signaling history. Cells that are consecutive posterior daughters (pp) have the highest β-catenin levels and are predicted to strongly activate POP-1 targets. Consecutive anterior daughters (aa) have the highest POP-1 levels and are predicted to most strongly repress POP-1 targets. Single-anterior and single-posterior daughters (pa, ap) are predicted to have intermediate levels of repression and activation, respectively. D) Proposed model for the potential role of context transcription factors in determining the type of TCF regulation. When POP-1 is present, all targets are repressed by high levels of nuclear POP-1 and activated by SYS-1 and moderate levels of POP-1. We hypothesize that POP-1 RNAi reveals the activity of the context factors co-regulating a gene. We predict genes requiring TCF for activation are co-regulated by weak context factors that cannot activate transcription in the absence of POP-1, while genes requiring TCF for repression are co-regulated by context factors that can activate robust expression independently. Genes that are both activated and repressed (dual) could be co-regulated by context factors that produce moderate expression in the absence of POP-1.</p

Posterior lineage-dependent genes are targets of TCF.

<p>* deletion lethal,</p><p>^† known embryonic target [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005585#pgen.1005585.ref040" target="_blank">40</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005585#pgen.1005585.ref064" target="_blank">64</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005585#pgen.1005585.ref067" target="_blank">67</a>],</p><p>^# known post-embryonic target [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005585#pgen.1005585.ref085" target="_blank">85</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005585#pgen.1005585.ref086" target="_blank">86</a>],</p><p>^{^} fosmid protein fusion reporter, so additional elements may lie outside the 5’ regulatory region.</p><p>Posterior lineage-dependent genes are targets of TCF.</p

A reporter of POP-1-dependent activation shows stronger activity in double-posterior lineages.

<p>A) POPTOP construct [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005585#pgen.1005585.ref059" target="_blank">59</a>], a minimal promoter driven by 7 TCF binding sites. B) Expression of POPTOP in the embryo. Expression is limited to descendants of posterior daughter cells (right branches, histone-mCherry reporter is stable even after transcription ceases). C) Detail of expression of POPTOP in the ABpl lineage. We infer that expression initiated in the common ancestor of multiple expressing cells, but visualization lags by ~30 minutes, consistent with previous estimates of the time required for transcription, translation and mCherry maturation [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005585#pgen.1005585.ref060" target="_blank">60</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005585#pgen.1005585.ref083" target="_blank">83</a>]. POPTOP activity for each cell is the average expression of that cell and its descendants (boxes). We then calculate differential activity between sister sublineages (e.g. ABplpppp HH sublineage minus ABplpppa “HL” sublineage). In the case marked, the SYS-1 High-High cell (HH) expresses POPTOP more strongly than its sister lineage (HL). D) POPTOP levels increase with number of previous divisions with high levels of nuclear SYS-1, as expected if it is specifically transcribed in posterior daughters. E) POPTOP sister asymmetry as outlined in panel C (SYS-1 high cells: red, SYS-1 low cells: grey) clustered by the time at which the division occurred. p-values test for significant differences between Xpp and Xap cells (Wilcoxon rank-sum test). POPTOP expression is more asymmetric in lineages of parent cells with high levels of nuclear SYS-1. Asymmetry is highest at the 100-cell stage, when most lineages initiate POPTOP expression. F) Enhancers with seven (<i>POPTOP</i>), six, and three TCF sites; cells with expressing daughters are marked by the number of consecutive high nuclear SYS-1 parents. A synthetic enhancer with a single TCF site showed no detectable embryonic expression (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005585#pgen.1005585.s015" target="_blank">S10 Fig</a>). Fewer TCF sites leads to more restricted expression in multiply posterior lineages.</p

Nuclear localization of β-catenins is asymmetric across most embryonic cells.

<p>A) Confocal image of Venus::SYS-1 in a 350 cell stage embryo. B) Quantification of nuclear localization for Venus::SYS-1 shows that cells with strong nuclear localization of β-catenin (red) are distributed across the A-P axis. Grey cells have little to no detectable nuclear Venus::SYS-1. C) Overview of naming rules. Posterior daughter cells are represented as right branches on lineage trees. Sister asymmetry is measured by subtracting expression between daughter cells. D) Mean nuclear GFP::WRM-1 levels across the ABplp lineage. Branch color represents nuclear fluorescence intensity on a scale from purple (weak nuclear depletion) to green (weak nuclear enrichment) to red (strong nuclear enrichment). Note stronger enrichment in posterior daughters of later divisions and rare divisions with reversed polarity (black arrow). E) Mean sister asymmetry in nuclear GFP::WRM-1 for each division assayed through bean stage (~600 cells). Colors denote orientation of division according to Sulston. F) Correlation between mean GFP::WRM-1 and Venus::SYS-1 asymmetry for each division through the 350-cell stage.</p