Climate Change, Coral Reef Ecosystems, and Management Options for Marine Protected Areas

Marine protected areas (MPAs) provide place-based management of marine ecosystems through various degrees and types of protective actions. Habitats such as coral reefs are especially susceptible to degradation resulting from climate change, as evidenced by mass bleaching events over the past two decades. Marine ecosystems are being altered by direct effects of climate change including ocean warming, ocean acidification, rising sea level, changing circulation patterns, increasing severity of storms, and changing freshwater influxes. As impacts of climate change strengthen they may exacerbate effects of existing stressors and require new or modified management approaches; MPA networks are generally accepted as an improvement over individual MPAs to address multiple threats to the marine environment. While MPA networks are considered a potentially effective management approach for conserving marine biodiversity, they should be established in conjunction with other management strategies, such as fisheries regulations and reductions of nutrients and other forms of land-based pollution. Information about interactions between climate change and more “traditional” stressors is limited. MPA managers are faced with high levels of uncertainty about likely outcomes of management actions because climate change impacts have strong interactions with existing stressors, such as land-based sources of pollution, overfishing and destructive fishing practices, invasive species, and diseases. Management options include ameliorating existing stressors, protecting potentially resilient areas, developing networks of MPAs, and integrating climate change into MPA planning, management, and evaluation

Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans.

In Caenorhabditis elegans, the dosage compensation complex (DCC) specifically binds to and represses transcription from both X chromosomes in hermaphrodites. The DCC is composed of an X-specific condensin complex that interacts with several proteins. During embryogenesis, DCC starts localizing to the X chromosomes around the 40-cell stage, and is followed by X-enrichment of H4K20me1 between 100-cell to comma stage. Here, we analyzed dosage compensation of the X chromosome between sexes, and the roles of dpy-27 (condensin subunit), dpy-21 (non-condensin DCC member), set-1 (H4K20 monomethylase) and set-4 (H4K20 di-/tri-methylase) in X chromosome repression using mRNA-seq and ChIP-seq analyses across several developmental time points. We found that the DCC starts repressing the X chromosomes by the 40-cell stage, but X-linked transcript levels remain significantly higher in hermaphrodites compared to males through the comma stage of embryogenesis. Dpy-27 and dpy-21 are required for X chromosome repression throughout development, but particularly in early embryos dpy-27 and dpy-21 mutations produced distinct expression changes, suggesting a DCC independent role for dpy-21. We previously hypothesized that the DCC increases H4K20me1 by reducing set-4 activity on the X chromosomes. Accordingly, in the set-4 mutant, H4K20me1 increased more from the autosomes compared to the X, equalizing H4K20me1 level between X and autosomes. H4K20me1 increase on the autosomes led to a slight repression, resulting in a relative effect of X derepression. H4K20me1 depletion in the set-1 mutant showed greater X derepression compared to equalization of H4K20me1 levels between X and autosomes in the set-4 mutant, indicating that H4K20me1 level is important, but X to autosomal balance of H4K20me1 contributes slightly to X-repression. Thus H4K20me1 is not only a downstream effector of the DCC [corrected].In summary, X chromosome dosage compensation starts in early embryos as the DCC localizes to the X, and is strengthened in later embryogenesis by H4K20me1

The X chromosome is not fully dosage compensated in early embryogenesis.

<p>(A) Timeline of X chromosome regulation during C. elegans embryogenesis. Zygotic transcription begins at the four-cell stage [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref100" target="_blank">100</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref101" target="_blank">101</a>], followed by expression of sex determination genes by the 28 cell-stage [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref032" target="_blank">32</a>]. This triggers DCC localization to the X chromosomes at about the 40-cell stage [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref021" target="_blank">21</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref022" target="_blank">22</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref028" target="_blank">28</a>] and H4K20me1 enrichment on the X chromosome starting at the 100-cell stage [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref018" target="_blank">18</a>]. (B) mRNA-seq expression values from hermaphrodites (y-axis) and mixed sex (x-axis) early embryos (4–40 cell stage) were plotted. X is shown in purple, and shifted slightly towards the hermaphrodite data. (C) Boxplot shows distribution of log₂ fold-difference between hermaphrodites and mixed sex early embryos. Horizontal lines indicate equal expression between sexes (log₂ fold difference = 0) and 2-fold more expression in hermaphrodites (log₂ fold difference = 0.415). The n numbers below boxes show the number of expressed genes for each chromosome. Compared to each of the autosomes, X chromosome expression is significantly higher in hermaphrodites (one-sided Wilcoxon rank sum test, *** = p < 10⁻³, ** = p < 10⁻², and * = p < 0.05.). (D) Differentially expressed genes (DESeq padj < 0.05) were sorted into three groups: up (higher) or downregulated (lower transcript levels) in hermaphrodites, and not differentially expressed. Distribution of these groups among the chromosomes indicated a significant enrichment of hermaphrodite upregulated genes on the X chromosome (Fisher’s exact test for enrichment, *** = p < 10⁻³, ** = p < 10⁻²). (E) Plots indicate the percentage of statistically similarly expressed transcripts (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#sec027" target="_blank">methods</a>) that were maternally deposited (oocyte FPKM>1 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref030" target="_blank">30</a>]).</p

Gene regulation by <i>dpy-27</i>, <i>dpy-21</i>, <i>set-4</i> and <i>set-1</i> across the X chromosome and autosomes.

<p>(A) K-means clustering was performed using log₂ ratios of expression in <i>dpy-27</i>/control RNAi, <i>dpy-21(e428)</i>/N2, <i>set-4(n4600)</i>/N2, <i>set-1(tm1821)</i> homozygous/heterozygous L3 worms. The clusters are indicated with a color and number to the right of the heat map. (B) GO term analyses indicate the enrichment of gene functions for each cluster compared to the rest of the X or autosomes. Additional GO terms are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.s012" target="_blank">S4 File</a>.</p

DCC-mediated transcriptional repression is applied continuously across the X chromosomal genes.

<p>(A) Box plots show the distribution of GRO-seq gene-body log₂ ratios in <i>sdc-2(y93</i>,<i>RNAi)</i> versus control mixed stage embryos taken from published data [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref043" target="_blank">43</a>]. Dosage compensated (blue) and non-compensated (yellow) genes were previously categorized by microarray experiments [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref042" target="_blank">42</a>]. On average, previously designated compensated and noncompensated classes showed similar upregulation of transcription upon <i>sdc-2(y93</i>,<i>RNAi)</i> treatment. Same analysis was performed using mRNA-seq data comparing <i>dpy-27</i> versus control RNAi in mixed embryos. In this case, noncompensated classes showed less upregulation measured by mRNA-seq. (B) A mixture model was used to represent the presence of subpopulations within an overall population, and applied to the GRO-seq expression ratios of all measured genes. This model identified two distributions similar to the empirical X and autosomal distributions. Values above modeled distributions show the mean for each distribution. (C, D) Same mixture model approach was used to analyze subpopulations within only the X chromosome using the GRO-seq (C), and <i>dpy-27(y56)</i> mRNA-seq (D) data in mixed embryos. Both subpopulations showed upregulation, thus the effect of the DCC appears continuous such that no large distinct class of genes completely escapes DCC regulation.</p

DCC represses zygotic expression of the X chromosome in early embryos.

<p>(A) K means clustering of expression in 2-cell [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref030" target="_blank">30</a>] and early hermaphrodite embryos (4–40 cell). Of the five clusters identified, one showed clearly increased expression between 2-cell and early embryos (#3). (B) Boxplots show expression levels for genes separated by clusters in 2-cell [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref030" target="_blank">30</a>] and early hermaphrodite and mixed sex embryos. (C) Newly expressed genes were identified by taking genes in cluster #3 that showed no expression in 2-cell embryos (FPKM<1). Boxplots show distribution of expression difference between sexes in early embryos. Both newly expressed, and all expressed (FPKM>1) genes were significantly higher in hermaphrodite X chromosomes compared to autosomes (one sided Wilcoxon rank-sum test, *** = p < 10⁻³, * = p < 0.05) (D) Expression level of early sex determination genes in hermaphrodites and mixed sex samples are shown for the indicated data sets. 2-cell stage expression data in hermaphrodite embryos were obtained from [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005698#pgen.1005698.ref030" target="_blank">30</a>]. Error bars show the standard error of the mean. (E) Log₂ expression ratios between <i>dpy-27(y56)</i> and N2 wild type show significant X derepression in <i>dpy-27(y56)</i> early embryos. <i>dpy-27(y56)</i> mutation affects expression of newly expressed zygotic genes (panel C) on the X chromosome compared to autosomes. Significance of X upregulation was tested using one sided Wilcoxon rank-sum test (*** = p < 10⁻³).</p