Gene expression across mammalian organ development

The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, macaque, mouse, rat, rabbit, opossum and chicken. Comparisons of gene expression patterns identified developmental stage correspondences across species, and differences in the timing of key events during the development of the gonads. We found that the breadth of gene expression and the extent of purifying selection gradually decrease during development, whereas the amount of positive selection and expression of new genes increase. We identified differences in the temporal trajectories of expression of individual genes across species, with brain tissues showing the smallest percentage of trajectory changes, and the liver and testis showing the largest. Our work provides a resource of developmental transcriptomes of seven organs across seven species, and comparative analyses that characterize the development and evolution of mammalian organs

Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage

Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage. The age of this system approximately coincides with the ages of the avian and two mammalian sex chromosomes systems. To compensate for the almost complete Y Chromosome degeneration, X-linked genes have become twofold up-regulated, restoring ancestral expression levels. The highly efficient dosage compensation mechanism of Anolis represents the only vertebrate case identified so far to fully support Ohno's original dosage compensation hypothesis. Further analyses reveal that X up-regulation occurs only in males and is mediated by a male-specific chromatin machinery that leads to global hyperacetylation of histone H4 at lysine 16 specifically on the X Chromosome. The green anole dosage compensation mechanism is highly reminiscent of that of the fruit fly, Drosophila melanogaster Altogether, our work unveils the convergent emergence of a Drosophila-like dosage compensation mechanism in an ancient reptilian sex chromosome system and highlights that the evolutionary pressures imposed by sex chromosome dosage reductions in different amniotes were resolved in fundamentally different ways

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

A large-scale comparative gene expression study reveals the different ways in which the chromosome-wide gene dosage reductions resulting from sex chromosome differentiation events were compensated during mammalian and avian evolution

Concerted downregulation of X-linked and autosomal genes in the brain of placental and marsupial (i.e., therian) mammals.

<p>Modules with specific expression states in the therian brain (module 563; 330 genes) or eutherian brain/cerebellum (module 634; 313 genes) are shown. Bars represent the weighted average expression of all genes in a module, for each sample (horizontal grey line, average bar height). The horizontal red line represents the cutoff of the biclustering algorithm; samples above the red line are considered to have a distinct expression state. Note that the modules shown are highly enriched for X-linked genes (module 563: 25 observed versus 8.5 expected, <i>p</i><10⁻³; module 634: 28 observed versus 8.3 expected, <i>p</i><10⁻⁴), as are modules 421, 507, 521, and 618, which display transcriptional downregulations in therians or eutherians and were all considered in the protein–protein interaction analyses (see main text and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#s3" target="_blank">Methods</a>). All modules can be explored in a searchable database: <a href="http://www.unil.ch/cbg/ISA/species" target="_blank">http://www.unil.ch/cbg/ISA/species</a>.</p

Male versus female expression levels of individual sex chromosomal genes in cerebellum from representative amniotes.

<p>Male to female (M∶F) gene expression ratios are plotted for individual genes (expressed in both sexes) on the human, mouse, and opossum X, platypus X₁ and X₅, and chicken Z chromosome for a representative tissue (cerebellum). Values are plotted on a log₂ scale to allow for linear and symmetrical patterns (e.g., 0.5 [log₂ ratio of −1]; 1 [log₂ ratio of 0]; and 2 [log₂ ratio of 1]). Median M∶F ratios for human, mouse, and opossum X, platypus X₅ and X₁ non-pseudoautosomal region, and chicken Z are indicated by orange lines. The distribution of individual M∶F ratios (orange vertical plots) is shown to the right of each main plot. Expression ratios of individual genes on the platypus X₁ chromosome are indicated by green circles (pseudoautosomal genes with 1∶1 orthologs on chicken Chromosomes Z, 3, or 13; see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328-Veyrunes1" target="_blank">[3]</a> for details), orange circles (non-pseudoautosomal/sex-linked genes with 1∶1 orthologs on chicken Chromosome 12 <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328-Veyrunes1" target="_blank">[3]</a>), or grey circles (pseudoautosomal or non-pseudoautosomal genes without clear 1∶1 chicken orthologs). Note that the respective medians for the platypus X₁ were calculated on the basis of genes with chicken 1∶1 orthologs, although the other genes in these regions show very similar patterns. See <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328.s021" target="_blank">Table S3</a> for platypus X₁ M∶F ratios for all six organs.</p

Sex chromosome homology relationships and current and inferred ancestral expression levels of genes on the mammalian (proto) X or avian Z chromosomes.

<p>(A) Sex chromosomes in the different mammals and birds and their corresponding homologous autosomal counterparts in species with non-homologous sex chromosome systems. (B) Left: median X (Z) to autosome expression level ratios (and 95% confidence intervals) of expressed genes on the current sex chromosomes in five representative amniotes that have 1∶1 orthologs in all studied species (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328.s003" target="_blank">Figure S3</a> for plots with all ten species). Middle: median X (Z) to autosome ratios of expressed genes on “proto-sex chromosomes,” as inferred from autosomal one-to-one orthologous genes from species with non-homologous sex chromosomes (see (A), main text, and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#s3" target="_blank">Methods</a> for details). Right: median current to ancestral X (Z)-linked gene expression ratios for genes expressed both on the current X and proto-X (normalized by expression levels of autosomal genes, respectively). Note that values are plotted on a log₂ scale to allow for linear and symmetrical patterns. Numbers of X (X₅, Z) conserved genes (i.e., genes with clear 1∶1 orthologs across the ten species) considered in these analyses are: 157 (human), 156 (chimp), 158 (gorilla), 156 (orang), 155 (macaque), 153 (mouse), 91 (opossum), 56 (platypus), 296 (chicken). See <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328.s003" target="_blank">Figure S3</a> for similar plot containing data for all ten species. See <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#s3" target="_blank">Methods</a> for details regarding the calculation of the different ratios. Statistically significant deviations from the reference values (0.5 [log₂ ratio of −1]; 1 [log₂ ratio of 0]; and 2 [log₂ ratio of 1]), as assessed by one-sample Wilcoxon signed rank tests (Benjamini-Hochberg corrected <i>p</i><0.05) are indicated to the right of each plot (oranges/blue boxes).</p

Median male versus female expression levels of mammalian X-linked and avian Z-linked genes in five somatic tissues.

<p>Top: Median male to female (M∶F) gene expression level ratios and 95% confidence intervals for five somatic tissues derived from nine mammals and one bird. M∶F ratio calculations are based on genes expressed in both sexes (RPKM>0). Values are plotted on a log₂ scale to allow for linear and symmetrical patterns (e.g., same distances for two-fold higher expression levels in males or females, respectively). Statistically significant deviations of M∶F ratios from key reference values (orange/blue boxes): 0.5 (log₂ ratio of −1); 1 (log₂ ratio of 0); and 2 (log₂ ratio of 1), as assessed by one-sample Wilcoxon signed rank tests (Bonferroni corrected <i>p</i><0.05). Numbers of X (X₅, Z) genes considered in the analysis are: 664 (human), 520 (chimp), 657 (gorilla), 606 (orang), 731 (macaque), 750 (mouse), 442 (opossum), 137 (platypus), 733 (chicken). Bottom: Schematic tree illustrating the phylogenetic relationships and sex chromosomes (homologous therian XY chromosomes in red; [partially] homologous platypus and bird sex chromosomes in blue) of the amniote lineages for which male and female expression was compared. Specifically, male and female expression values were compared for the therian X, platypus X₅ (highlighted in pink), and chicken Z chromosome. Approximate divergence time estimates (million years ago [Mya]) are based on previous studies <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328-Janecka1" target="_blank">[52]</a>–<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328-Kumar1" target="_blank">[55]</a>. Note that the expression ratios shown for eutherians are based on protein-coding genes from the entire X chromosome, that is, the ancestral part of the eutherian X (the so-called XCR) <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328-Ross1" target="_blank">[31]</a>, as well as the region that became X-linked during early eutherian evolution (termed XAR) <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328-Ross1" target="_blank">[31]</a>. Expression ratios for the XCR only are shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328.s001" target="_blank">Figure S1</a>.</p

Distributions of current and inferred ancestral expression levels of genes on the platypus (proto) X chromosomes/autosomes and chicken (proto) Z chromosome/autosomes.

<p>Distributions of expression levels of (proto) sex chromosome-linked genes (blue line) and (proto) autosomal genes (red line) are shown for cerebellum from platypus and chicken. Expression levels in the comparison of the current X (Z) and proto-X (Z) are normalized by the respective autosomal expression levels (rightmost plots). See <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328.s019" target="_blank">Table S1</a> for all tests of differences between X (Z) and autosomal expression distributions (all tissues).</p

Distributions of current and inferred ancestral expression levels of genes on the marsupial (proto) X chromosomes and autosomes.

<p>Distributions of expression levels of (proto) X-linked genes (blue line) and (proto) autosomal genes (red line) are shown for cerebellum and liver from opossum. Expression levels in the comparison of the current X and proto-X (right plots) are normalized by the respective autosomal expression levels. In all cases, the two plotted distributions are not significantly different from each other (Benjamini-Hochberg corrected <i>p</i>>0.05; Komolgorov-Smirnov test). See <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001328#pbio.1001328.s019" target="_blank">Table S1</a> for all tests of differences between X and autosomal expression distributions (all tissues).</p