Additional file 2: Table S3. of Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis

Quantitative genotypes for all 15,183 inferred CNV regions (CNVRs). chr represents the chromosome on which the CNVR is located, while start and end indicate the coordinates of the first respectively last CGH probe contained in the CNVR. length_kb is the estimated CNVR length in kilobases. CNV_detection_status indicates whether a CNVR contains only deletions (del), duplications (dup) or both (cnv) and eqtl_mapping indicates whether a given CNVR was detected in at least two individuals and was therefore used for cis-eQTL mapping (1) or not (0). The columns thereafter are the quantitative genotypes defined as an individual’s median log2-ratio of all CGH probes within a given CNVR. (XLSX 5415 kb

K_A<i>/K</i>_S Distributions for 475 Intact Retrocopies and 1,554 Retropseudogenes with <i>K</i>_S < 0.15

<p>Note that we tested that the differences observed for <i>K</i>_A<i>/K</i>_S < 0.5 are not explained by differences in GC content (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030357#s4" target="_blank">Materials and Methods</a> for details). The bin with <i>K</i>_A<i>/K</i>_S > 1.5 includes estimates where <i>K</i>_S = 0 (<i>K</i>_A<i>/K</i>_S = ∞).</p

Expression Pattern of Retrogenes and Parents Determined by RT-PCR

<p>Black boxes indicate retrogenes; hatched boxes indicate parental genes. Note that in all cases testis expression of the retrogene was the strongest, as indicated by the semiquantitative PCR procedure (data not shown).</p

Additional file 1: Figures S1 – S4 and Tables S1, S2, S4, S5. of Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis

Supplemental figures and tables on CNV calling and eQTL mapping. (DOCX 1151 kb

Evidence for Positive Selection on <i>PABP3</i> Codons

<p>The rectangles correspond to the different domains of the PABP1 protein: RNA poly(A)-tail-binding domains (vertical lines), RNA-binding domains (hatched), protein–protein interaction domain (white), and PABP homo-oligomerization domain (black). Positions of positively selected codons with high posterior probabilities (>0.95) are indicated by arrows.</p

K_S Distribution for 3,951 Retrocopies

<p>The peak at <i>K</i>_S ≈ 0.1 suggests a burst of retroposition on the primate lineage (see also text and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030357#sg001" target="_blank">Figure S1</a>). Retrocopies with <i>K</i>_S > 1 were pooled in a single bin.</p

Expression changes and chromatin architecture modifications in WBS cells.

<p>Changes in expression and chromatin structure in WBS (GM13472) versus Ctrl (GM07006) cells. Changes in histone marks are presented as the log2-fold ratio between WBS and Ctrl cells. Statistical analysis was performed by a 2-sample t-Test. Values in italics are not statistically different.</p><p>AREL  =  average relative expression level, BDL  =  below detection line, NS  =  no regions within gene were defined as significantly changed,</p><p>*most significant block according to SICER within the gene (FDR<1%).</p

Extensive chromatin interactions of seven genes flanking the WBSCR on human chromosome 7 (HSA7) in cells from a healthy control individual.

<p>(<b>A</b>) Windowed and normalized 4C signal of each of the seven viewpoints along the entire HSA7. The black ticks below each graph show the location of the Bricks (Blocks of Regulators In Chromosomal Kontext). The gene density across HSA7, as well as the windowed profiles of H4K20me1 and H3K27me3 marks in the same cell line are shown below. Some examples of strong correlation of gene-dense regions and high density of H4K20me1 marks with highly interacting regions are highlighted in blue. The mapping of the assessed genes/viewpoints and of the WBSCR is indicated at the bottom. The red box specifies the close-up shown in panel B. (<b>B</b>) Close-up of the windowed 4C signal of the seven viewpoints around the WBSCR for the region indicated with a red box on HSA7 (top panel). The windowed 4C signal is shown in grey, while the profile corrected 4C signal (after removal of the highly interacting neighboring background signal) is overlaid in black. The position of all genes are displayed at the bottom, and the mapping of the assessed viewpoints is highlighted by red and green arrows indicating if the corresponding genes are down- or upregulated in cells from WBS patients, respectively. Black arrows underscore the mapping of the viewpoint that is not modified in gene expression (<i>ZNF107</i>) and the newly identified interacting partners <i>AUTS2</i> and <i>CALN1</i>. The location of the WBSCR is indicated by a purple horizontal bar. A close-up of interactions within this WBSCR is provided in <b>Supplementary <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079973#pone.0079973.s004" target="_blank">Figure S4</a></b>.</p

Functional p53 responsive elements map within the zebrafish-specific EnSpm-N6_DR transposon.

<p>(<b>A</b>) Predicted p53 responsive elements (REs) and their respective sequences in the first intron of <i>Danio rerio trim8a</i> long allele, <i>trim8a</i> short allele and <i>trim8b</i>. The indicated positions for REs are calculated from the annotated transcription start site. (<b>B</b>) Responsiveness to <i>Danio rerio</i> p53 transactivation of the first intron of <i>trim8a</i> engineered to contain different combinations of REs. The assessed mutant constructs are schematically represented on the left. (<b>C</b>) Zebrafish p53-dependent transactivation assessment in luciferase reporter assays of <i>Danio rerio trim8a</i> long allele, <i>trim8a</i> short allele, <i>trim8b</i> and <i>Homo sapiens p21</i> and <i>TRIM8</i>.</p

Protein subnetwork of human orthologs of genes parasitized by EnSpm-N6_DR elements in zebrafish classified by their involvement in specific developmental pathways, such as neurogenesis, synaptic transmission and regulation of programmed cell death.

<p>The network is visualized in STRING action view with lines and arrows of different colors indicating diverse types of interaction: binding (blue), activation (green), inhibition (red), post-translational modifications (violet) and co-expression (yellow). Of note the recently published interaction between TRIM8 and p53 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046642#pone.0046642-Caratozzolo1" target="_blank">[34]</a> was added explicitly as it is not yet annotated within the STRING database.</p