Candidate regulatory variants.

<p>Candidate regulatory variants.</p

Vitamin D and folate acquisition, metabolism and gene sets analyzed in this study.

<p>The upper part shows metabolism of vitamin D (yellow arrows) and folate (black arrows). Vitamin D₃ can be obtained from the diet, but it is mainly synthesised in the skin from 7-dehydrocholesterol (7-DHC) in response to light. It is then transported into the liver where it is hydroxylated to produce 25-hydroxyvitamin D₃ which is subsequently converted into its active form 1α, 25- dihydroxy vitamin D₃. This is transported in blood by vitamin D binding protein (DBP) and binds vitamin D receptor (VDR). The lower part shows gene sets analyzed in this study. The circles are proportional to number of genes in each set. The numbers in blue or pink circles indicate number of genes in each set that were present in AmiGO using the search terms “Vitamin D” (blue) or “Folate” (pink). Additional vitamin D (Vit D or VD) and folate (FA) gene sets are shown in shades of yellow and grey, respectively. The vitamin D gene sets that were generated included vitamin D targets identified by ChIP-Seq (VDR targets), genes involved in vitamin D action in bones, kidneys and intestines and all proteins involved in the VDR activation complex, including those directly interacting with VDR (VDRIP) and RXR (RXRIP) receptors. Folate gene sets include enzymes and receptors involved in dietary folate uptake and transport (FAU), proteins involved in nucleic acid synthesis (NAS) and methylation. The latter were sub-divided into genes involved in metabolism of methionine (Met), homocysteine (HCV) and S-adenosyl methionine methylation (SAM). The small blue and pink circles indicate the number of genes in the manually curated vitamin D and folate gene sets, respectively, that were also identified by AmiGO.</p

Positive selection at the <i>CXXC1</i> locus.

<p>A ~6 kb region on chromosome 18 that spans <i>CXXC1</i> showing GENCODE (Version 19) transcript annotation. The three short-listed candidate regulatory variants driving the selection signal in East Asians are all located in ENCODE annotated regions of open chromatin, depicted in the DNase I Hypersensitivity Clusters in 125 cell lines track, and show ENCODE chromatin state segmentation associated with an active promoter site in nine human cell lines. The latter include lymphoblastoids [GM12878]; embryonic stem cells [H1-hESC]; chronic myelogenous leukemia [K562]; hepatocellular carcinoma [HepG2]; umbilical vein endothelial [HUVEC]; mammary epithelial [HMEC]; skeletal muscle myoblast [HSMM]; skin epidermal keratinocytes [NHEK] and lung fibroblasts [NHLF]). Positions of histone modifications in osteoblasts are indicated by shaded bands and the black shade signifies enrichment. In osteoblasts the position of the histone sequence variant, H2A.Z, that determines accessibility of the transcription start site (TSS) and histone modifications like H3K4me3 that are enriched around TSS (dark bands) encompasses the candidate regulatory variant site and show binding for many transcription factors. H3K4me1 and H3K27ac modifications and p300 marks are enriched around active enhancers and CTCF indicates insulator regions. The lower part of the figure shows median joining haplotype networks in this region that is in high LD (r² ≥ 0.95) in CHB. Phased haplotypes generated by the 1000 Genomes Project were used to construct this network. The derived C allele for the regulatory variant <i>rs59393148</i> lies on the branch leading towards the most frequent haplotype found in East Asians, and shows a star like expansion typical of a selection signal. Note the proximity of archaic human haplotypes with a subset of East Asian (ASN) and European Finnish samples. These samples lie on a divergent branch that is closer to the Neanderthal (Nea) and Denisovan (Den) haplotype when compared with the rest of the modern human population samples.</p

Positive selection at the <i>LRP5</i> locus.

<p>(A). A 140 kb region on chromosome 6 that spans <i>LRP5</i> showing GENCODE (Version 19) transcript annotation. Positions of 11 candidate regulatory variants and DNase I Hypersensitivity Clusters are shown along with the −log₁₀ of the combined p-values from frequency-spectrum-based analysis in three continental populations. The significance threshold is indicated by the dashed line and two non-overlapping 10 kb windows have a significant combined p-value in CHB. (B). A closer look at the 3’ selected region in East Asians (highlighted in blue). The region contains both variants with the highest derived allele frequency in East Asians (<i>rs649772</i> and <i>rs671494</i>) that lie in a DNase I hypersensitivity cluster and show ENCODE chromatin state segmentation associated with enhancer binding in several cell lines. In osteoblasts the variants lie within the histone sequence variant, H2A.Z, that determines accessibility of the transcription start site (dark bands) and there are additional H3K4me1 and H3K27ac histone modifications upstream of the variant. The candidate regulatory variant site also shows binding for many transcription factors. The lower part of the panel shows median joining haplotype networks in a ~20 kb region that is in high LD (r² ≥ 0.95) in CHB. Phased haplotypes generated by the 1000 Genomes Project were used to construct this network. The derived alleles for the regulatory variants <i>rs649772</i> and <i>rs671494</i> lie on the branch leading towards the most frequent haplotype found in East Asians and shows a star like expansion typical of a selection signal. The non-synonymous variant <i>rs3736228</i> (red line) that is associated with bone mineral density in genome wide association studies lies on a separate branch.</p

Mitogenomes of Polar Bodies and Corresponding Oocytes

<div><p>The objective of the present study was to develop an approach that could assess the chromosomal status and the mitochondrial DNA (mtDNA) content of oocytes and their corresponding polar bodies (PBs) with the goal of obtaining a comparative picture of the segregation process both for nuclear and mtDNA. After Whole Genome Amplification (WGA), sequencing of the whole mitochondrial genome was attempted to analyze the segregation of mutant and wild-type mtDNA during human meiosis. Three triads, composed of oocyte and corresponding PBs, were analyzed and their chromosome status was successfully assessed. The complete mitochondrial genome (mitogenome) was almost entirely sequenced in the oocytes (95.99% compared to 98.43% in blood), while the percentage of sequences obtained in the corresponding PB1 and PB2 was lower (69.70% and 69.04% respectively). The comparison with the mtDNA sequence in blood revealed no changes in the D-loop region for any of the cells of each triad. In the coding region of blood mtDNA and oocyte mtDNA sequences showed full correspondence, whereas all PBs had at least one change with respect to the blood-oocyte pairs. In all, 9 changes were found, either in PB1 or PB2: 4 in <i>MT-ND5</i>, 2 in <i>MT-RNR2</i>, and 1 each in <i>MT-ATP8</i>, <i>MT-ND4</i>, <i>MT-CYTB</i>. The full concordance between oocyte and blood in the 3 triads, and the relegation of changes to PBs, revealed the unexpected coexistence of different variants, giving a refined estimation of mitochondrial heteroplasmy. Should these findings be confirmed by additional data, an active mechanism could be postulated in the oocyte to preserve a condition of ‘normality’.</p></div

Age estimations (in years ± SD) of the selected haplotypes with star like genealogy in East Asians (ASN).

<p>Age estimations (in years ± SD) of the selected haplotypes with star like genealogy in East Asians (ASN).</p

An Ancient Mediterranean Melting Pot: Investigating the Uniparental Genetic Structure and Population History of Sicily and Southern Italy

<div><p>Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.</p></div

Positive selection in East Asians for genes regulated by vitamin D in bone.

<p>The y axis shows the −log₁₀ of the combined p-value summarized from individual frequency-spectrum-based analysis on sets of Vitamin D (A) and Folate (B) related genes in three continental populations. The dashed horizontal line depicts the threshold of the −log₁₀ p-value for multiple comparisons after applying the Bonferroni correction (13 populations x 9 gene sets). (C). Positive selection in East Asians for genes regulated by vitamin D in bone. African (AFR) populations included ASW (African Ancestry in Southwest USA), LWK (Luhya in Webuye, Kenya) and YRI (Yoruba in Ibadan, Nigeria). Asians (ASN) were represented by CHB (Han Chinese in Beijing, China), CHS (Han Chinese South China) and JPT (Japanese in Tokyo, Japan); Europeans (EUR) included CEU (Utah residents with ancestry from northern and western Europe), FIN (Finnish in Finland), GBR (British from England and Scotland, UK) and TSI (Tuscans in Italy). Americans (AMR) were CLM (Colombians from Medellin, Colombia), MXL (Mexican Ancestry in Los Angeles, California, USA) and PUR (Puerto Rican in Puerto Rico, USA).</p

Positive selection at the <i>RUNX2</i> locus.

<p>(A). A 350 kb region on chromosome 6 that spans <i>RUNX2</i> showing GENCODE (Version 19) transcript annotation and the extent of the selective sweep region identified in the archaic Neanderthal genome. The positions of 22 candidate regulatory variants and DNase I Hypersensitivity Clusters are shown along with the −log₁₀ of the combined p-values from frequency-spectrum-based analysis in three continental populations. The significance threshold is depicted by the dashed line and two non-overlapping 10 kb windows have a significant combined p-value in CHB and YRI. (B). A closer look at the first selected region in East Asians (highlighted in blue). The region contains the variant with the highest derived allele frequency in East Asians (<i>rs 2677100</i>) that overlies ENCODE chromatin state segmentation associated with an enhancer in K562 and is also associated with H3K4me1 and H3K27ac modifications in osteoblasts. The lower part of the panel shows median joining haplotype networks in a ~10 kb region that is in high LD (r² ≥ 0.95) in CHB. Phased haplotypes generated by the 1000 Genomes Project were used to construct this network. The derived T allele for the regulatory variant <i>rs2677100</i> lies on the branch leading towards the most frequent haplotype found in East Asians and shows a star like expansion typical of a selection signal.</p

Spatial Principal Component Analysis (sPCA) based on Y-chromosome haplogroups frequencies.

<p>The first two global components, sPC1 (a) and sPC2 (b), are depicted. Positive values are represented by black squares; negative values are represented by white squares; the size of the square is proportional to the absolute value of sPC scores.</p