• DNA methylation and body-mass index: a genome-wide analysis

      Dick, Katherine J.; Nelson, Christopher P.; Tsaprouni, Loukia G.; Sandling, Johanna K.; Aïssi, Dylan; Wahl, Simone; Meduri, Eshwar; Morange, Pierre-Emmanuel; Gagnon, France; Grallert, Harald; et al. (Lancet Publishing Group, 2014-03-13)
      Background Obesity is a major health problem that is determined by interactions between lifestyle and environmental and genetic factors. Although associations between several genetic variants and body-mass index (BMI) have been identified, little is known about epigenetic changes related to BMI. We undertook a genome-wide analysis of methylation at CpG sites in relation to BMI. Methods 479 individuals of European origin recruited by the Cardiogenics Consortium formed our discovery cohort. We typed their whole-blood DNA with the Infinium HumanMethylation450 array. After quality control, methylation levels were tested for association with BMI. Methylation sites showing an association with BMI at a false discovery rate q value of 0·05 or less were taken forward for replication in a cohort of 339 unrelated white patients of northern European origin from the MARTHA cohort. Sites that remained significant in this primary replication cohort were tested in a second replication cohort of 1789 white patients of European origin from the KORA cohort. We examined whether methylation levels at identified sites also showed an association with BMI in DNA from adipose tissue (n=635) and skin (n=395) obtained from white female individuals participating in the MuTHER study. Finally, we examined the association of methylation at BMI-Associated sites with genetic variants and with gene expression. Findings 20 individuals from the discovery cohort were excluded from analyses after quality-control checks, leaving 459 participants. After adjustment for covariates, we identified an association (q value ≤middot&05) between methylation at five probes across three different genes and BMI. The associations with three of these probes - cg22891070, cg27146050, and cg16672562, all of which are in intron 1 of HIF3A - were confirmed in both the primary and second replication cohorts. For every 0·1 increase in methylation β value at cg22891070, BMI was 3·6% (95% CI 2·9) higher in the discovery cohort, 2·7% (1·2) higher in the primary replication cohort, and 0·8% (0·4) higher in the second replication cohort. For the MuTHER cohort, methylation at cg22891070 was associated with BMI in adipose tissue (p=1·72×10) but not in skin (p=0·882). We observed a significant inverse correlation (p=0·005) between methylation at cg22891070 and expression of one HIF3A gene-expression probe in adipose tissue. Two single nucleotide polymorphisms - rs8102595 and rs3826795 - had independent associations with methylation at cg22891070 in all cohorts. However, these single nucleotide polymorphisms were not significantly associated with BMI. Interpretation Increased BMI in adults of European origin is associated with increased methylation at the HIF3A locus in blood cells and in adipose tissue. Our findings suggest that perturbation of hypoxia inducible transcription factor pathways could have an important role in the response to increased weight in people. Funding The European Commission, National Institute for Health Research, British Heart Foundation, and Wellcome Trust.
    • Genome size diversity in angiosperms and its influence on gene space

      Dodsworth, Steven; Leitch, Andrew R.; Leitch, Ilia J.; Queen Mary University of London; Royal Botanic Gardens, Kew (Elsevier Ltd, 2015-11-21)
      Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C = 5.7 Gb. One of the most crucial factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as ‘junk’ DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression.
    • Genome skimming for next-generation biodiversity analysis

      Dodsworth, Steven; Queen Mary University of London; Royal Botanic Gardens, Kew (Elsevier Ltd, 2015-07-20)
    • Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae)

      Dodsworth, Steven; Jang, Tae-Soo; Struebig, Monika; Chase, Mark W.; Weiss-Schneeweiss, Hanna; Leitch, Andrew R.; Queen Mary University of London; Royal Botanic Gardens, Kew; University of Vienna; University of Western Australia (Springer-Verlag Wien, 2016-11-01)
      Nicotiana sect. Repandae is a group of four allotetraploid species originating from a single allopolyploidisation event approximately 5 million years ago. Previous phylogenetic analyses support the hypothesis of N. nudicaulis as sister to the other three species. This is concordant with changes in genome size, separating those with genome downsizing (N. nudicaulis) from those with genome upsizing (N. repanda, N. nesophila, N. stocktonii). However, a recent analysis reflecting genome dynamics of different transposable element families reconstructed greater similarity between N. nudicaulis and the Revillagigedo Island taxa (N. nesophila and N. stocktonii), thereby placing N. repanda as sister to the rest of the group. This could reflect a different phylogenetic hypothesis or the unique evolutionary history of these particular elements. Here we re-examine relationships in this group and investigate genome-wide patterns in repetitive DNA, utilising high-throughput sequencing and a genome skimming approach. Repetitive DNA clusters provide support for N. nudicaulis as sister to the rest of the section, with N. repanda sister to the two Revillagigedo Island species. Clade-specific patterns in the occurrence and abundance of particular repeats confirm the original (N. nudicaulis (N. repanda (N. nesophila ? N. stocktonii))) hypothesis. Furthermore, overall repeat dynamics in the island species N. nesophila and N. stocktonii confirm their similarity to N. repanda and the distinctive patterns between these three species and N. nudicaulis. Together these results suggest that broad-scale repeat dynamics do in fact reflect evolutionary history and could be predicted based on phylogenetic distance.
    • Potential of herbariomics for studying repetitive DNA in angiosperms

      Dodsworth, Steven; Guignard, Maite S.; Christenhusz, Maarten J.M.; Cowan, Robyn S.; Knapp, Sandra; Maurin, Olivier; Struebig, Monika; Leitch, Andrew R.; Chase, Mark W.; Forest, Felix; et al. (Frontiers Media, 2018-10-29)
      Repetitive DNA has an important role in angiosperm genomes and is relevant to our understanding of genome size variation, polyploidisation and genome dynamics more broadly. Much recent work has harnessed the power of high-throughput sequencing (HTS) technologies to advance the study of repetitive DNA in flowering plants. Herbarium collections provide a useful historical perspective on genome diversity through time, but their value for the study of repetitive DNA has not yet been explored. We propose that herbarium DNA may prove as useful for studies of repetitive DNA content as it has for reconstructed organellar genomes and low-copy nuclear sequence data. Here we present a case study in the tobacco genus (Nicotiana; Solanaceae), showing that herbarium specimens can provide accurate estimates of the repetitive content of angiosperm genomes by direct comparison with recently-collected material. We show a strong correlation between the abundance of repeat clusters, e.g., different types of transposable elements and satellite DNA, in herbarium collections versus recent material for four sets of Nicotiana taxa. These results suggest that herbarium specimen genome sequencing (herbariomics) holds promise for both repeat discovery and analyses that aim to investigate the role of repetitive DNAs in genomic evolution, particularly genome size evolution and/or contributions of repeats to the regulation of gene space.
    • Repetitive DNA restructuring across multiple Nicotiana allopolyploidisation events shows a lack of strong cytoplasmic bias in influencing repeat turnover

      Dodsworth, Steven; Guignard, Maite S.; Pérez-Escobar, Oscar A.; Struebig, Monika; Chase, Mark W.; Leitch, Andrew R.; ; University of Bedfordshire; Queen Mary University of London; Royal Botanic Gardens, Kew; et al. (MDPI, 2020-02-19)
      Allopolyploidy is acknowledged as an important force in plant evolution. Frequent allopolyploidy in Nicotiana across different timescales permits the evaluation of genome restructuring and repeat dynamics through time. Here we use a clustering approach on high-throughput sequence reads to identify the main classes of repetitive elements following three allotetraploid events, and how these are inherited from the closest extant relatives of the maternal and paternal subgenome donors. In all three cases, there was a lack of clear maternal, cytoplasmic bias in repeat evolution, i.e., lack of a predicted bias towards maternal subgenome-derived repeats, with roughly equal contributions from both parental subgenomes. Different overall repeat dynamics were found across timescales of <0.5 (N. rustica L.), 4 (N. repanda Willd.) and 6 (N. benthamiana Domin) Ma, with nearly additive, genome upsizing, and genome downsizing, respectively. Lower copy repeats were inherited in similar abundance to the parental subgenomes, whereas higher copy repeats contributed the most to genome size change in N. repanda and N. benthamiana. Genome downsizing post-polyploidisation may be a general long-term trend across angiosperms, but at more recent timescales there is species-specific variance as found in Nicotiana.
    • Role of endogenous annexin-A1 in the regulation of thymocyte positive and negative selection

      Paschalidis, Nikolaos; Huggins, A.; Rowbotham, Nicola J.; Furmanski, Anna L.; Crompton, Tessa; Flower, R.J.; Perretti, M.; D'Acquisto, Fulvio; Queen Mary University of London (Taylor & Francis, 2010-02-15)
      We have recently shown that endogenous Annexin-A1 (AnxA1) plays a homeostatic regulatory role in mature T cells by modulating the strength of TCR signaling. In this study we investigated the role of endogenous AnxA1 in thymocyte maturation. Analysis of AnxA1(-/-) thymocyte populations at the immature CD4(-)CD8(-) double negative (DN) stage showed a proportional decrease in the DN1 and an increase in the DN3 subsets compared to control littermates. There were no significant differences in thymocyte numbers or proportions of CD4(+) and CD8(+) single positive (SP) populations between Anx1(-/-) and AnxA1(+/+) mice. However, when we crossed AnxA1(-/-) mice onto HY-TCR transgenic mice, we observed an increase in CD4(+)CD8(+) double positive (DP) and CD4 SP cells in male AnxA1(-/-)/HY-TCR compared to AnxA1(+/+)/HY-TCR. Conversely, female AnxA1(-/-)/HY-TCR mice showed an increase in DP and a decrease in CD8 (SP) cells compared to female AnxA1(+/+)/HY-TCR. Biochemical analysis of the signaling pathways responsible for these effects showed a decrease in anti-CD3-induced Erk phosphorylation and NFkappaB activation in AnxA1(-/-) thymocytes compared to control littermates. Together these findings demonstrate a role for endogenous AnxA1 in regulating both positive and negative selection of the TCR repertoire. These results suggest that targeting AnxA1 expression or function in T cells could represent a useful approach for the development of novel therapies for the treatment of autoimmune diseases.