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Genome biology [journal]
- Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance. [JOURNAL ARTICLE]
- Genome Biol 2013 May 22; 14(5):R42.
BACKGROUND:The extent to which development- and age-associated epigenetic changes are influenced by genetic, environmental and stochastic factors remains to be discovered. Twins provide an ideal model with which to investigate these influences but previous cross-sectional twin studies provide contradictory evidence of within-pair epigenetic drift over time. Longitudinal twin studies can potentially address this discrepancy.
RESULTS:In a pilot, genome-scale study of DNA from buccal epithelium, a relatively homogeneous tissue, we show that one third of the CpGs assayed show dynamic methylation between birth and 18 months. Although all classes of annotated genomic regions assessed show an increase in DNA methylation over time, probes located in intragenic regions, enhancers and low-density CpG promoters are significantly over-represented, while CpG islands and high-CpG density promoters are depleted among the most dynamic probes. Comparison of co-twins demonstrated that within-pair drift in DNA methylation in our cohort is specific to a subset of pairs, who show more differences at 18 months. The rest of the pairs show either minimal change in methylation discordance, or more similar, converging methylation profiles at 18 months. As with age-associated regions, sites that change in their level of within-pair discordance between birth and 18 months are enriched in genes involved in development, but the average magnitude of change is smaller than for longitudinal change.
CONCLUSIONS:Our findings suggest that DNA methylation in buccal epithelium is influenced by nonshared stochastic and environmental factors which could reflect a degree of epigenetic plasticity within an otherwise constrained developmental program.
- Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). [JOURNAL ARTICLE]
- Genome Biol 2013 May 10; 14(5):R41.
BACKGROUND:Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely-packed protuberances on its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.
RESULTS:The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101x and 5.2x. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has sixteen COG2132 multi-copper oxidase family proteins with root specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment.
CONCLUSIONS:The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.
- After the gold rush. [JOURNAL ARTICLE]
- Genome Biol 2013 May 7; 14(5):115.
- The future of genomic medicine is here. [JOURNAL ARTICLE]
- Genome Biol 2013 Mar 27; 14(3):304.
A report on the 6th annual Future of Genomic Medicine conference, held at the Scripps Seaside Forum, La Jolla, CA, USA, March 7-8, 2013.
- Clinical applications of sequencing take center stage. [JOURNAL ARTICLE]
- Genome Biol 2013 Mar 28; 14(3):303.
A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013.This year's Advances in Genome Biology and Technology (AGBT) meeting reflected the current state of 'next generation' sequencing (NGS) technologies: significantly reduced competition and innovation, and a strong focus on standardization and application. Announcements of technological breakthroughs - a hallmark of previous AGBT meetings - were markedly absent, but existing technologies continued to improve following the now expected exponential curve. Although applications ranged widely, there was a strong emphasis on clinical diagnosis.
- Pushing the (nuclear) envelope into meiosis. [JOURNAL ARTICLE]
- Genome Biol 2013 Mar 27; 14(3):110.
A recent study shows that a short isoform of a mammalian nuclear lamin is important for homologous chromosome interactions during meiotic prophase in mice.
- Sequestration: inadvertently killing biomedical research to score political points. [JOURNAL ARTICLE]
- Genome Biol 2013 Mar 27; 14(3):109.
- The passionate life of Simon Chan. [JOURNAL ARTICLE]
- Genome Biol 2013 Jan 30; 14(1):103.
- Raymond Gosling: the man who crystallized genes. [JOURNAL ARTICLE]
- Genome Biol 2013 Apr 25; 14(1):402.
On April 25th 1953, three publications in "Nature" forever changed the face of the life sciences in reporting the structure of DNA. Sixty years later, Raymond Gosling shares his memories of the race to the double helix.
- Sixty years of genome biology. [JOURNAL ARTICLE]
- Genome Biol 2013 Apr 25; 14(4):113.
Sixty years after Watson and Crick published the double helix model of DNA's structure, thirteen members of Genome Biology's Editorial Board select key advances in the field of genome biology subsequent to that discovery.