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Vardhman K. Rakyan
Queen Mary University of London
EpigenomicsDNA methylationEpigeneticsGeneticsBiology
70Publications
34H-index
7,205Citations
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Publications 75
Newest
#1Fredrika Asenius (UCL: University College London)
#2Tyler J. Gorrie-Stone (University of Essex)H-Index: 3
Last. David J. Williams (UCL: University College London)H-Index: 72
view all 10 authors...
Background: Epidemiological studies suggest that paternal obesity may increase the risk of fathering small for gestational age offspring. Studies in non-human mammals suggest that such associations could be mediated by DNA methylation changes in spermatozoa that influence offspring development in utero. Human obesity is associated with differential DNA methylation in peripheral blood. It is unclear, however, whether this differential DNA methylation is reflected in spermatozoa. We profiled genom...
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#1Robert LoweH-Index: 17
#2Amy F. DansonH-Index: 2
Last. Chris G. FaulkesH-Index: 35
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The naked mole-rat, Heterocephalus glaber (NMR), the longest-lived rodent, is of significance and interest in the study of biomarkers for ageing. Recent breakthroughs in this field have revealed 'epigenetic clocks' that are based on the temporal accumulation of DNA methylation at specific genomic sites. Here, we validate the hypothesis of an epigenetic clock in NMRs based on changes in methylation of targeted CpG sites. We initially analysed 51 CpGs in NMR livers spanning an age range of 39-1,14...
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#1Christopher G. Bell (QMUL: Queen Mary University of London)H-Index: 23
#2Robert Lowe (QMUL: Queen Mary University of London)H-Index: 17
Last. Vardhman K. Rakyan (QMUL: Queen Mary University of London)H-Index: 34
view all 21 authors...
Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of ...
12 CitationsSource
#1Alexander Payne (University of Nottingham)H-Index: 2
#2Nadine Holmes (University of Nottingham)H-Index: 3
Last. Matthew Loose (University of Nottingham)H-Index: 22
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23 CitationsSource
#1Alexander Payne (University of Nottingham)H-Index: 2
#2Nadine Holmes (University of Nottingham)H-Index: 3
Last. Matthew Loose (University of Nottingham)H-Index: 22
view all 4 authors...
Motivation: The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction. Nanopore sequencers output fast5 files containing signal data subsequently base called to fastq format. Optionally, ONT devices can collect data from all sequencing channels simultaneously in a bulk fast5 file enabling inspection of signal in any channel at any point. We sought to visualise this signal to inspect challenging or difficult to se...
28 CitationsSource
#1Amy F. Danson (QMUL: Queen Mary University of London)H-Index: 2
#2Sarah J. Marzi (QMUL: Queen Mary University of London)H-Index: 5
Last. Vardhman K. Rakyan (QMUL: Queen Mary University of London)H-Index: 34
view all 5 authors...
Environmental influences fluctuate throughout the life course of an organism. It is therefore important to understand how the timing of exposure impacts molecular responses. Herein, we examine the responses of two key molecular markers of dietary stress, namely variant-specific methylation at ribosomal DNA (rDNA) and small RNA distribution, including tRNA fragments, in a mouse model of protein restriction (PR) with exposure at pre- and/or post-weaning. We first confirm that pre-weaning PR exposu...
3 CitationsSource
#1Zdenko Herceg (IARC: International Agency for Research on Cancer)H-Index: 8
#2Akram Ghantous (IARC: International Agency for Research on Cancer)H-Index: 15
Last. Hector Hernandez-Vargas (IARC: International Agency for Research on Cancer)H-Index: 20
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The interaction between the (epi)genetic makeup of an individual and his/her environmental exposure record (exposome) is accepted as a determinant factor for a significant proportion of human malignancies. Recent evidence has highlighted the key role of epigenetic mechanisms in mediating gene-environment interactions and translating exposures into tumorigenesis. There is also growing evidence that epigenetic changes may be risk factor-specific (“fingerprints”) that should prove instrumental in t...
18 CitationsSource
#1Robert Lowe (QMUL: Queen Mary University of London)H-Index: 17
#2Carl Barton (QMUL: Queen Mary University of London)H-Index: 5
Last. Vardhman K. RakyanH-Index: 34
view all 14 authors...
Mammalian species exhibit a wide range of lifespans. To date, a robust and dynamic molecular readout of these lifespan differences has not yet been identified. Recent studies have established the existence of ageing-associated differentially methylated positions (aDMPs) in human and mouse. These are CpG sites at which DNA methylation dynamics show significant correlations with age. We hypothesise that aDMPs are pan-mammalian and are a dynamic molecular readout of lifespan variation among differe...
7 CitationsSource
#1Matthias Thurner (University of Oxford)H-Index: 4
#2Martijn van de Bunt (University of Oxford)H-Index: 24
Last. Mark I. McCarthy (University of Oxford)H-Index: 162
view all 15 authors...
Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n=17) and DNA methylation (whole-genome bisulphite sequencing, n=10) in human islets, generati...
38 CitationsSource
#1Matthias Thurner (University of Oxford)H-Index: 4
#2Martijn van de Bunt (University of Oxford)H-Index: 24
Last. Mark I. McCarthy (University of Oxford)H-Index: 162
view all 15 authors...
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