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DAMEfinder: a method to detect differential allele-specific methylation
BackgroundDNA methylation is a highly studied epigenetic signature that is associated with regulation of gene expression, whereby genes with high...
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Chronological set of E. coli O157:H7 bovine strains establishes a role for repeat sequences and mobile genetic elements in genome diversification
BackgroundEnterohemorrhagic Escherichia coli O157:H7 (EHEC) is a significant foodborne pathogen that resides asymptomatically within cattle and...
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Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation
BackgroundDespite its conserved role on gene expression and transposable element (TE) silencing, genome-wide CG methylation differs substantially...
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Insights into the genetic architecture of Phytophthora capsici root rot resistance in chile pepper (Capsicum spp.) from multi-locus genome-wide association study
BackgroundPhytophthora root rot, a major constraint in chile pepper production worldwide, is caused by the soil-borne oomycete, Phytophthora capsici ....
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Genetic map** of a major QTL promoting homoeologous chromosome pairing in a wheat landrace
Key messageCommon wheat landrace Kaixian-luohanmai carries a gene(s) that promotes homoeologous chromosome pairing. A major QTL responsible for this...
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Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters
BackgroundThere is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However,...
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Long Non-coding RNAs in Rheumatology
The last decade has seen an enormous increase in long non-coding RNA (lncRNA) research within rheumatology. LncRNAs are arbitrarily classed as...
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DNA methylation signatures in autism spectrum disorders
Autism Spectrum Disorders (ASD) are a group of neurodevelopmental disorders which includes autistic disorders, Asperger’s Syndrome and Pervasive...
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X inactivation in a mammal species with three sex chromosomes
X inactivation is a fundamental mechanism in eutherian mammals to restore a balance of X-linked gene products between XY males and XX females....
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Cloning by SCNT: Integrating Technical and Biology-Driven Advances
Somatic cell nuclear transfer (SCNT) into enucleated oocytes initiates nuclear reprogramming of lineage-committed cells to totipotency. Pioneer SCNT...
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Metabolic collateral lethal target identification reveals MTHFD2 paralogue dependency in ovarian cancer
Recurrent loss-of-function deletions cause frequent inactivation of tumour suppressor genes but often also involve the collateral deletion of...
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Sex differences in the intergenerational inheritance of metabolic traits
Strong evidence suggests that early-life exposures to suboptimal environmental factors, including those in utero, influence our long-term metabolic...
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Klinefelter Bone Microarchitecture Evolution with Testosterone Replacement Therapy
Klinefelter Syndrome (KS) patients, defined by a 47 XXY karyotype, have increased risk of fragility fractures. We have assessed bone...
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Classification of Long Noncoding RNAs by k-mer Content
K-mer based comparisons have emerged as powerful complements to BLAST-like alignment algorithms, particularly when the sequences being compared lack...
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Non-Invasive Identification of Sex in Cultured Bovine Embryos by UHPLC-MS/MS Metabolomics
IntroductionDifferent gene expression between male and female bovine embryos leads to metabolic differences.
ObjectiveWe used UHPLC-MS/MS to...
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Mechanisms of chromatin-based epigenetic inheritance
Multi-cellular organisms such as humans contain hundreds of cell types that share the same genetic information (DNA sequences), and yet have...
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Regulation of Gene Expression in Eukaryotes
Similar to prokaryotes, eukaryotes have also evolved with complex gene regulation mechanisms to control the expression of variety of genes in...
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Multi-species and multi-tissue methylation clocks for age estimation in toothed whales and dolphins
The development of a precise blood or skin tissue DNA Epigenetic Aging Clock for Odontocete (OEAC) would solve current age estimation inaccuracies...
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PCDH19 Pathogenic Variants in Males: Expanding the Phenotypic Spectrum
Protocadherin-19 (PCDH19) pathogenic variants cause an infantile onset epilepsy syndrome called Girls Clustering Epilepsy due to the vast majority of...
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Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
Probing epigenetic features on DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we use nanopore...
