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Article
Open AccessCharacterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling
The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due t...
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Article
Open AccessThe potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer
Three-dimensional (3D) epigenome remodeling is an important mechanism of gene deregulation in cancer. However, its potential as a target to counteract therapy resistance remains largely unaddressed. Here, we s...
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Article
Open AccessA first-in-class pan-lysyl oxidase inhibitor impairs stromal remodeling and enhances gemcitabine response and survival in pancreatic cancer
The lysyl oxidase family represents a promising target in stromal targeting of solid tumors due to the importance of this family in crosslinking and stabilizing fibrillar collagens and its known role in tumor ...
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Protocol
Target-Specific Profiling of RNA m5C Methylation Level Using Amplicon Sequencing
Map** the position and quantifying the level of 5-methylcytosine (m5C) as a modification in different types of cellular RNA is an important objective in the field of epitranscriptomics. Bisulfite conversion has...
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Article
Open AccessIdentification of DNA methylation biomarkers with potential to predict response to neoadjuvant chemotherapy in triple-negative breast cancer
Neoadjuvant chemotherapy (NAC) is used to treat triple-negative breast cancer (TNBC) prior to resection. Biomarkers that accurately predict a patient’s response to NAC are needed to individualise therapy and a...
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Article
Open AccessBRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer
BRG1 (encoded by SMARCA4) is a catalytic component of the SWI/SNF chromatin remodelling complex, with key roles in modulating DNA accessibility. Dysregulation of BRG1 is observed, but functionally uncharacterised...
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Article
Open AccessComprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels
DNA methylation is a well-studied epigenetic mark that is frequently altered in diseases such as cancer, where specific changes are known to reflect the type and severity of the disease. Therefore, there is a ...
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Article
Open AccessMultiple links between 5-methylcytosine content of mRNA and translation
5-Methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pu...
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Article
Open AccessAlterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer
Prostate cancer changes the phenotype of cells within the stromal microenvironment, including fibroblasts, which in turn promote tumour progression. Functional changes in prostate cancer-associated fibroblasts...
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Article
Open AccessEpigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer
Endocrine therapy resistance frequently develops in estrogen receptor positive (ER+) breast cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that 3-dimensional (3D) chromatin ...
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Article
Open AccessConstitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains
The architectural protein CTCF is a mediator of chromatin conformation, but how CTCF binding to DNA is orchestrated to maintain long-range gene expression is poorly understood. Here we perform RNAi knockdown t...
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Article
Open AccessMethylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes
Adipocytes support key metabolic and endocrine functions of adipose tissue. Lipid is stored in two major classes of depots, namely visceral adipose (VA) and subcutaneous adipose (SA) depots. Increased visceral...
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Article
Open AccessMonozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterised by the loss of upper and lower motor neurons. ALS exhibits high phenotypic variability including age and site of onset, an...
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Article
Open AccessIntegrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups
ATP-dependent chromatin remodelling complexes are responsible for establishing and maintaining the positions of nucleosomes. Chromatin remodellers are targeted to chromatin by transcription factors and non-cod...
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Article
Open AccessReplication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer
DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely un...
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Article
Open AccessEpigenomics of mammary gland development
Differentiation of stem cells into highly specialised cells requires gene expression changes brought about by remodelling of the chromatin architecture. During this lineage-commitment process, the majority of ...
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Article
Open AccessGuidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten
Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technolo...
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Protocol
Bisulphite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq)
Epigenetic regulation plays a critical role in gene expression, cellular differentiation, and disease. There is a complex interplay between the different layers of epigenetic information, including DNA methyla...
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Article
Open AccessAcetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer
Acetylation of the histone variant H2A.Z (H2A.Zac) occurs at active promoters and is associated with oncogene activation in prostate cancer, but its role in enhancer function is still poorly understood. Here w...
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Article
Open AccessComprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA
The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in resha** ...
