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Article
Open AccessCirculating cell-free DNA methylation mirrors alterations in cerebral patterns in epilepsy
DNA methylation profiling of circulating cell-free DNA (cfDNA) has rapidly become a promising strategy for biomarker identification and development. The cell-type-specific nature of DNA methylation patterns an...
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Article
Open AccessEpigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines
COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myelo...
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Article
Open AccessEpigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci
Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the princ...
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Article
Open AccessSampling time-dependent artifacts in single-cell genomics studies
Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample ...
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Article
Open AccessInflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis
Sepsis, a life-threatening organ dysfunction caused by a dysregulated systemic immune response to infection, associates with reduced responsiveness to subsequent infections. How such tolerance is acquired is n...
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Article
Open AccessIL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation
The role of cytokines in establishing specific transcriptional programmes in innate immune cells has long been recognized. However, little is known about how these extracellular factors instruct innate immune ...
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Article
Open AccessNF-κB-direct activation of microRNAs with repressive effects on monocyte-specific genes is critical for osteoclast differentiation
Monocyte-to-osteoclast conversion is a unique terminal differentiation process that is exacerbated in rheumatoid arthritis and bone metastasis. The mechanisms implicated in upregulating osteoclast-specific gen...
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Protocol
Chromatin Immunoprecipitation
Chromatin plays important functions in regulating many biological processes, including DNA transcription, replication, and repair. The use of chromatin immunoprecipitation (ChIP) assays has contributed enormou...
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Article
Open AccessPU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation
DNA methylation is a key epigenetic mechanism for driving and stabilizing cell-fate decisions. Local deposition and removal of DNA methylation are tightly coupled with transcription factor binding, although th...
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Article
Open AccessThe B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion
Epstein-Barr virus (EBV) infection is a well characterized etiopathogenic factor for a variety of immune-related conditions, including lymphomas, lymphoproliferative disorders and autoimmune diseases. EBV-medi...
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Chapter
Examining DNA–Protein Interactions with Genome-Wide Chromatin Immunoprecipitation Analysis
Understanding the mechanisms by which genomic information is hierarchically organized and used by different cell and tissue types under different physiological conditions requires the detailed analysis of the ...
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Article
A truncating mutation of HDAC2 in human cancers confers resistance to histone deacetylase inhibition
Disruption of histone acetylation patterns is a common feature of cancer cells, but very little is known about its genetic basis. We have identified truncating mutations in one of the primary human histone dea...
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Article
Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer
CpG island hypermethylation and global genomic hypomethylation are common epigenetic features of cancer cells. Less attention has been focused on histone modifications in cancer cells. We characterized post-tr...
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Article
The impact of MECP2 mutations in the expression patterns of Rett syndrome patients
Rett syndrome (RTT), the second most common cause of mental retardation in females, has been associated with mutations in MeCP2, the archetypical member of the methyl-CpG binding domain (MBD) family of protein...
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Article
Stage-specific chromosomal association of Drosophila dMBD2/3 during genome activation
The Drosophila gene dMBD2/3 encodes a protein with significant homologies to the mammalian methyl-DNA binding proteins MBD2 and MBD3. These proteins are essential components of chromatin complexes involved in ep...
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Article
Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation
Methylation of DNA at the dinucleotide CpG is essential for mammalian development and is correlated with stable transcriptional silencing1,2,3. This transcriptional silencing has recently been linked at a molecul...