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Article
cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers
The canonical BRG/BRM-associated factor (cBAF) complex is essential for chromatin opening at enhancers in mammalian cells. However, the nature of the open chromatin remains unclear. Here, we show that, in addi...
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Article
Open AccessTranscription modulates chromatin dynamics and locus configuration sampling
In living cells, the 3D structure of gene loci is dynamic, but this is not revealed by 3C and FISH experiments in fixed samples, leaving a notable gap in our understanding. To overcome these limitations, we ap...
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Article
Open AccessHuman centromere repositioning activates transcription and opens chromatin fibre structure
Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions ...
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Protocol
Predictive Polymer Models for 3D Chromosome Organization
Polymer simulations and predictive mechanistic modelling are increasingly used in conjunction with experiments to study the organization of eukaryotic chromosomes. Here we review some of the most prevalent mod...
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Article
cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing
Inappropriate stimulation or defective negative regulation of the type I interferon response can lead to autoinflammation. In genetically uncharacterized cases of the type I interferonopathy Aicardi–Goutières ...
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Article
Mechanistic modeling of chromatin folding to understand function
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organization and function. As datasets increase in size and complexity, it becomes a challenge to rea...
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Article
Negative supercoil at gene boundaries modulates gene topology
Transcription challenges the integrity of replicating chromosomes by generating topological stress and conflicts with forks1,2. The DNA topoisomerases Top1 and Top2 and the HMGB family protein Hmo1 assist DNA rep...
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Article
cGAS surveillance of micronuclei links genome instability to innate immunity
The cytoplasmic DNA sensor cGAS detects DNA in ruptured micronuclei and activates an innate immune response.
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Article
Regulation of transcriptional activators by DNA-binding domain ubiquitination
Ubiquitin is a key component of the regulatory network that maintains gene expression in eukaryotes, yet the molecular mechanism(s) by which non-degradative ubiquitination modulates transcriptional activator (...
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Article
Open AccessGenome organization: experiments and modeling
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Article
Open AccessEffects of DNA supercoiling on chromatin architecture
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of k...
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Article
Open AccessEffects of DNA supercoiling on chromatin architecture
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of k...
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Article
Characterisation of Osteoprotegerin Autoantibodies in Coeliac Disease
Autoantibodies neutralising the effect of the bone regulatory cytokine osteoprotegerin (OPG) have been described in a patient with severe osteoporosis and coeliac disease. This study aimed to determine the pre...
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Article
Open AccessGenomic profiling of type-1 adult diabetic and aged normoglycemic mouse liver
Hyperglycemia induces chromatin remodeling with consequences on differential gene expression in mouse hepatocytes, similar to what occurs during aging. The liver is the central organ for the regulation of gluc...
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Article
Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures
A genome-wide map** approach of DNA supercoiling in cells demonstrates that the genome is organized in supercoiling domains. Domains are formed and remodeled by transcription and topoisomerase activity and a...
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Article
DNA methylation in mouse embryonic stem cells and development
Mammalian development is associated with considerable changes in global DNA methylation levels at times of genomic reprogramming. Normal DNA methylation is essential for development but, despite considerable a...
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Article
Open AccessChromatin structure and evolution in the human genome
Evolutionary rates are not constant across the human genome but genes in close proximity have been shown to experience similar levels of divergence and selection. The higher-order organisation of chromosomes h...
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Article
The role of chromatin structure in regulating the expression of clustered genes
It is not only functionally related genes that cluster in the mammalian genome: there also seems to be general clustering of apparently unrelated genes.
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Article
Open AccessAltered protein dynamics of disease-associated lamin A mutants
Recent interest in the function of the nuclear lamina has been provoked by the discovery of lamin A/C mutations in the laminopathy diseases. However, it is not understood why mutations in lamin A give such a r...
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Article
The Williams syndrome transcription factor interacts with PCNA to target chromatin remodelling by ISWI to replication foci
Chromatin states have to be faithfully duplicated during DNA replication to maintain cell identity. It is unclear whether or how ATP-dependent chromatin-remodelling factors are involved in this process. Here w...
