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Articles by Boyan Bonev
Deciphering glioma susceptibility - Nature Cell Biology
The regulatory mechanisms that drive oncogene expression in gliomas remain poorly understood. A study now identifies a role for widespread rearrangements of the enhancer connectome. Such rearrangements are linked to known genetic risk variants, revealing how genetic predisposition contributes to malignancy.
Direct neuronal reprogramming of mouse astrocytes is associated with multiscale epigenome remodeling and requires Yy1 - Nature Neuroscience
Abstract Direct neuronal reprogramming is a promising approach to regenerate neurons from local glial cells. However, mechanisms of epigenome remodeling and co-factors facilitating this process are unclear. In this study, we combined single-cell multiomics with genome-wide profiling of three-dimensional nuclear architecture and DNA methylation in mouse astrocyte-to-neuron reprogramming mediated by Neurogenin2 (Ngn2) and its phosphorylation-resistant form (PmutNgn2), respectively.
Quorum-sensing, intra- and inter-species competition in the staphylococci
In Gram-positive bacteria such as Staphylococcus aureus and the coagulase-negative staphylococci (CoNS), the accessory gene regulator (agr) is a highly conserved but polymorphic quorum-sensing system involved in colonization, virulence and biofilm development. Signalling via agr depends on the interaction of an autoinducing peptide (AIP) with AgrC, a transmembrane sensor kinase that, once phosphorylated activates the response regulator AgrA.
Evolutionary conservation and cell type specificity of nuclear compartments in the brain
In the cell nucleus, radial genome organization relative to the nuclear lamina exhibits both cell type–specific variability and evolutionarily conserved distribution. A recent study by Ahanger, Delgado et al. explores the in vivo spatial distribution of the genome in the brain and identifies conserved genomic localization across mammalian species that are correlated with gene expression states.
Interactions of polymyxin B with lipopolysaccharide-containing membranes
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Decoding the organization, dynamics, and function of the 4D genome
Summary Understanding how complex cell-fate decisions emerge at the molecular level is a key challenge in developmental biology. Despite remarkable progress in decoding the contribution of the linear epigenome, how spatial genome architecture functionally informs changes in gene expression remains unclear.
Regulation of single-cell genome organization into TADs and chromatin nanodomains
Abstract The genome folds into a hierarchy of three-dimensional structures within the nucleus. At the sub-megabase scale, chromosomes form topologically associating domains (TADs)1,2,3,4. However, how TADs fold in single cells is elusive. Here, we reveal TAD features inaccessible to cell population analysis by using super-resolution microscopy.
4D Genome Rewiring during Oncogene-Induced and Replicative Senescence
Highlights • Deep multi-omics characterization of replicative and oncogene-induced senescence • Senescence-associated heterochromatin domains (SAHDs) form SAHFs via 3D changes • DNMT1 is required for SAHF formation via regulation of HMGA2 expression • SAHF formation leads to expression of SAHF-adjacent genes via 3D chromatin contacts Summary To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome,...
Multiscale 3D Genome Rewiring during Mouse Neural Development
Global Reorganization of the 3D Genome during Neural Differentiation Transcription Is Correlated with but Not Sufficient to Induce Insulation at TAD Boundaries De Novo Active Gene Promoters and the Bodies of Exon-Rich Genes Interact at Multiple Genomic Scales Polycomb-Mediated Interactions Are Disrupted Independently of H3K27me3 during Neural Differentiation Cell-Type Specific Chromatin Folding Is Organized around the Neural Transcription Factors Pax6, NeuroD2, and Tbr1 In Vivo...
Principles of assessing bacterial susceptibility to antibiotics using the agar diffusion method
Objectives The agar diffusion assay is one method for quantifying the ability of antibiotics to inhibit bacterial growth. Interpretation of results from this assay relies on model-dependent analysis, which is based on the assumption that antibiotics diffuse freely in the solid nutrient medium. In many cases, this assumption may be incorrect, which leads to significant deviations of the predicted behaviour from the experiment and to inaccurate assessment of bacterial susceptibility to antibiotics.
Organization and function of the 3D genome
Nature Reviews Genetics 17, 661–678 (2016)In the original version of this article, the statement that CCCTC-binding factor (CTCF) is conserved in most bilaterians was incorrectly referenced. Reference 58 has now been corrected in the online version of the article to cite Heger, P., Marin, B., Bartkuhn, M., Schierenberg, E. & Wiehe, T. The chromatin insulator CTCF and the emergence of metazoan diversity. Proc. Natl Acad. Sci. USA 109, 17507–17512 (2012). The authors apologize for this error.
Organization and function of the 3D genome
Detecting DNA fragments that preferentially interact together on the basis of their proximity in the three-dimensional (3D) space was first used in 1993 (Ref. 135) and subsequently improved and expanded in 2002 (Ref. 136) to form the basis of all chromosome conformation capture (3C) technologies, including Hi-C (a high-throughput derivative of 3C)13. The first step of most 3C-based methods involves the formaldehyde crosslinking of cells.
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