Chromatin organization in red triangles

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In eukaryotic cells, DNA is tightly packed in the form chromatin. The basic structure of chromatin is a nucleosome composed of 147 bp DNA wrapped around eight histone proteins; two copies of H2A, H2B, H3 and H4. These histone proteins are decorated with pa ...

BackgroundChromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple species, tissue types, and differentiati ...

In mammals the circadian clock drives daily behavioural and physiological changes that resonate with environmental cues, which can be observed, for example, in the intricate timing of rest during the night and activity during the day in humans. The circadi ...

Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is c ...

The 'acidic patch' is a highly electronegative cleft on the histone H2A-H2B dimer in the nucleosome. It is a fundamental motif for protein binding and chromatin dynamics, but the cellular impact of targeting this potentially therapeutic site with exogenous ...

BACKGROUND: The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD g ...

The question of how self-interacting chromatin domains in interphase chromosomes are structured and generated dominates current discussions on eukaryotic chromosomes. Numerical simulations using standard polymer models have been helpful in testing the vali ...

Hox gene clusters of jaw vertebrates display a tight genomic organization, which has no equivalent in any other bilateria genomes sequenced thus far. It was previously argued that such a topological consolidation toward a condensed, metagenic structure was ...

Gene expression is dynamic and heterogeneous across all cell types. It serves several fundamental functions such as adaptation for changing environment and developing tissue specific phenotype and functionality during development and in adult organism. Con ...

Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide in ...

Chromatin condensation plays an important role in the regulation of gene expression. Recently, it was shown that the transcriptional activation of Hoxd genes during vertebrate digit development involves modifications in 3D interactions within and around th ...

Chromatin organization in red triangles

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Deciphering the chromatin binding mechanisms of human HP1 variants at the single-molecule level

Comparison of computational methods for the identification of topologically associating domains

Rhythmic and clock-dependent chromatin loops regulate circadian gene expression

Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions

Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation

Large scale genomic reorganization of topological domains at the HoxD locus

Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S-pombe

Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci

Chromatin organization, transcription factor dynamics and gene expression in higher eukaryotes with superresolution imaging and single molecule tracking

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states