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Iterative correction of Hi-C data reveals hallmarks of chromosome organization
ICE (iterative correction and eigenvector decomposition) provides insight into inter- and intrachromosome interaction patterns.
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Open AccessChromosomal architecture changes upon cell differentiation
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Open AccessPolymer models of topological insulators
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Open AccessS cerevisiae genome as a confined equilibrium polymer brush
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Open AccessPolymer models of yeast S. cerevisiae genome organization
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Super-resolution imaging reveals distinct chromatin folding for different epigenetic states
Using super-resolution imaging to directly observe the three-dimensional organization of Drosophila chromatin at a scale spanning sizes from individual genes to entire gene regulatory domains, the authors find th...
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Open AccessGenome-wide transcription start site map** of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation
Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinf...
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Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
Using a single-nucleus Hi-C protocol, the authors find that spatial organization of chromatin during oocyte-to-zygote transition differs between paternal and maternal nuclei within a single-cell zygote.
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Article
FISH-ing for captured contacts: towards reconciling FISH and 3C
This Analysis explores the relationship between chromosome conformation capture (for example, Hi-C) and FISH datasets, and uses simulations to reconcile measurements from the two technologies.
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Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments
Accumulation of trimethylation of histone H3 at lysine 4 (H3K4me3) on immune-related gene promoters underlies robust transcription during trained immunity. However, the molecular basis for this remains unknown...
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Publisher Correction: Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments
In the version of this article initially published, ‘+’ and ‘–’ labels were missing from the graph keys at the bottom of Fig. 8d. The error has been corrected in the HTML and PDF versions of the article.
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Heterochromatin drives compartmentalization of inverted and conventional nuclei
The nucleus of mammalian cells displays a distinct spatial segregation of active euchromatic and inactive heterochromatic regions of the genome1,2. In conventional nuclei, microscopy shows that euchromatin is loc...
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Publisher Correction: Heterochromatin drives compartmentalization of inverted and conventional nuclei
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Open AccessThe genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos
Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes ...
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Open AccessThe 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data
The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal ( ...
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Open AccessAuthor Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data
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Open AccessLineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques
Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that ...
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Open AccessDiverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers
The relationships between chromosomal compartmentalization, chromatin state and function are poorly understood. Here by profiling long-range contact frequencies in HCT116 colon cancer cells, we distinguish thr...
