ArticlePloS one2015
Inter-chromosomal contact networks provide insights into Mammalian chromatin organization.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 46 citations in OpenAlex.
- Extrachromosomal DNA associates with nuclear condensates and reorganizes chromatin structures to enhance oncogenic transcription.Cancer cell · 2025Article
- SLUR(M)-py: a SLURM powered Pythonic pipeline for parallel processing of 3D (Epi)genomic profiles.Epigenomics · 2025Article
- Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories.Genome research · 2024Article
- Human Coronavirus Infection Reorganizes Spatial Genomic Architecture in Permissive Lung Cells.Research square · 2024Article
- Potential roles of inter-chromosomal interactions in cell fate determination.Frontiers in cell and developmental biology · 2024Review
- Mapping the semi-nested community structure of 3D chromosome contact networks.PLoS computational biology · 2023Article
- Satellite DNAs and human sex chromosome variation.Seminars in cell & developmental biology · 2022Review
- Comparative 3D genome architecture in vertebrates.BMC biology · 2022Article
- Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions.Nature communications · 2021Article
- Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.Cancer cell · 2021Article
- RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture.Frontiers in genetics · 2021Article
- Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.Nature communications · 2020Article
- Dynamic evolution of great ape Y chromosomes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Network-based method for regions with statistically frequent interchromosomal interactions at single-cell resolution.BMC bioinformatics · 2020Article
- Evidence of constraint in the 3D genome for trans-splicing in human cells.Science China. Life sciences · 2020Article
- Article
- Revealing Gene Function and Transcription Relationship by Reconstructing Gene-Level Chromatin Interaction.Computational and structural biotechnology journal · 2019Article
- Nuclear organization mediates cancer-compromised genetic and epigenetic control.Advances in biological regulation · 2018Review
- Computational Methods for Assessing Chromatin Hierarchy.Computational and structural biotechnology journal · 2018Review
- FOXO3 longevity interactome on chromosome 6.Aging cell · 2017Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent advent of conformation capture techniques has provided unprecedented insights into the spatial organization of chromatin. We present a large-scale investigation of the inter-chromosomal segment and gene contact networks in embryonic stem cells of two mammalian organisms: humans and mice. Both interaction networks are characterized by a high degree of clustering of genome regions and the existence of hubs. Both genomes exhibit similar structural characteristics such as increased flexibility of certain Y chromosome regions and co-localization of centromere-proximal regions. Spatial proximity is correlated with the functional similarity of genes in both species. We also found a significant association between spatial proximity and the co-expression of genes in the human genome. The structural properties of chromatin are also species specific, including the presence of two highly interactive regions in mouse chromatin and an increased contact density on short, gene-rich human chromosomes, thereby indicating their central nuclear position. Trans-interacting segments are enriched in active marks in human and had no distinct feature profile in mouse. Thus, in contrast to interactions within individual chromosomes, the inter-chromosomal interactions in human and mouse embryonic stem cells do not appear to be conserved.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.