ArticlePLoS computational biology2017
Analysis of the relationship between coexpression domains and chromatin 3D organization.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Focus on single-gene effects limits discovery and interpretation of complex-trait-associated variants.American journal of human genetics · 2026Article
- Smoothie: efficient inference and integration of spatial co-expression networks from denoised spatial transcriptomics data.Communications biology · 2026Article
- De novo rates of aProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis.Nature cancer · 2024Article
- The essential role of architectural noncoding RNARNA (New York, N.Y.) · 2024Article
- The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis.GigaScience · 2024Article
- Transcription factor expression is the main determinant of variability in gene co-activity.Molecular systems biology · 2023Article
- Gemini: memory-efficient integration of hundreds of gene networks with high-order pooling.Bioinformatics (Oxford, England) · 2023Article
- A benchmark of computational pipelines for single-cell histone modification data.Genome biology · 2023Article
- Evolutionary honing in and mutational replacement: how long-term directed mutational responses to specific environmental pressures are possible.Theory in biosciences = Theorie in den Biowissenschaften · 2023Review
- Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains.Frontiers in genetics · 2023Article
- Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis.Communications biology · 2022Article
- The evolutionarily conserved arginyltransferase 1 mediates a pVHL-independent oxygen-sensing pathway in mammalian cells.Developmental cell · 2022Article
- Making sense of the linear genome, gene function and TADs.Epigenetics & chromatin · 2022Article
- Regulatory mechanisms ensuring coordinated expression of functionally related genes.Trends in genetics : TIG · 2022Review
- Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer.Journal of translational medicine · 2021Article
- Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.PLoS computational biology · 2021Article
- Gravitational Force-Induced 3D Chromosomal Conformational Changes Are Associated with Rapid Transcriptional Response in Human T Cells.International journal of molecular sciences · 2021Article
- The molecular basis, genetic control and pleiotropic effects of local gene co-expression.Nature communications · 2021Article
- Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers.Genome biology · 2021Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene order is not random in eukaryotic chromosomes, and co-regulated genes tend to be clustered. The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional (3D) organization are still unclear however. Here we have adapted a recently described method for identifying chromatin topologically associating domains (TADs) to identify coexpression domains (which we term "CODs"). Using human normal breast and breast cancer RNA-seq data, we have identified approximately 500 CODs. CODs in the normal and breast cancer genomes share similar characteristics but differ in their gene composition. COD genes have a greater tendency to be coexpressed with genes that reside in other CODs than with non-COD genes. Such inter-COD coexpression is maintained over large chromosomal distances in the normal genome but is partially lost in the cancer genome. Analyzing the relationship between CODs and chromatin 3D organization using Hi-C contact data, we find that CODs do not correspond to TADs. In fact, intra-TAD gene coexpression is the same as random for most chromosomes. However, the contact profile is similar between gene pairs that reside either in the same COD or in coexpressed CODs. These data indicate that co-regulated genes in the genome present similar patterns of contacts irrespective of the frequency of physical chromatin contacts between them.
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