ArticlePLoS computational biology2018
4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Regulation of WNT16 in bone may involve upstream enhancers within CPED1.Scientific reports · 2025Article
- Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells.PLoS genetics · 2022Article
- CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression.Nature communications · 2021Article
- 3D reconstruction of genomic regions from sparse interaction data.NAR genomics and bioinformatics · 2021Article
- Age-related and disease locus-specific mechanisms contribute to early remodelling of chromatin structure in Huntington's disease mice.Nature communications · 2021Article
- Genetics and Genomics ofInternational journal of molecular sciences · 2021Article
- Chromatin topology and the timing of enhancer function at theProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Functional Assessment of Coding and Regulatory Variants From theJBMR plus · 2020Article
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Authors and funding
6 authors.
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Abstract
The use of 3C-based methods has revealed the importance of the 3D organization of the chromatin for key aspects of genome biology. However, the different caveats of the variants of 3C techniques have limited their scope and the range of scientific fields that could benefit from these approaches. To address these limitations, we present 4Cin, a method to generate 3D models and derive virtual Hi-C (vHi-C) heat maps of genomic loci based on 4C-seq or any kind of 4C-seq-like data, such as those derived from NG Capture-C. 3D genome organization is determined by integrative consideration of the spatial distances derived from as few as four 4C-seq experiments. The 3D models obtained from 4C-seq data, together with their associated vHi-C maps, allow the inference of all chromosomal contacts within a given genomic region, facilitating the identification of Topological Associating Domains (TAD) boundaries. Thus, 4Cin offers a much cheaper, accessible and versatile alternative to other available techniques while providing a comprehensive 3D topological profiling. By studying TAD modifications in genomic structural variants associated to disease phenotypes and performing cross-species evolutionary comparisons of 3D chromatin structures in a quantitative manner, we demonstrate the broad potential and novel range of applications of our method.
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