ArticleNucleic acids research2016
Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 23 citations in OpenAlex.
- STATISTICAL CURVE MODELS FOR INFERRING 3D CHROMATIN ARCHITECTURE.The annals of applied statistics · 2024Article
- Assessing chromatin relocalization in 3D using the patient rule induction method.Biostatistics (Oxford, England) · 2023Article
- Does multi-way, long-range chromatin contact data advance 3D genome reconstruction?BMC bioinformatics · 2023Article
- Can 3D diploid genome reconstruction from unphased Hi-C data be salvaged?NAR genomics and bioinformatics · 2022Article
- Principal curve approaches for inferring 3D chromatin architecture.Biostatistics (Oxford, England) · 2022Article
- Chromatin Hubs: A biological and computational outlook.Computational and structural biotechnology journal · 2022Review
- G1/S transcription factors assemble in increasing numbers of discrete clusters through G1 phase.The Journal of cell biology · 2020Article
- Assessing stationary distributions derived from chromatin contact maps.BMC bioinformatics · 2020Article
- The Functional 3D Organization of Unicellular Genomes.Scientific reports · 2019Article
- The Rabl configuration limits topological entanglement of chromosomes in budding yeast.Scientific reports · 2019Article
- Improved accuracy assessment for 3D genome reconstructions.BMC bioinformatics · 2018Article
- Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Regulation of genome organization and gene expression by nuclear mechanotransduction.Nature reviews. Molecular cell biology · 2017Review
- 3D clustering of co-regulated genes and its effect on gene expression.Current genetics · 2017Review
- Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome.Nucleic acids research · 2017Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The spatial organization of the genome influences cellular function, notably gene regulation. Recent studies have assessed the three-dimensional (3D) co-localization of functional annotations (e.g. centromeres, long terminal repeats) using 3D genome reconstructions from Hi-C (genome-wide chromosome conformation capture) data; however, corresponding assessments for continuous functional genomic data (e.g. chromatin immunoprecipitation-sequencing (ChIP-seq) peak height) are lacking. Here, we demonstrate that applying bump hunting via the patient rule induction method (PRIM) to ChIP-seq data superposed on a Saccharomyces cerevisiae 3D genome reconstruction can discover 'functional 3D hotspots', regions in 3-space for which the mean ChIP-seq peak height is significantly elevated. For the transcription factor Swi6, the top hotspot by P-value contains MSB2 and ERG11 - known Swi6 target genes on different chromosomes. We verify this finding in a number of ways. First, this top hotspot is relatively stable under PRIM across parameter settings. Second, this hotspot is among the top hotspots by mean outcome identified by an alternative algorithm, k-Nearest Neighbor (k-NN) regression. Third, the distance between MSB2 and ERG11 is smaller than expected (by resampling) in two other 3D reconstructions generated via different normalization and reconstruction algorithms. This analytic approach can discover functional 3D hotspots and potentially reveal novel regulatory interactions.
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