ArticleMolecular cancer research : MCR2017
Nucleome Analysis Reveals Structure-Function Relationships for Colon Cancer.
Article in Molecular cancer research : MCR, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed, 35 citations in OpenAlex.
- Article
- Effectiveness of machine learning at modeling the relationship between Hi-C data and copy number variation.Quantitative biology (Beijing, China) · 2024Article
- The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells.Cell proliferation · 2024Article
- Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line.BMC genomics · 2023Article
- Chromatin Mechanisms Driving Cancer.Cold Spring Harbor perspectives in biology · 2022Review
- Epithelial Cells in 2D and 3D Cultures Exhibit Large Differences in Higher-order Genomic Interactions.Genomics, proteomics & bioinformatics · 2022Article
- Article
- Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.Cancer cell · 2021Article
- TCF7L2 silencing results in altered gene expression patterns accompanied by local genomic reorganization.Neoplasia (New York, N.Y.) · 2021Article
- Bioinformatics for The Prognostic Value and Function of Cubilin (CUBN) in Colorectal Cancer.Medical science monitor : international medical journal of experimental and clinical research · 2020Article
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
- Disordered chromatin packing regulates phenotypic plasticity.Science advances · 2020Article
- Biomaterial Scaffolds Recruit an Aggressive Population of Metastatic Tumor CellsCancer research · 2019Article
- Single Chromosome Aneuploidy Induces Genome-Wide Perturbation of Nuclear Organization and Gene Expression.Neoplasia (New York, N.Y.) · 2019Article
- The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions.Genome biology · 2018Article
- Integrative detection and analysis of structural variation in cancer genomes.Nature genetics · 2018Article
- Visual Pattern-Driven Exploration of Big Data.2018 International Symposium on Big Data Visual and Immersive Analytics (BDVA) : Konstanz, Germany, October 17 -19, 2018. IEEE International Symposium on Big Data Visual and Immersive Analytics (4th : 2018 : Konstanz, Germany) · 2018Article
- HiGlass: web-based visual exploration and analysis of genome interaction maps.Genome biology · 2018Article
- Identification of copy number variations and translocations in cancer cells from Hi-C data.Bioinformatics (Oxford, England) · 2018Article
- HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples.IEEE transactions on visualization and computer graphics · 2018Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
Chromosomal translocations and aneuploidy are hallmarks of cancer genomes; however, the impact of these aberrations on the nucleome (i.e., nuclear structure and gene expression) is not yet understood. Here, the nucleome of the colorectal cancer cell line HT-29 was analyzed using chromosome conformation capture (Hi-C) to study genome structure, complemented by RNA sequencing (RNA-seq) to determine the consequent changes in genome function. Importantly, translocations and copy number changes were identified at high resolution from Hi-C data and the structure-function relationships present in normal cells were maintained in cancer. In addition, a new copy number-based normalization method for Hi-C data was developed to analyze the effect of chromosomal aberrations on local chromatin structure. The data demonstrate that at the site of translocations, the correlation between chromatin organization and gene expression increases; thus, chromatin accessibility more directly reflects transcription. In addition, the homogeneously staining region of chromosome band 8q24 of HT-29, which includes the MYC oncogene, interacts with various loci throughout the genome and is composed of open chromatin. The methods, described herein, can be applied to the assessment of the nucleome in other cell types with chromosomal aberrations.
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Registered trials
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.