Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

Wang, Xiaotao; Xu, Jie; Zhang, Baozhen; Hou, Ye; Song, Fan; Lyu, Huijue; Yue, Feng

doi:10.1038/s41592-021-01164-w

Cited by 107 publications

(120 citation statements)

References 51 publications

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“…A normalization similar to the above-mentioned approaches is applied to each CNV-block in the genome, separately, to remove the visibility bias CNVs create. Two recent examples for CNV-aware normalization are the NeoLoopFinder toolbox [144] and the HiNT tool [145] .…”

Section: How To Identify Changes In Ctcf Binding and 3d Genome Organi...mentioning

confidence: 99%

CTCF: A misguided jack-of-all-trades in cancer cells

Segueni

Noordermeer

2022

Computational and Structural Biotechnology Journal

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Section: How To Identify Changes In Ctcf Binding and 3d Genome Organi...mentioning

confidence: 99%

CTCF: A misguided jack-of-all-trades in cancer cells

Segueni

Noordermeer

2022

Computational and Structural Biotechnology Journal

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“…As DNA, folding may be considered at several levels, a compartment analysis was conducted at 0.25Mb resolution corresponding to open-closed chromatin domains in which the A and B compartments detected by Hi-C reflect the folding of chromosomes into euchromatin and heterochromatin, respectively. The alterations of copy number identified in MP41 and MP46 UM genomes (Supplementary Figure 8) can alter HiC interaction scores [24] (Supplementary Figure 9A, E and I, Supplementary Figure 10 A, E and I), and normalization is necessary to accurately decipher DNA topology. Multiple computational methods for HiC normalization were carried out (ICE, CAIC, and LOIC) on UM models and NM (Supplementary Figure 9 and 10) as performed previously on breast cancer cell lines [25].…”

Section: Resultsmentioning

confidence: 99%

Multi-omics comparison of malignant and normal uveal melanocytes reveals novel molecular features of uveal melanoma

Gentien

Saberi-Ansari

Servant

et al. 2022

Preprint

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Uveal Melanoma (UM) is a rare cancer resulting from the transformation of melanocytes residing in the uveal tract. Integrative analysis has identified four molecular and clinical subsets in UM. To improve our understanding of UM we performed extensive multi-omics characterization comparing pure melanoma populations obtained from two aggressive UM patient-derived xenograft models with normal choroidal melanocytes. Our study addresses for the first time DNA optical mapping, specific histone mark modifications, DNA topology analysis by Hi-C. Gene expression and cytogenetic analyses suggest that genomic instability is a hallmark of UM. Our study also identified a recurrent deletion in the BAP1 promoter which results in the absence of expression of BAP1 which is associated with high risk of metastases in UM patients. Chromatin topology changes are associated with up-regulation of PRAME, a recognized independent prognostic biomarker in UM and potential therapeutic target. Our findings illustrate how multi-omics integrative approaches can improve the understanding of tumorigenesis and reveals two novel mechanisms of gene expression dysregulation in UM.

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“…To identify new CDs in chromosome rearrangement areas, NeoLoopFinder was applied to help find newly emerged CDs in areas that had inversions, translocations, and deletions. [ 21 ]…”

Section: Methodsmentioning

confidence: 99%

“…[82] Neo-CDs Identification: To identify new CDs in chromosome rearrangement areas, NeoLoopFinder was applied to help find newly emerged CDs in areas that had inversions, translocations, and deletions. [21] Data Visualization: Integrative Genomics Viewer (IGV) was employed to interactively explore large comprehensive genomic data and visualize structural variations as described. [83] Annoroad Browser (https://github.…”

Section: Supporting Informationmentioning

confidence: 99%

Dynamic Interplay between Structural Variations and 3D Genome Organization in Pancreatic Cancer

et al. 2022

Advanced Science

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Structural variations (SVs) are the greatest source of variations in the genome and can lead to oncogenesis. However, the identification and interpretation of SVs in human cancer remain technologically challenging. Here, long-read sequencing is first employed to depict the signatures of structural variations in carcinogenesis of human pancreatic ductal epithelium. Then widespread reprogramming of the 3D chromatin architecture is revealed by an in situ Hi-C technique. Integrative analyses indicate that the distribution pattern of SVs among the 3D genome is highly cell-type specific and the bulk remodeling effects of SVs in the chromatin organization partly depend on intercellular genomic heterogeneity. Meanwhile, contact domains tend to minimize these disrupting effects of SVs within local adjacent genomic regions to maintain overall stability. Notably, complex genomic rearrangements involving two key driver genes CDKN2A and SMAD4 are identified, and their influence on the expression of oncogenes MIR31HG, MYO5B, etc., are further elucidated from both a linear view and 3D perspective. Overall, this work provides a genome-wide resource and highlights the impact, complexity, and dynamicity of the interplay between structural variations and high-order chromatin organization, which expands the current understanding of the pathogenesis of SVs in human cancer.

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Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

Cited by 107 publications

References 51 publications

CTCF: A misguided jack-of-all-trades in cancer cells

CTCF: A misguided jack-of-all-trades in cancer cells

Multi-omics comparison of malignant and normal uveal melanocytes reveals novel molecular features of uveal melanoma

Dynamic Interplay between Structural Variations and 3D Genome Organization in Pancreatic Cancer

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