DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis

Pan, Hong; Jiang, Hao; Xu, Weize; Lin, Dazhen; Xu, Qian; Cao, Gang; Li, Guoliang

doi:10.1101/764332

Cited by 3 publications

(3 citation statements)

References 18 publications

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“…First, quality control of raw fastq files was performed with FastQC v0.11.8 (Andrews, 2010). The DLO Hi-C tool (Hong et al, 2019) was used to process the Hi-C data generated by the Digestion-ligation-only Hi-C technique (Lin et al, 2018). This tool removes pair end tags (PETs) of self-ligation, re-ligation, and dangling pairs.…”

Section: Hi-c Data Processing and Breakpoint Detectionmentioning

confidence: 99%

Structural Variations of the 3D Genome Architecture in Cervical Cancer Development

Adeel

Jiang

Arega

et al. 2021

Front. Cell Dev. Biol.

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Human papillomavirus (HPV) integration is the major contributor to cervical cancer (CC) development by inducing structural variations (SVs) in the human genome. SVs are directly associated with the three-dimensional (3D) genome structure leading to cancer development. The detection of SVs is not a trivial task, and several genome-wide techniques have greatly helped in the identification of SVs in the cancerous genome. However, in cervical cancer, precise prediction of SVs mainly translocations and their effects on 3D-genome and gene expression still need to be explored. Here, we have used high-throughput chromosome conformation capture (Hi-C) data of cervical cancer to detect the SVs, especially the translocations, and validated it through whole-genome sequencing (WGS) data. We found that the cervical cancer 3D-genome architecture rearranges itself as compared to that in the normal tissue, and 24% of the total genome switches their A/B compartments. Moreover, translocation detection from Hi-C data showed the presence of high-resolution t(4;7) (q13.1; q31.32) and t(1;16) (q21.2; q22.1) translocations, which disrupted the expression of the genes located at and nearby positions. Enrichment analysis suggested that the disrupted genes were mainly involved in controlling cervical cancer-related pathways. In summary, we detect the novel SVs through Hi-C data and unfold the association among genome-reorganization, translocations, and gene expression regulation. The results help understand the underlying pathogenicity mechanism of SVs in cervical cancer development and identify the targeted therapeutics against cervical cancer.

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Section: Hi-c Data Processing and Breakpoint Detectionmentioning

confidence: 99%

Structural Variations of the 3D Genome Architecture in Cervical Cancer Development

Adeel

Jiang

Arega

et al. 2021

Front. Cell Dev. Biol.

Self Cite

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“…DLO Hi-C data were processed using the DLO Hi-C Tool (44). In detail, the linkers were filtered first.…”

Section: Dlo Hi-c Data Analysismentioning

confidence: 99%

“…The clean reads were mapped to one new merged genome that contained the swine genome (v 10.2) and PRV genome. The self-ligation and religation reads were removed using the DLO Hi-C Tool (44). The iterative correction method (45) was performed to normalize interaction matrixes at different resolutions to remove the bias of raw matrices.…”

Section: Dlo Hi-c Data Analysismentioning

confidence: 99%

RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription

et al. 2021

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Like most DNA viruses, herpesviruses precisely deliver their genomes into the sophisticatedly organized nuclei of the infected host cells to initiate subsequent transcription and replication. However, it remains elusive how the viral genome specifically interacts with the host genome and hijacks host transcription machinery. Using pseudorabies virus (PRV) as model virus, we performed chromosome conformation capture assays to demonstrate a genome-wide specific trans-species chromatin interaction between the virus and host. Our data show that the PRV genome is delivered by the host DNA binding protein RUNX1 into the open chromatin and active transcription zone. This facilitates virus hijacking host RNAPII to efficiently transcribe viral genes, which is significantly inhibited by either a RUNX1 inhibitor or RNA interference. Together, these findings provide insights into the chromatin interaction between viral and host genomes and identify new areas of research to advance the understanding of herpesvirus genome transcription.

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Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data

Adeel

Rehman

Zhang

et al. 2022

Genes

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Complex chromosomal rearrangements such as translocations play a critical role in oncogenesis. Translocation detection is vital to decipher their biological role in activating cancer-associated mechanisms. High-throughput chromosomal conformations capture (Hi-C) data have shown promising progress in unveiling the genome variations in a disease condition. Until now, multiple structural data (Hi-C)-based methods are available that can detect translocations in cancer genomes. However, the consistency and specificity of Hi-C-based translocation results still need to be validated with conventional methods. This study used Hi-C data of cancerous cell lines, namely lung cancer (A549), Chronic Myelogenous Leukemia (K562), and Acute Monocytic Leukemia (THP-1), to detect the translocations. The results were cross-validated through whole-genome sequencing (WGS) and paired-read analysis. Moreover, PCR amplification validated the presence of translocated reads in different chromosomes. By integrating different data types, we showed that the results of Hi-C data are as reliable as WGS and can be utilized as an assistive method for detecting translocations in the diseased genome. Our findings support the utility of Hi-C technology to detect the translocations and study their effects on the three-dimensional architecture of the genome in cancer condition.

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DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis

Cited by 3 publications

References 18 publications

Structural Variations of the 3D Genome Architecture in Cervical Cancer Development

Structural Variations of the 3D Genome Architecture in Cervical Cancer Development

RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription

Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data

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