Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture

Lin, Dazhen; Pan, Hong; Zhang, Siheng; Xu, Weize; Jamal, Muhammad; Yan, Keji; Lei, Yingying; Li, Liang; Ruan, Yijun; Fu, Zhen F.; Li, Guoliang; Cao, Gang

doi:10.1038/s41588-018-0111-2

Cited by 83 publications

(67 citation statements)

References 42 publications

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“…We used the 4-cutter restriction enzyme Mbol, whereas the other study used the 6-cutter restriction enzyme HindIII. MboI targets 7,227,513 sites in the human genome, which is about ten-fold more than HindIII (846,132), and thus could theoretically capture more chromosome contact information (Lin et al, 2018). Second, this discrepancy might depend on the genomic regions that were examined.…”

Section: Discussionmentioning

confidence: 99%

Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells

Higashijima

Matsui

Shimamura

et al. 2018

Preprint

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C.K.G.), kanki@lsbm.org (Y.K.) SUMMARY Lysine 9 di-methylation and lysine 27 tri-methylation of histone H3 (H3K9me2 and H3K27me3) are generally linked to gene repression. However, the functions of repressive histone methylation dynamics during inflammatory responses remain enigmatic. We found that tumor necrosis factor (TNF)-α rapidly induces the co-occupancy of lysine demethylases 7A (KDM7A) and 6A (UTX) with nuclear factor kappa-B (NF-κB) recruited elements in human endothelial cells. KDM7A and UTX demethylate H3K9me2 and H3K27me3, respectively, and both are required for activation of NF-κB-dependent inflammatory genes. Chromosome conformation capture-based methods demonstrated increased interactions between TNF-α-induced super enhancers at NF-κB-relevant loci, coinciding with KDM7A-and UTX-recruitment. Simultaneous inhibition of KDM7A and UTX significantly reduced leukocyte adhesion in mice, establishing the biological and potential translational relevance of this mechanism. Collectively, these findings suggest that rapid erasure of repressive histone marks by KDM7A and UTX is essential for NF-κB-dependent regulation of genes that control inflammatory responses of endothelial cells. (150 words) KEYWORDS Inflammation, atherosclerosis, histone modification enzyme, repressive histone mark, super enhancer, chromatin architecture, chromatin conformation change HIGHLIGHTS 1. KDM7A and UTX cooperatively control NF-κB-dependent transcription in vascular endothelial cells. 2. Demethylation of repressive histone marks by KDM7A and UTX is critical for early inflammatory responses. 3. KDM7A and UTX are associated with TNF-α-induced looping of super enhancers. 4. Pharmacological inhibition of KDM7A and UTX reduces leukocyte adhesive interactions with endothelial cells in mice.

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Section: Discussionmentioning

confidence: 99%

Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells

Higashijima

Matsui

Shimamura

et al. 2018

Preprint

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“…DLO Hi-C Tool was used to detect the linker of previously published DLO Hi-C data [10]. The test data includes 1 DLO Hi-C library of K562 cell line, 3 replicates of in situ DLO Hi-C library of K562 cell line and two replicates of in situ DLO Hi-C library of THP-1 cell line.…”

Section: Resultsmentioning

confidence: 99%

“…DLO Hi-C Tool was used to process DLO Hi-C and in situ DLO Hi-C datasets published by Lin et al [10]. We compared the computation time and the number of reads after every step.…”

Section: Pre-processingmentioning

confidence: 99%

“…Some of the paired-end reads are invalid interactions, such as re-ligation and self-ligation reads [10]. In addition, there are some duplicate reads produced by polymerase chain reaction (PCR).…”

Section: Classification Of Paired-end Reads Based On Alignmentmentioning

confidence: 99%

“…Although Hi-C has greatly advanced our understanding of the 3D organization of genomes, it is limited with high randomly ligated DNA noise, high cost and complex experimental procedures. To overcome the limitations of Hi-C method, we developed a simple, cost-effective and low-noise method, Digestion-Ligation-Only Hi-C (DLO Hi-C) [10]. The key advantages of DLO Hi-C are as follows.…”

Section: Introductionmentioning

confidence: 99%

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

Pan

Jiang

et al. 2019

Preprint

Self Cite

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Background: It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (Chromosome Conformation Capture) and its derived methods are now widely applied to investigate genome organizations and gene regulation. Digestion-Ligation-Only Hi-C (DLO Hi-C) is a new technology with high efficiency and effective cost for whole-genome chromosome conformation capture.Results: Here, we introduce DLO Hi-C Tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied DLO Hi-C Tool to different DLO Hi-C datasets, and demonstrated its ability of processing large data in multi-threading. Conclusions:DLO Hi-C Tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.

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Alteration of chromatin high‐order conformation associated with oxaliplatin resistance acquisition in colorectal cancer cells

Shang

Jiao

et al. 2023

Exploration

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Oxaliplatin is a first‐line chemotherapy drug widely adopted in colorectal cancer (CRC) treatment. However, a large proportion of patients tend to become resistant to oxaliplatin, causing chemotherapy to fail. At present, researches on oxaliplatin resistance mainly focus on the genetic and epigenetic alterations during cancer evolution, while the characteristics of high‐order three‐dimensional (3D) conformation of genome are yet to be explored. In order to investigate the chromatin conformation alteration during oxaliplatin resistance, we performed multi‐omics study by combining DLO Hi‐C, ChIP‐seq as well as RNA‐seq technologies on the established oxaliplatin‐resistant cell line HCT116‐OxR, as well as the control cell line HCT116. The results indicate that 19.33% of the genome regions have A/B compartments transformation after drug resistance, further analysis of the genes converted by A/B compartments reveals that the acquisition of oxaliplatin resistance in tumor cells is related to the reduction of reactive oxygen species and enhanced metastatic capacity. Our research reveals the spatial chromatin structural difference between CRC cells and oxaliplatin resistant cells based on the DLO Hi‐C and other epigenetic omics experiments. More importantly, we provide potential targets for oxaliplatin‐resistant cancer treatment and a new way to investigate drug resistance behavior under the perspective of 3D genome alteration.

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Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture

Cited by 83 publications

References 42 publications

Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells

Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells

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

Alteration of chromatin high‐order conformation associated with oxaliplatin resistance acquisition in colorectal cancer cells

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