Exonuclease combinations reduce noises in 3D genomics technologies

Kong, Siyuan; Li, Qing; Zhang, Gaolin; Li, Qiujia; Huang, Qitong; Huang, Lei; Zhang, Hui; Huang, Yinghua; Peng, Yanling; Qin, Baoming; Zhang, Yubo

doi:10.1093/nar/gkaa106

Cited by 6 publications

(3 citation statements)

References 50 publications

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“…Single-cell epigenomes have the potential to provide a deeper understanding of cell type-specific gene regulatory procedures and how they change during development in response to environmental cues and disease pathogenesis. The current experimental single-cell platforms for analyzing different epigenomic features focus on DNA modification, histone modification, DNA-protein interaction, chromatin accessibility, and 3D chromatin conformation ( Kong et al, 2020a ; Preissl et al, 2022 ).…”

Section: The Methodological Progress Of Single-cell Omics and Single-...mentioning

confidence: 99%

Single-cell omics: A new direction for functional genetic research in human diseases and animal models

Kong

Tian

et al. 2023

Front. Genet.

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Over the past decade, with the development of high-throughput single-cell sequencing technology, single-cell omics has been emerged as a powerful tool to understand the molecular basis of cellular mechanisms and refine our knowledge of diverse cell states. They can reveal the heterogeneity at different genetic layers and elucidate their associations by multiple omics analysis, providing a more comprehensive genetic map of biological regulatory networks. In the post-GWAS era, the molecular biological mechanisms influencing human diseases will be further elucidated by single-cell omics. This review mainly summarizes the development and trend of single-cell omics. This involves single-cell omics technologies, single-cell multi-omics technologies, multiple omics data integration methods, applications in various human organs and diseases, classic laboratory cell lines, and animal disease models. The review will reveal some perspectives for elucidating human diseases and constructing animal models.

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Section: The Methodological Progress Of Single-cell Omics and Single-...mentioning

confidence: 99%

Single-cell omics: A new direction for functional genetic research in human diseases and animal models

Kong

Tian

et al. 2023

Front. Genet.

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“…To investigate these “minor changes”, a number of 3D genomics techniques have been developed. These include chromosome conformation capture (3C)-based technologies, such as chromosome conformation capture-on-chip (4C) [ 34 ], chromosome conformation capture carbon copy (5C) [ 35 ], high-throughput/resolution chromosome conformation capture (Hi-C) [ 36 ], Single-cell Hi-C [ 37 ], eHi-C [ 38 ], in 3D genomics, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) [ 39 ], and related methods, which have enabled the discovery of transcriptional regulatory elements, especially enhancers, and their effects on gene expression ( Figure 1 ). In addition, various methods, such as self-transcribing active regulatory region sequencing (STARR-seq), chromatin immunoprecipitation sequencing (ChIP-seq) [ 40 , 41 ], DNase-seq, site-specific integration FACS-sequencing (SIF-seq), assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq), robust statistical estimation (ROSE) algorithm, in situ Hi-C followed by chromatin immunoprecipitation (HiChIP), have been widely used for the identification and annotation of enhancers and super enhancers (annotations of enhancer and super enhancer are described in detail in Section 4 ).…”

Section: The Development Of Precision Biologymentioning

confidence: 99%

Exploring the Role of Enhancer-Mediated Transcriptional Regulation in Precision Biology

Wang

Liu

Luo

et al. 2023

IJMS

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The emergence of precision biology has been driven by the development of advanced technologies and techniques in high-resolution biological research systems. Enhancer-mediated transcriptional regulation, a complex network of gene expression and regulation in eukaryotes, has attracted significant attention as a promising avenue for investigating the underlying mechanisms of biological processes and diseases. To address biological problems with precision, large amounts of data, functional information, and research on the mechanisms of action of biological molecules is required to address biological problems with precision. Enhancers, including typical enhancers and super enhancers, play a crucial role in gene expression and regulation within this network. The identification and targeting of disease-associated enhancers hold the potential to advance precision medicine. In this review, we present the concepts, progress, importance, and challenges in precision biology, transcription regulation, and enhancers. Furthermore, we propose a model of transcriptional regulation for multi-enhancers and provide examples of their mechanisms in mammalian cells, thereby enhancing our understanding of how enhancers achieve precise regulation of gene expression in life processes. Precision biology holds promise in providing new tools and platforms for discovering insights into gene expression and disease occurrence, ultimately benefiting individuals and society as a whole.

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“…Due to proximity ligation strategy in Hi-C, noise could be generated during the process (Kong and Zhang, 2019). Extracting reliable gene loops from the high-noise Hi-C data usually requires deep sequencing and significant bioinformatics efforts (Kong et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

BL-Hi-C reveals the 3D genome structure ofBrassicacrops with high efficiency and sensitivity

Zhang¹,

Zhao²,

Liang³

et al. 2023

Preprint

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High-throughput chromatin conformation capture (Hi-C) technologies can be used to investigate the three-dimensional genomic structure of plants. However, complex protocol and high background noise in Hi-C hinder its practical application in plant 3D genomics. Here, we took the approach of modified Bridge Linker Hi-C technology (BL-Hi-C) to explore plant 3D landscape. We modified the BL-Hi-C method by simplifing nuclei extraction step. By using Brassica rapa and Brassica oleracea, BL-Hi-C showed higher signal value and lower background noise than Hi-C. The high sensitivity of BL-Hi-C was further demonstrated by its capacity to identify gene loops involving BrFLC1, BrFLC2 and BrFLC3 which were undetectable in Hi-C. BL-Hi-C also showed promising performance with input as low as 100 mg leaf tissue. By analyzing of the generated data from BL-Hi-C, we found that the simulated 3D genome structure of B. rapa leaf cells was Bouquet configuration. Our results showed that the modified BL-Hi-C is a powerful tool for the investigation of plants' genomic organization, gene regulation, and genome assembly.

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Exonuclease combinations reduce noises in 3D genomics technologies

Cited by 6 publications

References 50 publications

Single-cell omics: A new direction for functional genetic research in human diseases and animal models

Single-cell omics: A new direction for functional genetic research in human diseases and animal models

Exploring the Role of Enhancer-Mediated Transcriptional Regulation in Precision Biology

BL-Hi-C reveals the 3D genome structure ofBrassicacrops with high efficiency and sensitivity

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