Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy

Li, Angsheng; Yin, Xianchen; Xu, Bingxiang; Wang, Dan-Yang; Han, Jimin; Wu, Yi; Deng, Yun; Xiong, Ying; Zhang, Zhihua

doi:10.1038/s41467-018-05691-7

Cited by 63 publications

(105 citation statements)

References 40 publications

(81 reference statements)

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“…2f). Notably, 1.5 Mb, the average size of CD that we can best read off from the 50-kb resolution Hi-C data [17] used in this study, is also similar to the domain size detected by a recently proposed TAD detection algorithm called deDoC [53]. In essence, the concept of "graph structural entropy" used in deDoC is also based on global pattern recognition.…”

Section: Discussionsupporting

confidence: 60%

A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C

Kim

Bak

Liu

et al. 2019

Preprint

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Identifying chromatin domains (CDs) from Hi-C data is currently a central problem in genome research. Here we present Multi-CD (https://github.com/multi-cd), a unified method to discover CDs at various genomic scales. Integrating approaches from polymer physics, financial market fluctuation analysis and Bayesian inference, Multi-CD identifies the CDs that best represent the global pattern of correlation manifested in Hi-C, and reveals the multi-scale structure of chromosome. At each scale, the CDs are consistent with the results of existing methods, as well as with biological data from independent sources. CD solutions compared across different scales and cell types allow us to quantify the hierarchy between four major families of CDs, and to glean the principles of chromatin organization: (i) Sub-TADs, TADs, and meta-TADs constitute a robust hierarchical structure. (ii) The assemblies of compartments and TAD-based domains are governed by distinct organizational principles. (iii) Sub-TADs are the common building blocks of chromosome architecture. CDs acquired from our interpretation of Hi-C data using Multi-CD not only provide new insights into chromatin organization, but also offer a quantitative account for its cell-type-dependence and function.with γ ij = (σ ii + σ jj − 2σ ij )/2, where σ ij (= δr i · δr j ) is the positional covariance, determined by the topology of polymer network [42]. Indeed, distance distributions measured using fluorescence measurement between chromatin loci justifies this hypothesis (see Fig. S1). Importantly, our interpretation of chromosome conformation as a locally equilibrated, quasi-stable polymer network enables a one-to-one mapping of the contact probability p ij = rc 0 dxP (x; γ ij ) to the positional covariance σ ij , and hence to the cross-correlation matrix, (C) ij = σ ij / √ σ ii σ jj (see Methods). The cross-correlation matrix C normalizes the wide numer-

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Section: Discussionsupporting

confidence: 60%

A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C

Kim

Bak

Liu

et al. 2019

Preprint

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“…We next determined if the methods for defining individual TADs influenced the accuracy in detecting TAD splits and mergers. We replaced our default TAD identification method with each of the four state-of-the-art methods [21], including the HiCseq [22], TopDom [16], DomainCaller [4], and IC-finder [15]. The results indicated that the default method in TADsplimer outperformed HiCseq, TopDom, DomainCaller, and IC-finder ( Fig.…”

Section: Simulation Data Demonstrated Superior Performance Of Tadsplimermentioning

confidence: 99%

“…Many algorithms have been developed to define TADs in a single Hi-C sample [4,5,[14][15][16][17]]. However, systematically analyzing the reorganization of TADs in response to biological stimuli remains a technical challenge.…”

Section: Introductionmentioning

confidence: 99%

TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription

et al. 2020

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We present TADsplimer, the first computational tool to systematically detect topologically associating domain (TAD) splits and mergers across the genome between Hi-C samples. TADsplimer recaptures splits and mergers of TADs with high accuracy in simulation analyses and defines hundreds of TAD splits and mergers between pairs of different cell types, such as endothelial cells and fibroblasts. Our work reveals a key role for TAD remodeling in epigenetic regulation of transcription and delivers the first tool for the community to perform dynamic analysis of TAD splits and mergers in numerous biological and disease models.

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“…We next asked if there is also genome widely changes of the TADs in response to the thermal stresses, as observed in Drosophila (Djekidel et al, 2015). By applying a recently developed algorithm deDoc to our Hi-C data (Li et al, 2018), we identified 2107, 2207 and 1967 TADs in NM, HS and CS, at 10Kb resolution respectively. The accuracy of TADs boundaries was evidenced by the enrichment of CTCF, and SMC3 ChIP-seq peaks.…”

Section: Tad Structure Are Stable After the Thermal Stressesmentioning

confidence: 99%

“…A/B compartment profile is called by analyzing the first eigevector of KR normalized contact maps at 100Kb resolution (Lieberman-Aiden et al, 2009b). The compartment with higher H3K27ac ChIP-Seq signals were determined as compartment A. TADs were called using deDoc at 10Kb resolutions (Li et al, 2018).…”

Section: Hi-c and Hichip Data Processingmentioning

confidence: 99%

Widespread transcriptional responses to the thermal stresses are prewired in human 3D genome

Wang

et al. 2019

Preprint

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Temperature changes is one of the most common environmental stress that consequences with massive phenotypic responses for almost all the life forms. The dysregulation of heat shock (HS) response genes had been found associated with various severe diseases, including cancer. Although the HS response has been well studied in animal cells, it remains elusive whether or not the cells response to cold shock (CS) similarly. Here, we comprehensively compared the changes of gene expression, epigenetic marks (H3K4me3 and H3K27ac), binding of genome architecture proteins (CTCF, SMC3 and Pol II) and chromatin conformation after HS and CS in human cells. Widespread expression change was observed after both HS and CS. Remarkably, we identified distinguished characters in those thermal stress responded genes at nearly all levels of chromatin architecture, i.e, the compartment, topological associated domain, chromatin loops and transcription elongation regulators, in the normal condition. However, the global chromatin architecture remains largely stable after both CS and HS. Interestingly, the thermal stresses responded genes are prone to spatial clustering even before the temperature changes.Our data suggested that the transcriptional response to the thermal stresses maybe independent to the changes of the high-level chromatin architecture, e.g., compartments and TAD, while it may be more dependent on the precondition of the chromatin and epigenetic settings at the normal condition.

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Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy

Cited by 63 publications

References 40 publications

A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C

A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C

TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription

Widespread transcriptional responses to the thermal stresses are prewired in human 3D genome

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