Analysis methods for studying the 3D architecture of the genome

Loss of multi-level 3D genome organization during breast cancer progression

Breast cancer entails intricate alterations in genome organization and expression. However, how three-dimensional (3D) chromatin structure changes in the progression from a normal to a breast cancer malignant state remains unknown. To address this, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) are overall maintained, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observe a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identify a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene is inserted into a highly active subcompartment on chromosome 10. This insertion is accompanied by the formation of de novo enhancer contacts and activation of MYC , illustrating how structural genomic variants can alter the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the loss of genome organization at multiple scales during breast cancer progression revealing novel relationships between genome 3D structure and oncogenic processes.

scHiCyclePred: a deep learning framework for predicting cell cycle phases from single-cell Hi-C data using multi-scale interaction information

The emergence of single-cell Hi-C (scHi-C) technology has provided unprecedented opportunities for investigating the intricate relationship between cell cycle phases and the three-dimensional (3D) structure of chromatin. However, accurately predicting cell cycle phases based on scHi-C data remains a formidable challenge. Here, we present scHiCyclePred, a prediction model that integrates multiple feature sets to leverage scHi-C data for predicting cell cycle phases. scHiCyclePred extracts 3D chromatin structure features by incorporating multi-scale interaction information. The comparative analysis illustrates that scHiCyclePred surpasses existing methods such as Nagano_method and CIRCLET across various metrics including accuracy (ACC), F1 score, Precision, Recall, and balanced accuracy (BACC). In addition, we evaluate scHiCyclePred against the previously published CIRCLET using the dataset of complex tissues (Liu_dataset). Experimental results reveal significant improvements with scHiCyclePred exhibiting improvements of 0.39, 0.52, 0.52, and 0.39 over the CIRCLET in terms of ACC, F1 score, Precision, and Recall metrics, respectively. Furthermore, we conduct analyses on three-dimensional chromatin dynamics and gene features during the cell cycle, providing a more comprehensive understanding of cell cycle dynamics through chromatin structure. scHiCyclePred not only offers insights into cell biology but also holds promise for catalyzing breakthroughs in disease research. Access scHiCyclePred on GitHub at https:// github.com/HaoWuLab-Bioinformatics/ scHiCyclePred .

CTPredictor: A comprehensive and robust framework for predicting cell types by integrating multi-scale features from single-cell Hi-C data

Single-cell Hi-C (scHi-C) has emerged as a powerful technology for deciphering cell-to-cell variability in three-dimensional (3D) chromatin organization, providing insights into genome-wide chromatin interactions and their correlation with cellular functions. Nevertheless, the accurate identification of cell types across different datasets remains a formidable challenge, hindering comprehensive investigations into genome structure. In response, we introduce CTPredictor, an innovative computational method that integrates multi-scale features to accurately predict cell types in various datasets. CTPredictor strategically incorporates three distinct feature sets, namely, small intra-domain contact probability (SICP), smoothed small intra-domain contact probability (SSICP), and smoothed bin contact probability (SBCP). The resulting fusion classification model significantly enhances the accuracy of cell type prediction based on single-cell Hi-C data (scHi-C). Rigorous benchmarking against established methods and three conventional machine learning approaches demonstrates the robust performance of CTPredictor, positioning it as an advanced tool for cell type prediction within scHi-C data. Beyond its prediction capabilities, CTPredictor holds promise in illuminating 3D genome structures and their functional significance across a wide array of biological processes.

Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells

The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition and significance of the three-dimensional chromatin structure, summarize the technologies available for studying it, and describe the research progress on the chromatin spatial structure of dendritic cells, macrophages, T cells, B cells, and neutrophils.

Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness

BACKGROUND

Chromosome is one of the most fundamental part of cell biology where DNA holds the hierarchical information. DNA compacts its size by forming loops, and these regions house various protein particles, including CTCF, SMC3, H3 histone. Numerous sequencing methods, such as Hi-C, ChIP-seq, and Micro-C, have been developed to investigate these properties. Utilizing these data, scientists have developed a variety of loop prediction techniques that have greatly improved their methods for characterizing loop prediction and related aspects.

RESULTS

In this study, we categorized 22 loop calling methods and conducted a comprehensive study of 11 of them. Additionally, we have provided detailed insights into the methodologies underlying these algorithms for loop detection, categorizing them into five distinct groups based on their fundamental approaches. Furthermore, we have included critical information such as resolution, input and output formats, and parameters. For this analysis, we utilized the GM12878 Hi-C datasets at 5 KB, 10 KB, 100 KB and 250 KB resolutions. Our evaluation criteria encompassed various factors, including memory usages, running time, sequencing depth, and recovery of protein-specific sites such as CTCF, H3K27ac, and RNAPII.

CONCLUSION

This analysis offers insights into the loop detection processes of each method, along with the strengths and weaknesses of each, enabling readers to effectively choose suitable methods for their datasets. We evaluate the capabilities of these tools and introduce a novel Biological, Consistency, and Computational robustness score ( B C C score ) to measure their overall robustness ensuring a comprehensive evaluation of their performance.

Computational methods for analysing multiscale 3D genome organization

Recent progress in whole-genome mapping and imaging technologies has enabled the characterization of the spatial organization and folding of the genome in the nucleus. In parallel, advanced computational methods have been developed to leverage these mapping data to reveal multiscale three-dimensional (3D) genome features and to provide a more complete view of genome structure and its connections to genome functions such as transcription. Here, we discuss how recently developed computational tools, including machine-learning-based methods and integrative structure-modelling frameworks, have led to a systematic, multiscale delineation of the connections among different scales of 3D genome organization, genomic and epigenomic features, functional nuclear components and genome function. However, approaches that more comprehensively integrate a wide variety of genomic and imaging datasets are still needed to uncover the functional role of 3D genome structure in defining cellular phenotypes in health and disease.

Revisiting Assessment of Computational Methods for Hi-C Data Analysis

The performances of algorithms for Hi-C data preprocessing, the identification of topologically associating domains, and the detection of chromatin interactions and promoter-enhancer interactions have been mostly evaluated using semi-quantitative or synthetic data approaches, without utilizing the most recent methods, since 2017. In this study, we comprehensively evaluated 24 popular state-of-the-art methods for the complete end-to-end pipeline of Hi-C data analysis, using manually curated or experimentally validated benchmark datasets, including a CRISPR dataset for promoter-enhancer interaction validation. Our results indicate that, although no single method exhibited superior performance in all situations, HiC-Pro, DomainCaller, and Fit-Hi-C2 showed relatively balanced performances of most evaluation metrics for preprocessing, topologically associating domain identification, and chromatin interaction/promoter-enhancer interaction detection, respectively. The comprehensive comparison presented in this manuscript provides a reference for researchers to choose Hi-C analysis tools that best suit their needs.

Hi-C Analysis to Identify Genome-Wide Chromatin Structural Aberration in Cancer

Hi-C is a method that analyzes genome-wide chromatin structure using next-generation sequencer. Chromatin structure is crucial for regulating transcription or replication, and Hi-C has revealed the hierarchical chromatin structures, such as loop, domain , and compartment structures. Aberrant alteration of these structures causes disease, and a number of structural aberrations in cancer cells have been reported recently. Besides, Hi-C can identify chromosome rearrangements that frequently occurred in cancer. Therefore, Hi-C is a powerful technique to analyze epigenomic and genomic aberrations in tumorigenesis. Here we will introduce the basic protocol of Hi-C in experimental and analytical aspects.

DeepPHiC: predicting promoter-centered chromatin interactions using a novel deep learning approach

MOTIVATION

Promoter-centered chromatin interactions, which include promoter-enhancer (PE) and promoter-promoter (PP) interactions, are important to decipher gene regulation and disease mechanisms. The development of next-generation sequencing technologies such as promoter capture Hi-C (pcHi-C) leads to the discovery of promoter-centered chromatin interactions. However, pcHi-C experiments are expensive and thus may be unavailable for tissues/cell types of interest. In addition, these experiments may be underpowered due to insufficient sequencing depth or various artifacts, which results in a limited finding of interactions. Most existing computational methods for predicting chromatin interactions are based on in situ Hi-C and can detect chromatin interactions across the entire genome. However, they may not be optimal for predicting promoter-centered chromatin interactions.

RESULTS

We develop a supervised multi-modal deep learning model, which utilizes a comprehensive set of features such as genomic sequence, epigenetic signal, anchor distance, evolutionary features and DNA structural features to predict tissue/cell type-specific PE and PP interactions. We further extend the deep learning model in a multi-task learning and a transfer learning framework and demonstrate that the proposed approach outperforms state-of-the-art deep learning methods. Moreover, the proposed approach can achieve comparable prediction performance using predefined biologically relevant tissues/cell types compared to using all tissues/cell types in the pretraining especially for predicting PE interactions. The prediction performance can be further improved by using computationally inferred biologically relevant tissues/cell types in the pretraining, which are defined based on the common genes in the proximity of two anchors in the chromatin interactions.

AVAILABILITY AND IMPLEMENTATION

https://github.com/lichen-lab/DeepPHiC.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Methods for the Differential Analysis of Hi-C Data

The 3D organization of chromatin within the nucleus enables dynamic regulation and cell type-specific transcription of the genome. This is true at multiple levels of resolution: on a large scale, with chromosomes occupying distinct volumes (chromosome territories); at the level of individual chromatin fibers, which are organized into compartmentalized domains (e.g., Topologically Associating Domains-TADs), and at the level of short-range chromatin interactions between functional elements of the genome (e.g., enhancer-promoter loops).The widespread availability of Chromosome Conformation Capture (3C)-based high-throughput techniques has been instrumental in advancing our knowledge of chromatin nuclear organization. In particular, Hi-C has the potential to achieve the most comprehensive characterization of chromatin 3D interactions, as it is theoretically able to detect any pair of restriction fragments connected as a result of ligation by proximity.This chapter will illustrate how to compare the chromatin interactome in different experimental conditions, starting from pre-computed Hi-C contact matrices, how to visualize the results, and how to correlate the observed variations in chromatin interaction strength with changes in gene expression.

The 3D Genome: From Structure to Function

The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding factor domains, cohesin, and chromatin structures are the prominent identified components that encode the 3D structure of the genome. Although TADs are the major contributors to 3D genome organization, they are absent in Arabidopsis. However, a few research groups have reported the presence of TAD-like structures in the plant kingdom.

scHiCStackL: a stacking ensemble learning-based method for single-cell Hi-C classification using cell embedding

Single-cell Hi-C data are a common data source for studying the differences in the three-dimensional structure of cell chromosomes. The development of single-cell Hi-C technology makes it possible to obtain batches of single-cell Hi-C data. How to quickly and effectively discriminate cell types has become one hot research field. However, the existing computational methods to predict cell types based on Hi-C data are found to be low in accuracy. Therefore, we propose a high accuracy cell classification algorithm, called scHiCStackL, based on single-cell Hi-C data. In our work, we first improve the existing data preprocessing method for single-cell Hi-C data, which allows the generated cell embedding better to represent cells. Then, we construct a two-layer stacking ensemble model for classifying cells. Experimental results show that the cell embedding generated by our data preprocessing method increases by 0.23, 1.22, 1.46 and 1.61$\%$ comparing with the cell embedding generated by the previously published method scHiCluster, in terms of the Acc, MCC, F1 and Precision confidence intervals, respectively, on the task of classifying human cells in the ML1 and ML3 datasets. When using the two-layer stacking ensemble framework with the cell embedding, scHiCStackL improves by 13.33, 19, 19.27 and 14.5 over the scHiCluster, in terms of the Acc, ARI, NMI and F1 confidence intervals, respectively. In summary, scHiCStackL achieves superior performance in predicting cell types using the single-cell Hi-C data. The webserver and source code of scHiCStackL are freely available at http://hww.sdu.edu.cn:8002/scHiCStackL/ and https://github.com/HaoWuLab-Bioinformatics/scHiCStackL, respectively.

Understanding 3D genome organization by multidisciplinary methods

Understanding how chromatin is folded in the nucleus is fundamental to understanding its function. Although 3D genome organization has been historically difficult to study owing to a lack of relevant methodologies, major technological breakthroughs in genome-wide mapping of chromatin contacts and advances in imaging technologies in the twenty-first century considerably improved our understanding of chromosome conformation and nuclear architecture. In this Review, we discuss methods of 3D genome organization analysis, including sequencing-based techniques, such as Hi-C and its derivatives, Micro-C, DamID and others; microscopy-based techniques, such as super-resolution imaging coupled with fluorescence in situ hybridization (FISH), multiplex FISH, in situ genome sequencing and live microscopy methods; and computational and modelling approaches. We describe the most commonly used techniques and their contribution to our current knowledge of nuclear architecture and, finally, we provide a perspective on up-and-coming methods that open possibilities for future major discoveries.

The 3D Genome Structure of Single Cells

The spatial organization of the genome in the cell nucleus is pivotal to cell function. However, how the 3D genome organization and its dynamics influence cellular phenotypes remains poorly understood. The very recent development of single-cell technologies for probing the 3D genome, especially single-cell Hi-C (scHi-C), has ushered in a new era of unveiling cell-to-cell variability of 3D genome features at an unprecedented resolution. Here, we review recent developments in computational approaches to the analysis of scHi-C, including data processing, dimensionality reduction, imputation for enhancing data quality, and the revealing of 3D genome features at single-cell resolution. While much progress has been made in computational method development to analyze single-cell 3D genomes, substantial future work is needed to improve data interpretation and multimodal data integration, which are critical to reveal fundamental connections between genome structure and function among heterogeneous cell populations in various biological contexts.

Combining artificial intelligence: deep learning with Hi-C data to predict the functional effects of non-coding variants

MOTIVATION

Although genome-wide association studies (GWASs) have identified thousands of variants for various traits, the causal variants and the mechanisms underlying the significant loci are largely unknown. In this study, we aim to predict non-coding variants that may functionally affect translation initiation through long-range chromatin interaction.

RESULTS

By incorporating the Hi-C data, we propose a novel and powerful deep learning model of artificial intelligence to classify interacting and non-interacting fragment pairs and predict the functional effects of sequence alteration of single nucleotide on chromatin interaction and thus on gene expression. The changes in chromatin interaction probability between the reference sequence and the altered sequence reflect the degree of functional impact for the variant. The model was effective and efficient with the classification of interacting and non-interacting fragment pairs. The predicted causal SNPs that had a larger impact on chromatin interaction were more likely to be identified by GWAS and eQTL analyses. We demonstrate that an integrative approach combining artificial intelligence-deep learning with high throughput experimental evidence of chromatin interaction leads to prioritizing the functional variants in disease- and phenotype-related loci and thus will greatly expedite uncover of the biological mechanism underlying the association identified in genomic studies.

AVAILABILITY AND IMPLEMENTATION

Source code used in data preparing and model training is available at the GitHub website (https://github.com/biocai/DeepHiC).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Integrative Analysis of Genome, 3D Genome, and Transcriptome Alterations of Clinical Lung Cancer Samples

Genomic studies of cancer cell alterations, such as mutations, copy number variations (CNVs), and translocations, greatly promote our understanding of the genesis and development of cancer. However, the 3D genome architecture of cancers remains less studied due to the complexity of cancer genomes and technical difficulties. To explore the 3D genome structure in clinical lung cancer, we performed Hi-C experiments using paired normal and tumor cells harvested from patients with lung cancer, combining with RNA-seq analysis. We demonstrated the feasibility of studying 3D genome of clinical lung cancer samples with a small number of cells (1 × 10⁴), compared the genome architecture between clinical samples and cell lines of lung cancer, and identified conserved and changed spatial chromatin structures between normal and cancer samples. We also showed that Hi-C data can be used to infer CNVs and point mutations in cancer. By integrating those different types of cancer alterations, we showed significant associations between CNVs, 3D genome, and gene expression. We propose that 3D genome mediates the effects of cancer genomic alterations on gene expression through altering regulatory chromatin structures. Our study highlights the importance of analyzing 3D genomes of clinical cancer samples in addition to cancer cell lines and provides an integrative genomic analysis pipeline for future larger-scale studies in lung cancer and other cancers.

HCMB: A stable and efficient algorithm for processing the normalization of highly sparse Hi-C contact data

The high-throughput genome-wide chromosome conformation capture (Hi-C) method has recently become an important tool to study chromosomal interactions where one can extract meaningful biological information including P(s) curve, topologically associated domains, A/B compartments, and other biologically relevant signals. Normalization is a critical pre-processing step of downstream analyses for the elimination of systematic and technical biases from chromatin contact matrices due to different mappability, GC content, and restriction fragment lengths. Especially, the problem of high sparsity puts forward a huge challenge on the correction, indicating the urgent need for a stable and efficient method for Hi-C data normalization. Recently, some matrix balancing methods have been developed to normalize Hi-C data, such as the Knight-Ruiz (KR) algorithm, but it failed to normalize contact matrices with high sparsity. Here, we presented an algorithm, Hi-C Matrix Balancing (HCMB), based on an iterative solution of equations, combining with linear search and projection strategy to normalize the Hi-C original interaction data. Both the simulated and experimental data demonstrated that HCMB is robust and efficient in normalizing Hi-C data and preserving the biologically relevant Hi-C features even facing very high sparsity. HCMB is implemented in Python and is freely accessible to non-commercial users at GitHub: https://github.com/HUST-DataMan/HCMB.

Identifying high-confidence capture Hi-C interactions using CHiCANE

The ability to identify regulatory interactions that mediate gene expression changes through distal elements, such as risk loci, is transforming our understanding of how genomes are spatially organized and regulated. Capture Hi-C (CHi-C) is a powerful tool to delineate such regulatory interactions. However, primary analysis and downstream interpretation of CHi-C profiles remains challenging and relies on disparate tools with ad-hoc input/output formats and specific assumptions for statistical modeling. Here we present a data processing and interaction calling toolkit (CHiCANE), specialized for the analysis and meaningful interpretation of CHi-C assays. In this protocol, we demonstrate applications of CHiCANE to region capture Hi-C (rCHi-C) and promoter capture Hi-C (pCHi-C) libraries, followed by quality assessment of interaction peaks, as well as downstream analysis specific to rCHi-C and pCHi-C to aid functional interpretation. For a typical rCHi-C/pCHi-C dataset this protocol takes up to 3 d for users with a moderate understanding of R programming and statistical concepts, although this is dependent on dataset size and compute power available. CHiCANE is freely available at https://cran.r-project.org/web/packages/chicane .

HiCRep.py: fast comparison of Hi-C contact matrices in Python

MOTIVATION

Hi-C is the most widely used assay for investigating genome-wide 3D organization of chromatin. When working with Hi-C data, it is often useful to calculate the similarity between contact matrices in order to assess experimental reproducibility or to quantify relationships among Hi-C data from related samples. The HiCRep algorithm has been widely adopted for this task, but the existing R implementation suffers from run time limitations on high-resolution Hi-C data or on large single-cell Hi-C datasets.

RESULTS

We introduce a Python implementation of HiCRep and demonstrate that it is much faster and consumes much less memory than the existing R implementation. Furthermore, we give examples of HiCRep's ability to accurately distinguish replicates from non-replicates and to reveal cell type structure among collections of Hi-C data.

AVAILABILITY AND IMPLEMENTATION

HiCRep.py and its documentation are available with a GPL license at https://github.com/Noble-Lab/hicrep. The software may be installed automatically using the pip package installer.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants

Expression quantitative trait loci (eQTLs) studies provide associations of genetic variants with gene expression but fall short of pinpointing functionally important eQTLs. Here, using H3K27ac HiChIP assays, we mapped eQTLs overlapping active cis-regulatory elements that interact with their target gene promoters (promoter-interacting eQTLs, pieQTLs) in five common immune cell types (Database of Immune Cell Expression, Expression quantitative trait loci and Epigenomics (DICE) cis-interactome project). This approach allowed us to identify functionally important eQTLs and show mechanisms that explain their cell-type restriction. We also devised an approach to eQTL discovery that relies on HiChIP-based promoter interaction maps as a structural framework for deciding which SNPs to test for association with gene expression, and observe ultra-long-distance pieQTLs (>1 megabase away), including several disease-risk variants. We validated the functional role of pieQTLs using reporter assays, CRISPRi, dCas9-tiling guides and Cas9-mediated base-pair editing. In this article we present a method for functional eQTL discovery and provide insights into relevance of noncoding variants for cell-specific gene regulation and for disease association beyond conventional eQTL mapping.

FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data

Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool and powerful Python API with a broad feature set covering matrix generation, analysis, and visualisation for C-like data ( https://github.com/vaquerizaslab/fanc ). Due to its compatibility with the most prevalent Hi-C storage formats, FAN-C can be used in combination with a large number of existing analysis tools, thus greatly simplifying Hi-C matrix analysis.

Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation

We present MUSTACHE, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. MUSTACHE employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in contact maps. MUSTACHE is scalable to kilobase-resolution maps and reports loops that are highly consistent between replicates and between Hi-C and Micro-C datasets. Compared to other loop callers, such as HiCCUPS and SIP, MUSTACHE recovers a higher number of published ChIA-PET and HiChIP loops as well as loops linking promoters to regulatory elements. Overall, MUSTACHE enables an efficient and comprehensive analysis of chromatin loops. Available at: https://github.com/ay-lab/mustache .

GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data

Advances in the study of chromosome conformation capture technologies, such as Hi-C technique - capable of capturing chromosomal interactions in a genome-wide scale - have led to the development of three-dimensional chromosome and genome structure reconstruction methods from Hi-C data. The three dimensional genome structure is important because it plays a role in a variety of important biological activities such as DNA replication, gene regulation, genome interaction, and gene expression. In recent years, numerous Hi-C datasets have been generated, and likewise, a number of genome structure construction algorithms have been developed.

In this work, we outline the construction of a novel Genome Structure Database (GSDB) to create a comprehensive repository that contains 3D structures for Hi-C datasets constructed by a variety of 3D structure reconstruction tools. The GSDB contains over 50,000 structures from 12 state-of-the-art Hi-C data structure prediction algorithms for 32 Hi-C datasets.

GSDB functions as a centralized collection of genome structures which will enable the exploration of the dynamic architectures of chromosomes and genomes for biomedical research. GSDB is accessible at http://sysbio.rnet.missouri.edu/3dgenome/GSDB

Exonuclease combinations reduce noises in 3D genomics technologies

Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source, which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of annulation and increased the valid-pairs ratio from ∼40% to ∼80% for enhanced interaction detection in standard Hi-C. This strategy is applicable for development of various 3D genomics technologies, or optimization of Hi-C sequencing efficiency.

FreeHi-C spike-in simulations for benchmarking differential chromatin interaction detection

High-throughput genome-wide chromatin conformation capture assay (Hi-C) is routinely used to profile long-range genomic interactions and three-dimensional organization of genomes. A key application of Hi-C is the comparative analysis of genomic interactions across different time points, cellular conditions, or multiple stimuli. While operating characteristics of methods for Hi-C data processing such as normalization, pairwise interaction and higher-order organization detection have been relatively well studied, properties of methods for differential chromatin interaction detection are less investigated. We have recently developed FreeHi-C to enable data-driven non-parametric simulations from Hi-C experiments. Here, we extend FreeHi-C with a user/data-driven spike-in module to facilitate comparisons of differential chromatin interaction detection methods where the ground truth differential chromatin interactions are known under a wide variety of settings. We use FreeHi-C to benchmark four differential chromatin interaction detection methods, namely HiCcompare, multiHiCcompare, diffHic, and Selfish, using three comparative analysis settings with different sequencing depths and spike-in proportions. This comparison reveals distinguished performances in terms of the standard metrics such as the false discovery rate control, detection power, significance order, precision-recall curve, and receiver operating characteristic curve as well as overall genomic properties of the types of differential chromatin interactions detectable by each method. Furthermore, it highlights the lack of power for all methods in small replication settings.

Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci

BACKGROUND

Chromatin 3D conformation plays important roles in regulating gene or protein functions. High-throughout chromosome conformation capture (3C)-based technologies, such as Hi-C, have been exploited to acquire the contact frequencies among genomic loci at genome-scale. Various computational tools have been proposed to recover the underlying chromatin 3D structures from in situ Hi-C contact map data. As connected residuals in a polymer, neighboring genomic loci have intrinsic mutual dependencies in building a 3D conformation. However, current methods seldom take this feature into account.

RESULTS

We present a method called ShNeigh, which combines the classical MDS technique with local dependence of neighboring loci modeled by a Gaussian formula, to infer the best 3D structure from noisy and incomplete contact frequency matrices. We validated ShNeigh by comparing it to two typical distance-based algorithms, ShRec3D and ChromSDE. The comparison results on simulated Hi-C dataset showed that, while keeping the high-speed nature of classical MDS, ShNeigh can recover the true structure better than ShRec3D and ChromSDE. Meanwhile, ShNeigh is more robust to data noise. On the publicly available human GM06990 Hi-C data, we demonstrated that the structures reconstructed by ShNeigh are more reproducible between different restriction enzymes than by ShRec3D and ChromSDE, especially at high resolutions manifested by sparse contact maps, which means ShNeigh is more robust to signal coverage.

CONCLUSIONS

Our method can recover stable structures in high noise and sparse signal settings. It can also reconstruct similar structures from Hi-C data obtained using different restriction enzymes. Therefore, our method provides a new direction for enhancing the reconstruction quality of chromatin 3D structures.

Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

Fit-Hi-C is a programming application to compute statistical confidence estimates for Hi-C contact maps to identify significant chromatin contacts. By fitting a monotonically non-increasing spline, Fit-Hi-C captures the relationship between genomic distance and contact probability without any parametric assumption. The spline fit together with the correction of contact probabilities with respect to bin- or locus-specific biases accounts for previously characterized covariates impacting Hi-C contact counts. Fit-Hi-C is best applied for the study of mid-range (e.g., 20 kb-2 Mb for human genome) intra-chromosomal contacts; however, with the latest reimplementation, named FitHiC2, it is possible to perform genome-wide analysis for high-resolution Hi-C data, including all intra-chromosomal distances and inter-chromosomal contacts. FitHiC2 also offers a merging filter module, which eliminates indirect/bystander interactions, leading to significant reduction in the number of reported contacts without sacrificing recovery of key loops such as those between convergent CTCF binding sites. Here, we describe how to apply the FitHiC2 protocol to three use cases: (i) 5-kb resolution Hi-C data of chromosome 5 from GM12878 (a human lymphoblastoid cell line), (ii) 40-kb resolution whole-genome Hi-C data from IMR90 (human lung fibroblast), and (iii) budding yeast whole-genome Hi-C data at a single restriction cut site (EcoRI) resolution. The procedure takes ~12 h with preprocessing when all use cases are run sequentially (~4 h when run parallel). With the recent improvements in its implementation, FitHiC2 (8 processors and 16 GB memory) is also scalable to genome-wide analysis of the highest resolution (1 kb) Hi-C data available to date (~48 h with 32 GB peak memory). FitHiC2 is available through Bioconda, GitHub and the Python Package Index.

Evaluation of 3D Chromatin Interactions Using Hi-C

The invention of Hi-C has greatly facilitated 3D genome research through an unbiased probing of 3D chromatin interactions. It produces enormous amount of sequencing data that capture multiscale chromatin conformation structures. In the last decade, numerous computational methods have been developed to analyze Hi-C data and predict A/B compartments, topologically associating domains (TADs), and significant chromatin contacts. This chapter introduced the iHiC package that provides several utilities to facilitate Hi-C data analysis with public software and demonstrated its application to a Hi-C dataset generated for mouse embryonic stem (ES) cells.

The Functional 3D Organization of Unicellular Genomes

Genome conformation capture techniques permit a systematic investigation into the functional spatial organization of genomes, including functional aspects like assessing the co-localization of sets of genomic elements. For example, the co-localization of genes targeted by a transcription factor (TF) within a transcription factory. We quantify spatial co-localization using a rigorous statistical model that measures the enrichment of a subset of elements in neighbourhoods inferred from Hi-C data. We also control for co-localization that can be attributed to genomic order. We systematically apply our open-sourced framework, spatial-mHG, to search for spatial co-localization phenomena in multiple unicellular Hi-C datasets with corresponding genomic annotations. Our biological findings shed new light on the functional spatial organization of genomes, including: In C. crescentus, DNA replication genes reside in two genomic clusters that are spatially co-localized. Furthermore, these clusters contain similar gene copies and lay in genomic vicinity to the ori and ter sequences. In S. cerevisae, Ty5 retrotransposon family element spatially co-localize at a spatially adjacent subset of telomeres. In N. crassa, both Proteasome lid subcomplex genes and protein refolding genes jointly spatially co-localize at a shared location. An implementation of our algorithms is available online.

HiCeekR: A Novel Shiny App for Hi-C Data Analysis

The High-throughput Chromosome Conformation Capture (Hi-C) technique combines the power of the Next Generation Sequencing technologies with chromosome conformation capture approach to study the 3D chromatin organization at the genome-wide scale. Although such a technique is quite recent, many tools are already available for pre-processing and analyzing Hi-C data, allowing to identify chromatin loops, topological associating domains and A/B compartments. However, only a few of them provide an exhaustive analysis pipeline or allow to easily integrate and visualize other omic layers. Moreover, most of the available tools are designed for expert users, who have great confidence with command-line applications. In this paper, we present HiCeekR (https://github.com/lucidif/HiCeekR), a novel R Graphical User Interface (GUI) that allows researchers to easily perform a complete Hi-C data analysis. With the aid of the Shiny libraries, it integrates several R/Bioconductor packages for Hi-C data analysis and visualization, guiding the user during the entire process. Here, we describe its architecture and functionalities, then illustrate its capabilities using a publicly available dataset.

The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook

Cancer is a complex disease at many different levels. The molecular phenomenology of cancer is also quite rich. The mutational and genomic origins of cancer and their downstream effects on processes such as the reprogramming of the gene regulatory control and the molecular pathways depending on such control have been recognized as central to the characterization of the disease. More important though is the understanding of their causes, prognosis, and therapeutics. There is a multitude of factors associated with anomalous control of gene expression in cancer. Many of these factors are now amenable to be studied comprehensively by means of experiments based on diverse omic technologies. However, characterizing each dimension of the phenomenon individually has proven to fall short in presenting a clear picture of expression regulation as a whole. In this review article, we discuss some of the more relevant factors affecting gene expression control both, under normal conditions and in tumor settings. We describe the different omic approaches that we can use as well as the computational genomic analysis needed to track down these factors. Then we present theoretical and computational frameworks developed to integrate the amount of diverse information provided by such single-omic analyses. We contextualize this within a systems biology-based multi-omic regulation setting, aimed at better understanding the complex interplay of gene expression deregulation in cancer.

Analysis of the structural variability of topologically associated domains as revealed by Hi-C

Three-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associated domains (TADs), building blocks of chromosome structure, are genomic regions with higher contact frequencies within the region than outside the region. A central question is the degree to which TADs are conserved or vary between conditions. We analyze 137 Hi-C samples from 9 studies under 3 measures to quantify the effects of various sources of biological and experimental variation. We observe significant variation in TAD sets between both non-replicate and replicate samples, and provide initial evidence that this variability does not come from genetic sequence differences. The effects of experimental protocol differences are also measured, demonstrating that samples can have protocol-specific structural changes, but that TADs are generally robust to lab-specific differences. This study represents a systematic quantification of key factors influencing comparisons of chromosome structure, suggesting significant variability and the potential for cell-type-specific structural features, which has previously not been systematically explored. The lack of observed influence of heredity and genetic differences on chromosome structure suggests that factors other than the genetic sequence are driving this structure, which plays an important role in human disease and cellular functioning.

Visualising three-dimensional genome organisation in two dimensions

The three-dimensional organisation of the genome plays a crucial role in developmental gene regulation. In recent years, techniques to investigate this organisation have become more accessible to labs worldwide due to improvements in protocols and decreases in the cost of high-throughput sequencing. However, the resulting datasets are complex and can be challenging to analyse and interpret. Here, we provide a guide to visualisation approaches that can aid the interpretation of such datasets and the communication of biological results.

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

HiChIP/PLAC-seq is increasingly becoming popular for profiling 3D chromatin contacts among regulatory elements and for annotating functions of genetic variants. Here we describe FitHiChIP, a computational method for loop calling from HiChIP/PLAC-seq data, which jointly models the non-uniform coverage and genomic distance scaling of contact counts to compute statistical significance estimates. We also develop a technique to filter putative bystander loops that can be explained by stronger adjacent loops. Compared to existing methods, FitHiChIP performs better in recovering contacts reported by Hi-C, promoter capture Hi-C and ChIA-PET experiments and in capturing previously validated promoter-enhancer interactions. FitHiChIP loop calls are reproducible among replicates and are consistent across different experimental settings. Our work also provides a framework for differential HiChIP analysis with an option to utilize ChIP-seq data for further characterizing differential loops. Even though designed for HiChIP, FitHiChIP is also applicable to other conformation capture assays.

HiChIP/PLAC-seq assay is popular for profiling 3D genome interactions among regulatory elements at kilobase resolution. Here the authors describe FitHiChIP an empirical null-based, flexible computational method for statistical significance estimation and loop calling from HiChIP data.

Rich Chromatin Structure Prediction from Hi-C Data

Recent studies involving the 3-dimensional conformation of chromatin have revealed the important role it has to play in different processes within the cell. These studies have also led to the discovery of densely interacting segments of the chromosome, called topologically associating domains. The accurate identification of these domains from Hi-C interaction data is an interesting and important computational problem for which numerous methods have been proposed. Unfortunately, most existing algorithms designed to identify these domains assume that they are non-overlapping whereas there is substantial evidence to believe a nested structure exists. We present a methodology to predict hierarchical chromatin domains using chromatin conformation capture data. Our method predicts domains at different resolutions, calculated using intrinsic properties of the chromatin data, and effectively clusters these to construct the hierarchy. At each individual level, the domains are non-overlapping in such a way that the intra-domain interaction frequencies are maximized. We show that our predicted structure is highly enriched for actively transcribing housekeeping genes and various chromatin markers, including CTCF, around the domain boundaries. We also show that large-scale domains, at multiple resolutions within our hierarchy, are conserved across cell types and species. We also provide comparisons against existing tools for extracting hierarchical domains. Our software, Matryoshka, is written in C++11 and licensed under GPL v3; it is available at https://github.com/COMBINE-lab/matryoshka.

Reconstructing spatial organizations of chromosomes through manifold learning

Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in a high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the three-dimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility. Unlike previous methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances, our model directly embeds the neighboring affinities from Hi-C space into 3D Euclidean space. Extensive validations demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also provided a physically and physiologically valid 3D representations of the organizations of chromosomes. Furthermore, we for the first time apply the modeled chromatin structures to recover long-range genomic interactions missing from original Hi-C data.

Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data

Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish technical artefacts from valid read pairs originating from true chromatin interactions.

C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries

Studies performed using Hi-C and other high-throughput whole-genome C-methods have demonstrated that 3D organization of eukaryotic genomes is functionally relevant. Unfortunately, ultra-deep sequencing of Hi-C libraries necessary to detect loop structures in large vertebrate genomes remains rather expensive. However, many studies are in fact aimed at determining the fine-scale 3D structure of comparatively small genomic regions up to several Mb in length. Such studies typically focus on the spatial structure of domains of coregulated genes, molecular mechanisms of loop formation, and interrogation of functional significance of GWAS-revealed polymorphisms. Therefore, a handful of molecular techniques based on Hi-C have been developed to address such issues. These techniques commonly rely on in-solution hybridization of Hi-C/3C-seq libraries with pools of biotinylated baits covering the region of interest, followed by deep sequencing of the enriched library. Here, we describe a new protocol of this kind, C-TALE (Chromatin TArget Ligation Enrichment). Preparation of hybridization probes from bacterial artificial chromosomes and an additional round of enrichment make C-TALE a cost-effective alternative to existing many-versus-all C-methods.

R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi-C Datasets

The three-dimensional (3D) interactions of chromatin regulate cell-type-specific gene expression, recombination, X-chromosome inactivation, and many other genomic processes. High-throughput chromatin conformation capture (Hi-C) technologies capture the structure of the chromatin on a global scale by measuring all-vs.-all interactions and can provide new insights into genomic regulation. The workflow presented here describes how to analyze and interpret a comparative Hi-C experiment. We describe the process of obtaining Hi-C data from public repositories and give suggestions for pre-processing pipelines for users who intend to analyze their own raw data. We then describe the data normalization and comparative analysis process. We present three protocols describing the use of the multiHiCcompare, diffHic, and FIND R packages, respectively, to perform a comparative analysis of Hi-C experiments. Finally, visualization of the results and downstream interpretation of the differentially interacting regions are discussed. The bulk of this tutorial uses the R programming environment, and the processes described can be performed with most operating systems and a single computer. © 2019 by John Wiley & Sons, Inc.

Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes

The new advances in various experimental techniques that provide complementary information about the spatial conformations of chromosomes have inspired researchers to develop computational methods to fully exploit the merits of individual data sources and combine them to improve the modeling of chromosome structure. Here we propose GEM-FISH, a method for reconstructing the 3D models of chromosomes through systematically integrating both Hi-C and FISH data with the prior biophysical knowledge of a polymer model. Comprehensive tests on a set of chromosomes, for which both Hi-C and FISH data are available, demonstrate that GEM-FISH can outperform previous chromosome structure modeling methods and accurately capture the higher order spatial features of chromosome conformations. Moreover, our reconstructed 3D models of chromosomes revealed interesting patterns of spatial distributions of super-enhancers which can provide useful insights into understanding the functional roles of these super-enhancers in gene regulation.

An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data

Over the past decade, methods for predicting three-dimensional (3-D) chromosome and genome structures have proliferated. This has been primarily due to the development of high-throughput, next-generation chromosome conformation capture (3C) technologies, which have provided next-generation sequencing data about chromosome conformations in order to map the 3-D genome structure. The introduction of the Hi-C technique-a variant of the 3C method-has allowed researchers to extract the interaction frequency (IF) for all loci of a genome at high-throughput and at a genome-wide scale. In this review we describe, categorize, and compare the various methods developed to map chromosome and genome structures from 3C data-particularly Hi-C data. We summarize the improvements introduced by these methods, describe the approach used for method evaluation, and discuss how these advancements shape the future of genome structure construction.

Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance

Recent studies have demonstrated that chromatin architecture is linked to the progression of cancers. However, the roles of 3D structure and its dynamics in hormone-dependent breast cancer and endocrine resistance are largely unknown. Here we report the dynamics of 3D chromatin structure across a time course of estradiol (E2) stimulation in human estrogen receptor α (ERα)-positive breast cancer cells. We identified subsets of temporally highly dynamic compartments predominantly associated with active open chromatin and found that these highly dynamic compartments showed higher alteration in tamoxifen-resistant breast cancer cells. Remarkably, these compartments are characterized by active chromatin states, and enhanced ERα binding but decreased transcription factor CCCTC-binding factor (CTCF) binding. We finally identified a set of ERα-bound promoter-enhancer looping genes enclosed within altered domains that are enriched with cancer invasion, aggressiveness or metabolism signaling pathways. This large-scale analysis expands our understanding of high-order temporal chromatin reorganization underlying hormone-dependent breast cancer.

TAD fusion score: discovery and ranking the contribution of deletions to genome structure

Deletions that fuse two adjacent topologically associating domains (TADs) can cause severe developmental disorders. We provide a formal method to quantify deletions based on their potential disruption of the three-dimensional genome structure, denoted as the TAD fusion score. Furthermore, we show that deletions that cause TAD fusion are rare and under negative selection in the general population. Finally, we show that our method correctly gives higher scores to deletions reported to cause various disorders, including developmental disorders and cancer, in comparison to the deletions reported in the 1000 Genomes Project. The TAD fusion score tool is publicly available at https://github.com/HormozdiariLab/TAD-fusion-score .

Measuring the reproducibility and quality of Hi-C data

BACKGROUND

Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study.

RESULTS

Using real and simulated data, we profile the performance of several recently proposed methods for assessing reproducibility of population Hi-C data, including HiCRep, GenomeDISCO, HiC-Spector, and QuASAR-Rep. By explicitly controlling noise and sparsity through simulations, we demonstrate the deficiencies of performing simple correlation analysis on pairs of matrices, and we show that methods developed specifically for Hi-C data produce better measures of reproducibility. We also show how to use established measures, such as the ratio of intra- to interchromosomal interactions, and novel ones, such as QuASAR-QC, to identify low-quality experiments.

CONCLUSIONS

In this work, we assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices. Through this extensive validation and benchmarking of Hi-C data, we describe best practices for reproducibility and quality assessment of Hi-C experiments. We make all software publicly available at http://github.com/kundajelab/3DChromatin_ReplicateQC to facilitate adoption in the community.

Identification of rheumatoid arthritis causal genes using functional genomics

Over the past decade, genome-wide association studies have contributed a wealth of knowledge to our understanding of polygenic disorders such as rheumatoid arthritis. As the size of sample cohorts has improved so too have the computational and experimental methods used to robustly define variants associated with disease susceptibility. The challenge now remains to translate these findings into improved understanding of disease aetiology and patient care. Whilst much of the focus of translating the findings of genome-wide association studies has been on global analysis of all variants identified, careful functional study of individual disease susceptibility loci will be required in order to refine our understanding of how individual variants contribute to disease risk. Here, we present the argument behind such an approach and describe some of the novel tools being used to investigate risk loci. This includes the use of chromosomal conformation capture techniques and modifications of the CRISPR-Cas9 system, with several examples of their implementation being described.

Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies

Current Hi-C analysis approaches are unable to account for reads that align to multiple locations, and hence underestimate biological signal from repetitive regions of genomes. We developed and validated mHi-C, a multi-read mapping strategy to probabilistically allocate Hi-C multi-reads. mHi-C exhibited superior performance over utilizing only uni-reads and heuristic approaches aimed at rescuing multi-reads on benchmarks. Specifically, mHi-C increased the sequencing depth by an average of 20% resulting in higher reproducibility of contact matrices and detected interactions across biological replicates. The impact of the multi-reads on the detection of significant interactions is influenced marginally by the relative contribution of multi-reads to the sequencing depth compared to uni-reads, cis-to-trans ratio of contacts, and the broad data quality as reflected by the proportion of mappable reads of datasets. Computational experiments highlighted that in Hi-C studies with short read lengths, mHi-C rescued multi-reads can emulate the effect of longer reads. mHi-C also revealed biologically supported bona fide promoter-enhancer interactions and topologically associating domains involving repetitive genomic regions, thereby unlocking a previously masked portion of the genome for conformation capture studies.

Computational methods for analyzing and modeling genome structure and organization

Recent advances in chromosome conformation capture technologies have led to the discovery of previously unappreciated structural features of chromatin. Computational analysis has been critical in detecting these features and thereby helping to uncover the building blocks of genome architecture. Algorithms are being developed to integrate these architectural features to construct better three-dimensional (3D) models of the genome. These computational methods have revealed the importance of 3D genome organization to essential biological processes. In this article, we review the state of the art in analytic and modeling techniques with a focus on their application to answering various biological questions related to chromatin structure. We summarize the limitations of these computational techniques and suggest future directions, including the importance of incorporating multiple sources of experimental data in building a more comprehensive model of the genome. This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Mechanistic Models.