ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Li, Guoliang; Fullwood, Melissa J.; Han, Xu; Mulawadi, Fabianus Hendriyan; Velkov, Stoyan; Vega, Vinsensius B.; Ariyaratne, Pramila; Mohamed, Yusoff Bin; Ooi, Hong; Tennakoon, Chandana; Wei, Chia Lin; Ruan, Yijun; Sung, Wing-Kin

doi:10.1186/gb-2010-11-2-r22

Cited by 286 publications

(268 citation statements)

References 16 publications

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“…In such approaches, when a long-range interaction within or between chromosomes is described, this is often a statistical definition, meaning that two (multifragment) regions have a higher probability for making contacts compared with other regions at a similar distance on the same chromosome or elsewhere on other chromosomes. For a more thorough statistical definition of 4C, HiC, or ChIA-PET interactions, we refer to Lieberman-Aiden et al (2009), Li et al (2010, , and Yaffe and Tanay (2011).…”

Section: Interpretation Of Chromosome Capture Experiments: Further Comentioning

confidence: 99%

A decade of 3C technologies: insights into nuclear organization

Wit

Laat²

2012

Genes Dev.

657

487

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Over the past 10 years, the development of chromosome conformation capture (3C) technology and the subsequent genomic variants thereof have enabled the analysis of nuclear organization at an unprecedented resolution and throughput. The technology relies on the original and, in hindsight, remarkably simple idea that digestion and religation of fixed chromatin in cells, followed by the quantification of ligation junctions, allows for the determination of DNA contact frequencies and insight into chromosome topology. Here we evaluate and compare the current 3C-based methods (including 4C [chromosome conformation capture-on-chip], 5C [chromosome conformation capture carbon copy], HiC, and ChIA-PET), summarize their contribution to our current understanding of genome structure, and discuss how shape influences genome function.For more than a century, researchers have been making inquiries into the organization of the nucleus, the largest and most easily discernable organelle in the eukaryotic cell. Early in the 20th Century, Cajal (1903) identified subnuclear structures that were later named Cajal bodies. Twenty-five years later, Heitz (1928) observed differentially staining chromatin in interphase nuclei of mosses and described it as heterochromatin and euchromatin. Interest in nuclear structure was further fueled by the realization that the nucleus contains genetic material in the form of DNA fibers. In humans, when unwound, the DNA measures ;2 m, ;200,000 times the diameter of an average mammalian cell nucleus. Packing DNA inside the nucleus therefore imposes tremendous organizational challenges. While already conceptually interesting, the shape of the genome becomes even more fascinating when one realizes that it also relates to genome functioning. Although we are still far from understanding this exact relationship, breakthrough technologies are now available for the systematic and detailed analysis of nuclear organization.Traditionally, nuclear organization is studied by microscopy, and thus it is appropriate to start by highlighting some important observations made under the microscope.However, the emphasis of this review is on novel genomics strategies that are based on chromosome conformation capture (3C) technology. Ten years ago, Dekker et al. (2002) developed 3C technology, a biochemical strategy to analyze contact frequencies between selected genomic sites in cell populations. Since then, various 3C-derived genomics methods have been developed. In comparison with microscopy, 3C-based methods enable more systematic DNA topology studies at a higher resolution: These technologies can put observations made on single genes in selected cells in the context of genomic behavior in cell populations. The generated DNA contact maps start teaching us the rules that dictate genome structure and functioning inside the cell. As we explain here, these rules are probabilistic, not deterministic, implying that they cannot predict the shape and functioning of the genome in individual cells. To investigate this, microscopy i...

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Section: Interpretation Of Chromosome Capture Experiments: Further Comentioning

confidence: 99%

A decade of 3C technologies: insights into nuclear organization

Wit

Laat²

2012

Genes Dev.

657

487

View full text Add to dashboard Cite

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“…ChIA-PET Tool (http://chiapet.gis.a-star.edu.sg/ downloads/chia-pet-tools) -исторически первый пакет программного обеспечения для обработки данных ChIA-PET [27]. Пакет предназначен для операционных систем Unix/Linux, имеет открытый исходный код.…”

Section: компьютерные инструменты анализа трёхмерной организации геноunclassified

Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data

et al. 2017

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The study spatial chromosome structure and chromosome folding in the interphase cell nucleus is an important challenge of world science. Detection of eukaryotic genome regions that physically interact with each other could be done by modern sequencing technologies. A basic method of chromosome folding by total sequencing of contacting DNA fragments is HI-C. Long-range chromosomal interactions play an important role in gene transcription and regulation. The study of chromosome interactions, 3D (three-dimensional) genome structure and its effect on gene transcription allows revealing fundamental biological processes from a viewpoint of structural regulation and are important for cancer research. The technique of chromatin immunoprecipitation and subsequent sequencing (ChIP-seq) make possible to determine binding sites of transcription factors that regulate expression of eukaryotic genes; genome transcription factors binding maps have been. The ChIA-PET technology allows exploring not only target protein binding sites, but also pairs of such sites on proximally located and interacting with each other chromosomes co-located in three-dimensional space of the cell nucleus. Here we discuss the principles of the construction of genomic maps and matrices of chromosome contacts according to ChIA-PET and Hi-C data that capture the chromosome conformation and overview existing software for 3D genome analysis including in house programs of gene location analysis in topological domains.

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“…PET interactions were identified and classified following the approach in Li et al (2010), with modifications described by Tang et al (2015), using a PET cutoff of 4-PET clusters with counts <4 are considered not significant, and these weak interactions are grouped with PET singletons. Although we prefer this analysis method, several methods are available for calling PET interactions (Paulsen et al 2014;He et al 2015;Phanstiel et al 2015), and the output of any of these methods is suitable as input to 3D-GNOME.…”

Section: Chia-pet Datamentioning

confidence: 99%

“…Although recent Hi-C experiments have achieved kilobase (kb) resolution (Rao et al 2014), obtaining such resolution requires extremely deep sequencing of billions of reads, which is impractical and prohibitive to many applications. On the other hand, ChIA-PET achieves mapping resolutions at the element level (protein factor binding sites) and requires just moderate sequencing depth (Li et al 2010). Previously, ChIA-PET data was only analyzed for high-frequency chromatin interactions mediated by specific protein factors (Fullwood et al 2009;Li et al 2012;Kieffer-Kwon et al 2013).…”

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confidence: 99%

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

et al. 2016

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ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides information at all genomic scales of interest, from the high-resolution locations of binding sites and enriched chromatin interactions mediated by specific protein factors, to the low resolution of nonenriched interactions that reflect topological neighborhoods of higher-order chromosome folding. This multilevel nature of ChIA-PET data offers an opportunity to use multiscale 3D models to study structural-functional relationships at multiple length scales, but doing so requires a structural modeling platform. Here, we report the development of 3D-GNOME (3-Dimensional Genome Modeling Engine), a complete computational pipeline for 3D simulation using ChIA-PET data. 3D-GNOME consists of three integrated components: a graph-distance-based heat map normalization tool, a 3D modeling platform, and an interactive 3D visualization tool. Using ChIA-PET and Hi-C data derived from human B-lymphocytes, we demonstrate the effectiveness of 3D-GNOME in building 3D genome models at multiple levels, including the entire genome, individual chromosomes, and specific segments at megabase (Mb) and kilobase (kb) resolutions of single average and ensemble structures. Further incorporation of CTCF-motif orientation and high-resolution looping patterns in 3D simulation provided additional reliability of potential biologically plausible topological structures.

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ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

Abstract: ChIA-PET Tool can be used to process long-range chromatin interaction data. Results are visualized on a user-friendly genome browser.

Cited by 286 publications

References 16 publications

A decade of 3C technologies: insights into nuclear organization

A decade of 3C technologies: insights into nuclear organization

Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

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