Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gülsoy, Günhan; Deng, Xinxian; Cook, Savannah; Ware, Carol B.; Krumm, Anton; Shendure, Jay; Blau, C. Anthony; Distèche, Christine M.; Noble, William Stafford; Duan, Zhijun

doi:10.1038/nmeth.3205

Cited by 185 publications

(200 citation statements)

References 52 publications

(101 reference statements)

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“…Crosslinked nuclei were then prepared as described in Duan et al (19). In situ DNase Hi-C was performed as described previously (43,55). For each experiment, ∼2 × 10 8 isolated yeast nuclei were used.…”

Section: Methodsmentioning

confidence: 99%

Form and function of topologically associating genomic domains in budding yeast

Eser

Chandler-Brown

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The genome of metazoan cells is organized into topologically associating domains (TADs) that have similar histone modifications, transcription level, and DNA replication timing. Although similar structures appear to be conserved in fission yeast, computational modeling and analysis of high-throughput chromosome conformation capture (Hi-C) data have been used to argue that the small, highly constrained budding yeast chromosomes could not have these structures. In contrast, herein we analyze Hi-C data for budding yeast and identify 200-kb scale TADs, whose boundaries are enriched for transcriptional activity. Furthermore, these boundaries separate regions of similarly timed replication origins connecting the longknown effect of genomic context on replication timing to genome architecture. To investigate the molecular basis of TAD formation, we performed Hi-C experiments on cells depleted for the Forkhead transcription factors, Fkh1 and Fkh2, previously associated with replication timing. Forkhead factors do not regulate TAD formation, but do promote longer-range genomic interactions and control interactions between origins near the centromere. Thus, our work defines spatial organization within the budding yeast nucleus, demonstrates the conserved role of genome architecture in regulating DNA replication, and identifies a molecular mechanism specifically regulating interactions between pericentric origins. A n important distinction between eukaryotic and prokaryotic cells is the presence of the eukaryotic nucleus, which compartmentalizes the cell. It is becoming increasingly clear that the eukaryotic nuclear compartment contains additional layers of spatial organization, including the nucleolus, splicing bodies, transcriptional foci, and the peripheral localization of telomeres (1, 2). In addition, high-throughput chromosome conformation capture (Hi-C) technologies have recently revealed the spatial organization of chromatin into topologically associating domains (TADs) on the 100-kb to 1-Mb scale for mammals (3, 4), as well as the fly Drosophila melanogaster (5), the worm Caenorhabditis elegans (6), and the fission yeast Schizosaccharomyces pombe (7). Loci within a TAD are much more likely to interact with one another than with loci outside the domain (5,8,9).In metazoans, topological domains play important roles in coordinating the DNA-templated processes of replication and transcription (10-12). Chromatin within a TAD tends to have similar histone modifications, and consequently euchromatic or heterochromatic state, so that the genome is organized into self-associated globules that are either permissive or repressive of transcription. Repressive TADs are likely to be associated with the nuclear periphery (8). In addition to coordinating transcription, TADs also coordinate replication so that replication origins within a domain activate synchronously.That TAD nuclear organization is important for transcription and replication has motivated much recent work on the molecular mechanisms underlying TAD formation. The...

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Section: Methodsmentioning

confidence: 99%

Form and function of topologically associating genomic domains in budding yeast

Eser

Chandler-Brown

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…The type of data produced with Hi-C is therefore more comprehensive than what other 3C-type methods usually yield, as was previously described in detail (111). The production of Hi-C libraries is similar to the production of 3C libraries: cell populations are first chemically fixed with formaldehyde, and the chromatin is digested with a restriction enzyme or DNase I, which was recently reported to achieve higher resolutions (112). The restriction fragment overhangs are then filled with Klenow enzyme and a mixture of deoxynucleoside triphosphates (dNTPs) that includes biotin-14-dCTP.…”

Section: Inferring Genome Organizationmentioning

confidence: 99%

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

Fraser

Williamson

Bickmore

et al. 2015

Microbiol Mol Biol Rev

203

174

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SUMMARY In humans, nearly two meters of genomic material must be folded to fit inside each micrometer-scale cell nucleus while remaining accessible for gene transcription, DNA replication, and DNA repair. This fact highlights the need for mechanisms governing genome organization during any activity and to maintain the physical organization of chromosomes at all times. Insight into the functions and three-dimensional structures of genomes comes mostly from the application of visual techniques such as fluorescence in situ hybridization (FISH) and molecular approaches including chromosome conformation capture (3C) technologies. Recent developments in both types of approaches now offer the possibility of exploring the folded state of an entire genome and maybe even the identification of how complex molecular machines govern its shape. In this review, we present key methodologies used to study genome organization and discuss what they reveal about chromosome conformation as it relates to transcription regulation across genomic scales in mammals.

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“…To circumvent this issue, two alternatives were developed. In the first, restriction enzymes were replaced by DNase I in order to digest crosslinked chromatin in two human cell lines, resulting in a Hi-C map with a resolution up to 2 kb (Ma et al 2015). Combining DNase I Hi-C output with DNA sequence capture, the authors dissected the 3D-interactome of lincRNA promoters in human H1 ES and K562 cells.…”

Section: Technical Limitations and Further Improvements In Hi-c Technmentioning

confidence: 99%

Chromosome conformation capture technologies and their impact in understanding genome function

2016

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It has been more than a decade since the first chromosome conformation capture (3C) assay was described. The assay was originally devised to measure the frequency with which two genomic loci interact within the three-dimensional (3D) nuclear space. Over time, this method has evolved both qualitatively and quantitatively, from detection of pairwise interaction of two unique loci to generating maps for the global chromatin interactome. Combined with the analysis of the epigenetic chromatin context, these advances led to the unmasking of general genome folding principles. The evolution of 3C-based methods has been supported first by the revolution in ChIP and then by sequencingbased approaches, methods that were primarily tools to study the unidimensional genome. The gradual improvement of 3C-based methods illustrates how the field adapted to the need to gradually address more subtle questions, beginning with enquiries of reductionist nature to reach more holistic perspectives, as the technology advanced, in a process that is greatly improving our knowledge on genome behavior and regulation. Here, we describe the evolution of 3C and other 3C-based methods for the analysis of chromatin interactions, along with a brief summary of their contribution in uncovering the significance of the threedimensional world within the nucleus. We also discuss their inherent limitations and caveats in order to provide a critical view of the power and the limits of this technology.

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Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

Cited by 185 publications

References 52 publications

Form and function of topologically associating genomic domains in budding yeast

Form and function of topologically associating genomic domains in budding yeast

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

Chromosome conformation capture technologies and their impact in understanding genome function

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