The hierarchy of the 3D genome.

By J. Gibcus, Job Dekker. Molecules and Cells, 2013

710 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/cd8bb043295a71f232c93f7af61b7770f9ef8977

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Plant Science

Citations in the corpus

Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes (2014, positive): “The ChIA-PET technique was used because it yields high-resolution (~4kb) genome-wide interaction data, which is important because most loops involved in transcriptional regulation are between 1 and 100kb (Gibcus and Dekker, 2013).”
Modification of enhancer chromatin: what, how and why? (2013, background): “the looping model has gained extensive support with the emergence of technologies such as chromosome conformation capture (3C) and its derivatives 4C and 5C (reviewed in de Wit and de Laat, 2012; Gibcus and Dekker, 2013).”
YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, positive): “Enhancer-promoter interactions generally occur within larger chromosomal loop structures formed by the interaction of CTCF proteins bound to each of the loop anchors (Gibcus and Dekker, 2013; Gorkin et al., 2014; Hnisz et al., 2016a; Merkenschlager and Nora, 2016).”
Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization (2017, neutral): “We next sought to investigate to what extent CTCF disruption affects higher-order segregation of active and inactive chromosome domains into A- and B- compartments (Gibcus and Dekker, 2013; Lieberman-Aiden et al., 2009).”
Editing DNA methylation in the mammalian genome (2016, neutral): “Transcriptional enhancers normally interact with their target genes through the formation of DNA loops (Gibcus and Dekker, 2013; Gorkin et al., 2014; Kagey et al., 2010), which typically are constrained within larger CTCF-mediated loops called insulated neighborhoods (Dowen et al.”
Single-Cell and Single-Molecule Analysis of Gene Expression Regulation (2016, background): “organized structures in which chromosomes fold into complex 3D conformations (55).”
Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus (2018, methodology): “These correspond to locations of active and inactive transcription (Gibcus and Dekker, 2013).”
Formation of Chromosomal Domains by Loop Extrusion (2015, background): “, 2015), and several TADs often reside within a single contiguous compartment (Gibcus and Dekker, 2013; Gorkin et al., 2014) (Supplemental Notes).”
Activation of proto-oncogenes by disruption of chromosome neighborhoods (2015, background): “Transcriptional enhancers normally interact with their target genes through the formation of DNA loops (5-7), which typically are constrained within larger CTCF-cohesin mediated loops called insulated neighborhoods (8-10), which in turn can form clusters that contribute to topologically associating ”
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells (2018, background): “In one view, it has been proposed that TADs represent a fundamental physical unit of the genome organization within individual cells, which promote intradomain chromatin interactions but inhibit interdomain interactions through spatial segregation (6, 14, 15).”
Transcriptional Addiction in Cancer (2017, neutral): “…neighborhoods are the mechanistic basis of higher-order chromosome structures, such as topologically associating domains (TADs), and form a chromosome scaffold that is largely preserved throughout development (Gibcus and Dekker, 2013; Gorkin et al., 2014; Phillips-Cremins and Corces, 2013).”
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data (2013, background): “50 for a more extensive discussion).”
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function (2015, positive): “…2007), and the genome-wide pattern of CTCF occupancy is cell-type specific (Kim et al., 2007; Shen et al., 2012; Wang et al., 2012); however, CBSs are enriched at constitutive boundaries of topologically associated domains (TADs) (Dixon et al., 2012; Gibcus and Dekker, 2013; Zuin et al., 2014).”
Regulation of disease-associated gene expression in the 3D genome (2016, neutral): “101) .”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, positive): “…modeling based on data from recently developed chromosome conformation capture technology provides unprecedentedly detailed insights into the spatial organization of genomes (Cavalli and Misteli, 2013; Dekker et al., 2013; Engreitz et al., 2013; Gibcus and Dekker, 2013; Kimura et al., 2013).”