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Open AccessJournal ArticleDOI

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

Luca Giorgetti, +12 more
- 08 May 2014 - 
- Vol. 157, Iss: 4, pp 950-963
TLDR
It is demonstrated that contacts between potential regulatory elements occur in the context of fluctuating structures rather than stable loops and proposed that such fluctuations may contribute to asymmetric expression in the Xic during X inactivation.
About: 
This article is published in Cell.The article was published on 2014-05-08 and is currently open access. It has received 444 citations till now. The article focuses on the topics: Chromosome conformation capture & Population.

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Citations
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Journal ArticleDOI

Single-cell chromatin accessibility reveals principles of regulatory variation

Jason D. Buenrostro, +7 more
- 23 Jul 2015 - 
TL;DR: A robust method for mapping the accessible genome of individual cells by assay for transposase-accessible chromatin using sequencing (ATAC-seq) integrated into a programmable microfluidics platform is developed and single-cell analysis of DNA accessibility provides new insight into cellular variation of the ‘regulome’.
Journal ArticleDOI

Formation of Chromosomal Domains by Loop Extrusion

Geoffrey Fudenberg, +6 more
- 31 May 2016 - 
TL;DR: This model produces TADs and finer-scale features of Hi-C data because each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops.
Journal ArticleDOI

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

Elphège P. Nora, +8 more
- 18 May 2017 - 
TL;DR: The data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading, and provides new fundamental insights into the rules governing mammalian genome organization.
Journal ArticleDOI

Organization and function of the 3D genome.

Boyan B. Bonev, +3 more
- 01 Nov 2016 - 
TL;DR: The insights into chromatin architecture that have been gained through recent technological developments in quantitative biology, genomics and cell and molecular biology approaches are discussed and how these new concepts have been used to address important biological questions in development and disease are explained.
Journal ArticleDOI

The 3D Genome as Moderator of Chromosomal Communication

Job Dekker, +1 more
- 10 Mar 2016 - 
TL;DR: A view of the interphase 3D genome characterized by extensive physical compartmentalization and insulation on the one hand and facilitated long-range interactions on the other is presented.
References
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Journal ArticleDOI

Equation of state calculations by fast computing machines

N. Metropolis, +4 more
- 01 Jun 1953 - 
TL;DR: In this article, a modified Monte Carlo integration over configuration space is used to investigate the properties of a two-dimensional rigid-sphere system with a set of interacting individual molecules, and the results are compared to free volume equations of state and a four-term virial coefficient expansion.
Journal ArticleDOI

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Jesse R. Dixon, +10 more
- 17 May 2012 - 
TL;DR: It is found that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.
Journal ArticleDOI

A guided tour into subcellular colocalization analysis in light microscopy

Susanne Bolte, +1 more
- 01 Dec 2006 - 
TL;DR: A novel toolbox for subcellular colocalization analysis under ImageJ is created that integrates current global statistic methods and a novel object‐based approach to assess proteins residing on intracellular structures by fluorescence microscopy.
Journal ArticleDOI

Spatial partitioning of the regulatory landscape of the X-inactivation centre

Elphège P. Nora, +26 more
- 17 May 2012 - 
TL;DR: In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, this study sets the stage for the full genetic dissection of the mouse X-inactivation centre.
Journal ArticleDOI

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

Tom Sexton, +8 more
- 03 Feb 2012 - 
TL;DR: A high-resolution chromosomal contact map derived from a modified genome-wide chromosome conformation capture approach applied to Drosophila embryonic nuclei is presented, laying the foundation for detailed studies of chromosome structure and function in a genetically tractable system.
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Topological domains in mammalian genomes identified by analysis of chromatin interactions

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Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

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- 09 Oct 2009 - 

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Suhas S.P. Rao, +15 more
- 18 Dec 2014 - 

Spatial partitioning of the regulatory landscape of the X-inactivation centre

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- 17 May 2012 - 

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

Takashi Nagano, +8 more
- 03 Oct 2013 -