Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

J Dekker, MA Marti-Renom, LA Mirny - Nature Reviews Genetics, 2013‏ - nature.com
How DNA is organized in three dimensions inside the cell nucleus and how this affects the
ways in which cells access, read and interpret genetic information are among the longest …

Long-range control of gene expression: emerging mechanisms and disruption in disease

DA Kleinjan, V Van Heyningen - The American Journal of Human Genetics, 2005‏ - cell.com
Transcriptional control is a major mechanism for regulating gene expression. The complex
machinery required to effect this control is still emerging from functional and evolutionary …

Chromatin organization by an interplay of loop extrusion and compartmental segregation

J Nuebler, G Fudenberg, M Imakaev, N Abdennur… - Biophysical …, 2018‏ - cell.com
Eukaryotic chromatin, is far from being simply a randomly arranged polymer in the cell
nucleus. Rather, Hi-C and imaging reveal a high degree of spatial organization on various …

Capturing chromosome conformation

J Dekker, K Rippe, M Dekker, N Kleckner - science, 2002‏ - science.org
We describe an approach to detect the frequency of interaction between any two genomic
loci. Generation of a matrix of interaction frequencies between sites on the same or different …

[ספר][B] Physical biology of the cell

R Phillips, J Kondev, J Theriot, H Garcia - 2012‏ - taylorfrancis.com
Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics
for undergraduate or graduate students. It maps the huge and complex landscape of cell …

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for map** interactions between genomic elements

J Dostie, TA Richmond, RA Arnaout, RR Selzer… - Genome …, 2006‏ - genome.cshlp.org
Physical interactions between genetic elements located throughout the genome play
important roles in gene regulation and can be identified with the Chromosome Conformation …

Loo** and interaction between hypersensitive sites in the active β-globin locus

B Tolhuis, RJ Palstra, E Splinter, F Grosveld, W De Laat - Molecular cell, 2002‏ - cell.com
Eukaryotic transcription can be regulated over tens or even hundreds of kilobases. We show
that such long-range gene regulation in vivo involves spatial interactions between …

Targeted sequencing by proximity ligation for comprehensive variant detection and local haploty**

PJP De Vree, E De Wit, M Yilmaz… - Nature …, 2014‏ - nature.com
Despite developments in targeted gene sequencing and whole-genome analysis
techniques, the robust detection of all genetic variation, including structural variants, in and …

The second decade of 3C technologies: detailed insights into nuclear organization

A Denker, W De Laat - Genes & development, 2016‏ - genesdev.cshlp.org
The relevance of three-dimensional (3D) genome organization for transcriptional regulation
and thereby for cellular fate at large is now widely accepted. Our understanding of the …

Theoretical analysis of epigenetic cell memory by nucleosome modification

IB Dodd, MA Micheelsen, K Sneppen, G Thon - Cell, 2007‏ - cell.com
Chromosomal regions can adopt stable and heritable alternative states resulting in bistable
gene expression without changes to the DNA sequence. Such epigenetic control is often …