Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman Aiden,Nynke L. van Berkum,Louise Williams,Maxim Imakaev,Tobias Ragoczy,Tobias Ragoczy,Agnes Telling,Agnes Telling,Ido Amit,Bryan R. Lajoie,Peter J. Sabo,Michael O. Dorschner,Richard Sandstrom,Bradley E. Bernstein,Bradley E. Bernstein,Michaël Bender,Mark Groudine,Mark Groudine,Andreas Gnirke,John A. Stamatoyannopoulos,Leonid A. Mirny,Eric S. Lander,Eric S. Lander,Job Dekker +23 more
TLDR
Hi-C is described, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing and demonstrates the power of Hi-C to map the dynamic conformations of entire genomes.Abstract:
We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.read more
Citations
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Epigenetic Regulation: A New Frontier for Biomedical Engineers
TL;DR: This review provides biomedical engineers with an overview of the principles of epigenetics, methods of study, recent findings in epigenetic regulation in health and disease, and computational and sequencing tools for epigenetics analysis, with an emphasis on the cardiovascular system.
Journal ArticleDOI
Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution
Pelin Sahlén,Ilgar Abdullayev,Ilgar Abdullayev,Daniel Ramsköld,Daniel Ramsköld,Liudmila Matskova,Nemanja Rilakovic,Britta Lötstedt,Thomas J. Albert,Joakim Lundeberg,Rickard Sandberg,Rickard Sandberg +11 more
TL;DR: HiCap, which combines a 4-cutter restriction enzyme Hi-C with sequence capture of promoter regions with results close to single-enhancer resolution, is developed and applied to mouse embryonic stem cells.
Journal ArticleDOI
Multiscale simulation of DNA.
TL;DR: The most recent theoretical methods that have been considered to study DNA, from the electron to the chromosome, are described, enriching knowledge on this fascinating molecule.
Journal ArticleDOI
LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation
Francesca Telese,Qi Ma,Patricia Montilla Perez,Dimple Notani,Soohwan Oh,Wenbo Li,Davide Comoletti,Kenneth A. Ohgi,Havilah Taylor,Michael G. Rosenfeld +9 more
TL;DR: The epigenetic signature of the neuronal enhancers required for transcriptional regulation of synaptic plasticity genes during memory formation is identified, linking this to Reelin signaling, revealing an unprecedented role for its intracellular domain in the regulation of synaptically generated signals.
Journal ArticleDOI
Effect of nuclear architecture on the efficiency of double-strand break repair
TL;DR: The results challenge present models that posit an active scanning of the whole nuclear volume by the broken chromosomal end and demonstrate that the search for homology is a limiting step in homologous recombination, and emphasize the importance of nuclear organization in genome maintenance.
References
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