The role of loops on the order of eukaryotes and prokaryotes

FEBS Letters
Andreas Hofmann, Dieter W Heermann


The study of the three-dimensional organization of chromatin has recently gained much focus in the context of novel techniques for detecting genome-wide contacts using next-generation sequencing. These chromosome conformation capture-based methods give a deep topological insight into the architecture of the genome inside the nucleus. Several recent studies observe a compartmentalization of chromatin interactions into spatially confined domains. This structural feature of interphase chromosomes is not only supported by conventional studies assessing the interaction data of millions of cells, but also by analysis on the level of a single cell. We first present and examine the different models that have been proposed to elucidate these topological domains in eukaryotes. Then we show that a model which relies on the dynamic formation of loops within domains can account for the experimentally observed contact maps. Interestingly, the topological domain structure is not only found in mammalian genomes, but also in bacterial chromosomes.


Jan 21, 2016·Biophysical Journal·Thomas J LampoAndrew J Spakowitz
Mar 12, 2016·Cell·Job Dekker, Leonid A Mirny
May 24, 2016·Cell Reports·Geoffrey FudenbergLeonid A Mirny
Nov 15, 2016·Nucleus·C A BrackleyDavide Marenduzzo
Jun 13, 2017·Nature Methods·Geoffrey Fudenberg, Maxim V Imakaev
Dec 21, 2017·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Tejal AgarwalApratim Chatterji
May 8, 2018·Cold Spring Harbor Symposia on Quantitative Biology·Geoffrey FudenbergLeonid A Mirny
Dec 15, 2019·Genes·Colleen J Lawrimore, Kerry Bloom
Mar 16, 2018·Physical Review Letters·K E PolovnikovM V Tamm


Apr 3, 2001·Nature Reviews. Genetics·Thomas Cremer, C Cremer
Feb 16, 2002·Science·Job DekkerNancy Kleckner
Jul 17, 2004·Genes & Development·Lisa PostowNicholas R Cozzarelli
Oct 8, 2004·The EMBO Journal·Michèle ValensFrédéric Boccard
Feb 28, 2006·Biophysical Journal·Davide MarenduzzoPeter R Cook
Aug 4, 2006·Proceedings of the National Academy of Sciences of the United States of America·Suckjoon Jun, Bela Mulder
Jan 19, 2007·Nature Reviews. Genetics·Christian LanctôtThomas Cremer
Aug 30, 2008·PLoS Computational Biology·Angelo Rosa, Ralf Everaers
Nov 28, 2008·Critical Reviews in Biochemistry and Molecular Biology·Martijn S LuijsterburgRemus T Dame
Feb 24, 2009·Proceedings of the National Academy of Sciences of the United States of America·Julio Mateos-LangerakSandra Goetze
Jul 1, 2009·Cell·Jennifer E Phillips, Victor G Corces
Sep 16, 2009·The Journal of Cell Biology·Peter R Cook, Davide Marenduzzo
May 13, 2010·Journal of Visualized Experiments : JoVE·Nynke L van BerkumEric S Lander
Jul 17, 2010·Nature Reviews. Microbiology·Suckjoon Jun, Andrew Wright
Jan 20, 2011·PloS One·Manfred Bohn, Dieter W Heermann
Mar 8, 2011·Journal of Cell Science·Mariliis Tark-DameDieter W Heermann
Apr 8, 2011·Current Opinion in Cell Biology·Dieter W Heermann
May 17, 2011·Physical Biology·Anton V Persikov, Mona Singh
Oct 28, 2011·Molecular Microbiology·Remus T DameHelmut Schiessel
Dec 21, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Pascal ReissDieter W Heermann
Apr 18, 2012·Experimental Cell Research·Dieter W Heermann
Jun 1, 2012·PloS One·Hansjoerg Jerabek, Dieter W Heermann
Sep 8, 2012·Nature·Amartya SanyalJob Dekker
Sep 19, 2012·Proceedings of the National Academy of Sciences of the United States of America·Mariano BarbieriMario Nicodemi
Jan 8, 2013·Journal of Bacteriology·Axel Cournac, Jacqueline Plumbridge
Feb 19, 2013·Nature Structural & Molecular Biology·Catherine NaughtonNick Gilbert
Mar 8, 2013·Current Opinion in Cell Biology·Andrea Smallwood, Bing Ren
Mar 12, 2013·Molecular Cell·Johan H Gibcus, Job Dekker
Mar 19, 2013·Cell·Wendy A Bickmore, Bas van Steensel
Apr 16, 2013·Nucleic Acids Research·Yoko ItoAdele Murrell
May 28, 2013·Cell·Jennifer E Phillips-CreminsVictor G Corces
Sep 12, 2013·Molecular Systems Biology·Barbara Di VenturaVictor Sourjik

Related Concepts

Chromosome Structures
Chromatin Loop
Caulobacter crescentus
Caulobacter vibrioides
Decompression Sickness

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.