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Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization

Ivan Junier, Olivier Martin, François Képès, Hanah Margalit
2010 PLoS Computational Biology  
Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization  ...  Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close-by.  ...  Marsili and M. Weigt for helpful comments. This work was supported by the Sixth European Research Framework (project number 034952, GENNETEC project), PRES UniverSud Paris, CNRS and Genopole.  ... 
doi:10.1371/journal.pcbi.1000678 pmid:20169181 pmcid:PMC2820526 fatcat:tbfj3nmr5ngptf4epoxdg3bgza

A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation

Miriam Fritsche, Songling Li, Dieter W. Heermann, Paul A. Wiggins
2011 Nucleic Acids Research  
Investigating this assumption, we find the DNA chain to self-organize into several topologically distinguishable domains where the interplay between the entropic repulsion of chromosomal loops and their  ...  Computational modeling shows that confinement-induced organization is able to overcome the chromosome's propensity to mix by the formation of topological domains.  ...  For this work, the bwGRiD parallel computing facilities (http://, member of the German D-Grid initiative, funded by the Ministry for Education and Research and the Ministry for Science,  ... 
doi:10.1093/nar/gkr779 pmid:21976727 pmcid:PMC3273793 fatcat:ey7ndbdaljhihk7bkw3hdx4xom

The genome in space and time: Does form always follow function?

Zhijun Duan, Carl Anthony Blau
2012 Bioessays  
However, our understanding of the mechanisms underlying both the topological organization of genomes and the various nuclear processes is still largely incomplete.  ...  Recent systematic studies using newly developed genomic approaches have revealed common mechanisms and principles that underpin the spatial organization of eukaryotic genomes and allow them to respond  ...  Acknowledgments We are grateful to Tony Krumm, Mark Groudine, Marshall Horwitz, and Xinxian Deng for critical reading, comments, and suggestions.  ... 
doi:10.1002/bies.201200034 pmid:22777837 pmcid:PMC3638008 fatcat:prq7getm3bg2laqkdi72hnkqge

Epigenetics of antigen-receptor gene assembly

Cornelis Murre
2007 Current Opinion in Genetics and Development  
Acknowledgements I thank Suchit Jhujhunwala, Menno van Zelm, Roy Riblet, Mandy Peak, Tobias Knoch and Doug Smith for stimulating discussions regarding chromatin topology.  ...  Work on this subject in the author's laboratory was supported by the NIH.  ...  The IgK and L light chain loci are also organized into distinct DNA elements, encoding V H , J H and C H segments.  ... 
doi:10.1016/j.gde.2007.08.006 pmid:17920858 pmcid:PMC2151926 fatcat:iarhoe3trjex3pmiz7owapuvo4

The Role of Chromosome Domains in Shaping the Functional Genome

Tom Sexton, Giacomo Cavalli
2015 Cell  
Research at the G.C. lab is supported by grants from the European Research Council (ERC-2008-AdG No 232947), the CNRS, the European Network of Excellence EpiGeneSys, the Agence Nationale de la Recherche  ...  Research at the T.S. lab is supported by INSERM, the ATIP-Avenir program, and the Laboratoire d'Excellence INRT.  ...  However, the known effects of RNA polymerase binding and elongation on local DNA topology (Lavelle, 2014) suggest that gene expression programs and chromatin organization could have a profound effect  ... 
doi:10.1016/j.cell.2015.02.040 pmid:25768903 fatcat:kvjww3bwkzgltm2evauit5mkga


2008 Kobunshi  
GI POFs are expected as local area network media in home and office.  ...  In the first step of the dopant diffusion co-extrusion process, a polymer bulk, which includes dopant with a high refractive index and the homo polymer bulk are melted in the core and cladding extruder  ...  Co.) coated on top of the nanoparticles, induced by the LSP field in few nanometer-wide nanogaps separating corners of the neighboring gold nanoblocks.  ... 
doi:10.1295/kobunshi.57.962 fatcat:daqulzlzqbgolp43f4csexcahq

CTCF, Cohesin, and Chromatin in Human Cancer

Sang-Hyun Song, Tae-You Kim
2017 Genomics & Informatics  
Such spatial genomic organization is functionally important for the spatial disposition of chromosomes to control cell fate during development and differentiation.  ...  Their dynamic interactions in three dimensions within the nucleus regulate gene transcription by changing the chromatin architecture.  ...  The spatial folding of chromosomes and their organization in the nucleus have profound effects on gene expression [5, 6] .  ... 
doi:10.5808/gi.2017.15.4.114 pmid:29307136 pmcid:PMC5769866 fatcat:iq3xejrubjgpxkuajssgvjqkg4

In This Issue

2014 Cell  
Optogenetic inhibition of the relevant neuronal circuit reduced both the synchrony and the correct behavior, suggesting a role for this neural oscillation in spatial working memory.  ...  The authors find strong selection in genes related to fatty acid metabolism, pigmentation, and cardiovascular function, reflecting the unique adaptations in response to Arctic climates and a hyperlipid  ...  In this disease, mitochondrial abnormalities are caused by hyperactivation of the DNA damage sensor PARP1 and reduced NAD+-SIRT1-PGC-1a signaling.  ... 
doi:10.1016/j.cell.2014.04.021 fatcat:2zhs7efwhvglvez5mme4zusgoy

The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

Suchit Jhunjhunwala, Menno C. van Zelm, Mandy M. Peak, Steve Cutchin, Roy Riblet, Jacques J.M. van Dongen, Frank G. Grosveld, Tobias A. Knoch, Cornelis Murre
2008 Cell  
Acknowledgements The text of this chapter is partly reprinted from the paper "Chromatin architecture and the generation of antigen receptor diversity", Cell, 138(3), 2009.  ...  is partly reprinted from the paper "The 3D-Structure of the Immunoglobulin Heavy Chain Locus: Implications for Long-Range Genomic  ...  These observations reveal how the Igh topology permits DNA elements that are separated by large genomic distances to be localized in relatively close spatial proximity.  ... 
doi:10.1016/j.cell.2008.03.024 pmid:18423198 pmcid:PMC2771211 fatcat:yxb5rqkg6feslbgbamntum2kyq

Spatial Organization of Chromatin: Transcriptional Control of Adaptive Immune Cell Development

Jagan M. R. Pongubala, Cornelis Murre
2021 Frontiers in Immunology  
Higher-order spatial organization of the genome into chromatin compartments (permissive and repressive), self-associating domains (TADs), and regulatory loops provides structural integrity and offers diverse  ...  In particular, chromatin regulatory loops, which bring enhancer and associated transcription factors in close spatial proximity to target gene promoters, play essential roles in regulating gene expression  ...  and CM is supported by the National Institutes of Health (NIH) (AI00880, AI09599 and AI102853).  ... 
doi:10.3389/fimmu.2021.633825 pmid:33854505 pmcid:PMC8039525 fatcat:ixmxcc7ycfaqfler3fwtm4kyii

High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization

Asli Yildirim, Michael Feig
2018 Nucleic Acids Research  
These findings shed light on the correlation between the spatial organization of the genome and biological functions.  ...  Models were built as a plectonemically supercoiled circular DNA and by incorporating chromosome conformation capture based data to generate an ensemble of base pair resolution models consistent with the  ...  force data for DNA-DNA interactions at different ion concentrations.  ... 
doi:10.1093/nar/gky141 pmid:29529244 pmcid:PMC5934669 fatcat:q2p77xwc2je2jc533227w3pxfm

Chromosome Intermingling: Mechanical Hotspots for Genome Regulation

Caroline Uhler, G.V. Shivashankar
2017 Trends in Cell Biology  
In this review, we first discuss different modes of mechanotransduction to the nucleus. Then we highlight the role of the spatial organization of chromosomes for integrating these signals.  ...  In particular, we emphasize the importance of chromosome intermingling for gene regulation.  ...  GVS was funded by the Mechanobiology Institute, Singapore, MOE-Tier3 grant Singapore and IFOM, Milan Italy. We thank members of the Uhler and Shivashankar laboratories for useful discussions.  ... 
doi:10.1016/j.tcb.2017.06.005 pmid:28728836 fatcat:ryqjmpxwvfbn3hrxskoid3elwe

The spatial biology of transcription and translation in rapidly growing Escherichia coli

Somenath Bakshi, Heejun Choi, James C. Weisshaar
2015 Frontiers in Microbiology  
Monte Carlo simulations of a polymer bead model built to mimic the chromosomal DNA and ribosomes (either 70S-polysomes or 30S and 50S subunits) explain spatial segregation or mixing of ribosomes and nucleoids  ...  There they initiate co-transcriptional translation, which is an important mechanism for maintaining RNAP forward progress and protecting the nascent mRNA chain.  ...  Acknowledgments Different aspects of this research were supported by the grants CHE-1213860 from the US National Science Foundation and R01-GM094510 and R01-GM093265 from the National Institutes of Health  ... 
doi:10.3389/fmicb.2015.00636 pmid:26191045 pmcid:PMC4488752 fatcat:jch6trvg3rg7dkz2efwc6woj3e

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

Vincenzo G Benza, Bruno Bassetti, Kevin D Dorfman, Vittore F Scolari, Krystyna Bromek, Pietro Cicuta, Marco Cosentino Lagomarsino
2012 Reports on progress in physics (Print)  
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid).  ...  The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organised at various length scales.  ...  Acknowledgments The authors are very grateful to Bianca Sclavi for discussions, feedback and help with the revision of this manuscript, and to Mario Nicodemi, Andrea Parmeggiani, Eric Siggia,  ... 
doi:10.1088/0034-4885/75/7/076602 pmid:22790781 fatcat:2b7s5pjzfzf75k3pbd4ulx3sia

Genome maintenance in the context of 4D chromatin condensation

Sonia Yu, Fan Yang, Wen H. Shen
2016 Cellular and Molecular Life Sciences (CMLS)  
We will also highlight the importance of the spatially-and-temporally-conscious orchestration of chromatin remodeling to ensure high-fidelity genetic transmission.  ...  The eukaryotic genome is packaged in the three-dimensional nuclear space by forming loops, domains and compartments in a hierarchical manner.  ...  Acknowledgments Work in the authors' laboratory is supported by NIH grant R01GM100478.  ... 
doi:10.1007/s00018-016-2221-2 pmid:27098512 pmcid:PMC4956502 fatcat:zjjvldolkzak7h37ot26m6jgxq
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