The Influence of the Cylindrical Shape of the Nucleosomes and H1 Defects on Properties of Chromatin
We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes, and the distance d between the in and outgoing DNA strands orthogonal to the axis of the co...
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| Veröffentlicht in: | Biophysical journal 2008-06, Vol.94 (11), p.4165-4172 |
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| creator | Diesinger, Philipp M. Heermann, Dieter W. |
| description | We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes, and the distance
d between the in and outgoing DNA strands orthogonal to the axis of the corresponding nucleosome cylinder. Factoring these chromatin features in, one gets essential changes in the chromatin phase diagram: Not only the shape of the excluded-volume borderline changes but also the orthogonal distance
d has a dramatic influence on the forbidden area. Furthermore, we examined the influence of H1 defects on the properties of the chromatin fiber. Thus, we present two possible strategies for chromatin compaction: The use of very dense states in the phase diagram in the gaps in the excluded-volume, borderline, or missing H1 histones can lead to very compact fibers. The chromatin fiber might use both of these mechanisms to compact itself at least locally. Line densities computed within the model coincident with the experimental values. |
| doi_str_mv | 10.1529/biophysj.107.113902 |
| format | Article |
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d between the in and outgoing DNA strands orthogonal to the axis of the corresponding nucleosome cylinder. Factoring these chromatin features in, one gets essential changes in the chromatin phase diagram: Not only the shape of the excluded-volume borderline changes but also the orthogonal distance
d has a dramatic influence on the forbidden area. Furthermore, we examined the influence of H1 defects on the properties of the chromatin fiber. Thus, we present two possible strategies for chromatin compaction: The use of very dense states in the phase diagram in the gaps in the excluded-volume, borderline, or missing H1 histones can lead to very compact fibers. The chromatin fiber might use both of these mechanisms to compact itself at least locally. Line densities computed within the model coincident with the experimental values.</description><identifier>ISSN: 0006-3495</identifier><identifier>EISSN: 1542-0086</identifier><identifier>DOI: 10.1529/biophysj.107.113902</identifier><identifier>PMID: 18234821</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Binding Sites ; Biophysical Theory and Modeling ; Cellular biology ; Chromatin ; Chromatin - chemistry ; Chromatin - ultrastructure ; Computer Simulation ; Deoxyribonucleic acid ; DNA ; Eukaryotes ; Histones - chemistry ; Histones - ultrastructure ; Macromolecular Substances - chemistry ; Models, Chemical ; Models, Molecular ; Molecular biology ; Molecular Conformation ; Nucleosomes - chemistry ; Nucleosomes - ultrastructure ; Protein Binding</subject><ispartof>Biophysical journal, 2008-06, Vol.94 (11), p.4165-4172</ispartof><rights>2008 The Biophysical Society</rights><rights>Copyright Biophysical Society Jun 1, 2008</rights><rights>Copyright © 2008, Biophysical Society</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c516t-a570d717989887ee56453a7e885edfe18afbd592412c58a8cc51a075d7f652aa3</citedby><cites>FETCH-LOGICAL-c516t-a570d717989887ee56453a7e885edfe18afbd592412c58a8cc51a075d7f652aa3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2480696/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://dx.doi.org/10.1529/biophysj.107.113902$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,3550,27924,27925,45995,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18234821$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Diesinger, Philipp M.</creatorcontrib><creatorcontrib>Heermann, Dieter W.</creatorcontrib><title>The Influence of the Cylindrical Shape of the Nucleosomes and H1 Defects on Properties of Chromatin</title><title>Biophysical journal</title><addtitle>Biophys J</addtitle><description>We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes, and the distance
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d has a dramatic influence on the forbidden area. Furthermore, we examined the influence of H1 defects on the properties of the chromatin fiber. Thus, we present two possible strategies for chromatin compaction: The use of very dense states in the phase diagram in the gaps in the excluded-volume, borderline, or missing H1 histones can lead to very compact fibers. The chromatin fiber might use both of these mechanisms to compact itself at least locally. Line densities computed within the model coincident with the experimental values.</description><subject>Binding Sites</subject><subject>Biophysical Theory and Modeling</subject><subject>Cellular biology</subject><subject>Chromatin</subject><subject>Chromatin - chemistry</subject><subject>Chromatin - ultrastructure</subject><subject>Computer Simulation</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Eukaryotes</subject><subject>Histones - chemistry</subject><subject>Histones - ultrastructure</subject><subject>Macromolecular Substances - chemistry</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Molecular biology</subject><subject>Molecular Conformation</subject><subject>Nucleosomes - chemistry</subject><subject>Nucleosomes - ultrastructure</subject><subject>Protein Binding</subject><issn>0006-3495</issn><issn>1542-0086</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNp9kUtv1DAUhS0EotPCL0BCEQu6yuDrxI8sQELDo5UqQKKsLY9zQzxK7NROKs2_x9UM5bHoytI93zm27yHkBdA1cNa82bow9fu0WwOVa4CqoewRWQGvWUmpEo_JilIqyqpu-Ak5TWlHKTBO4Sk5AcWqWjFYEXvdY3Hpu2FBb7EIXTHnwWY_ON9GZ81QfO_NdC98WeyAIYURU2F8W1xA8QE7tHMqgi--xTBhnF0WM7_pYxjN7Pwz8qQzQ8Lnx_OM_Pj08XpzUV59_Xy5eX9VWg5iLg2XtJUgG9UoJRG5qHllJCrFse0QlOm2LW9YDcxyZZTNNkMlb2UnODOmOiPvDrnTsh2xtejnaAY9RTeauNfBOP2v4l2vf4ZbzWpFRSNywPkxIIabBdOsR5csDoPxGJaklahrRjmvM_n6QVJSWXGlIIOv_gN3YYk-r0Ez4KIBUVUZqg6QjSGliN39m4Hqu671767zQOpD19n18u_v_vEcy83A2wOAeem3DqNO1t3V3LqYK9NtcA9e8AtAiLx6</recordid><startdate>20080601</startdate><enddate>20080601</enddate><creator>Diesinger, Philipp M.</creator><creator>Heermann, Dieter W.</creator><general>Elsevier Inc</general><general>Biophysical Society</general><general>The Biophysical Society</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AF</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>S0X</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20080601</creationdate><title>The Influence of the Cylindrical Shape of the Nucleosomes and H1 Defects on Properties of Chromatin</title><author>Diesinger, Philipp M. ; Heermann, Dieter W.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c516t-a570d717989887ee56453a7e885edfe18afbd592412c58a8cc51a075d7f652aa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Binding Sites</topic><topic>Biophysical Theory and Modeling</topic><topic>Cellular biology</topic><topic>Chromatin</topic><topic>Chromatin - chemistry</topic><topic>Chromatin - ultrastructure</topic><topic>Computer Simulation</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Eukaryotes</topic><topic>Histones - chemistry</topic><topic>Histones - ultrastructure</topic><topic>Macromolecular Substances - chemistry</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Molecular biology</topic><topic>Molecular Conformation</topic><topic>Nucleosomes - chemistry</topic><topic>Nucleosomes - ultrastructure</topic><topic>Protein Binding</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Diesinger, Philipp M.</creatorcontrib><creatorcontrib>Heermann, Dieter W.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>SIRS Editorial</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Biophysical journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Diesinger, Philipp M.</au><au>Heermann, Dieter W.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Influence of the Cylindrical Shape of the Nucleosomes and H1 Defects on Properties of Chromatin</atitle><jtitle>Biophysical journal</jtitle><addtitle>Biophys J</addtitle><date>2008-06-01</date><risdate>2008</risdate><volume>94</volume><issue>11</issue><spage>4165</spage><epage>4172</epage><pages>4165-4172</pages><issn>0006-3495</issn><eissn>1542-0086</eissn><abstract>We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes, and the distance
d between the in and outgoing DNA strands orthogonal to the axis of the corresponding nucleosome cylinder. Factoring these chromatin features in, one gets essential changes in the chromatin phase diagram: Not only the shape of the excluded-volume borderline changes but also the orthogonal distance
d has a dramatic influence on the forbidden area. Furthermore, we examined the influence of H1 defects on the properties of the chromatin fiber. Thus, we present two possible strategies for chromatin compaction: The use of very dense states in the phase diagram in the gaps in the excluded-volume, borderline, or missing H1 histones can lead to very compact fibers. The chromatin fiber might use both of these mechanisms to compact itself at least locally. Line densities computed within the model coincident with the experimental values.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>18234821</pmid><doi>10.1529/biophysj.107.113902</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Binding Sites Biophysical Theory and Modeling Cellular biology Chromatin Chromatin - chemistry Chromatin - ultrastructure Computer Simulation Deoxyribonucleic acid DNA Eukaryotes Histones - chemistry Histones - ultrastructure Macromolecular Substances - chemistry Models, Chemical Models, Molecular Molecular biology Molecular Conformation Nucleosomes - chemistry Nucleosomes - ultrastructure Protein Binding |
| title | The Influence of the Cylindrical Shape of the Nucleosomes and H1 Defects on Properties of Chromatin |
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