https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2018Lei_DNABennet 2026-05-24T19:52:48Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2018Lei_DNABennet&diff=4853&oldid=prev 2024-11-12T09:31:17Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:31, 12 November 2024</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Citation ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Citation ==</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Molecular Organization </del>of <del style="font-weight: bold; text-decoration: none;">the Early Stages of Nucleosome Phase Separation Visualized by Cryo</del>-Electron Tomography, <del style="font-weight: bold; text-decoration: none;">Meng Zhang</del>, <del style="font-weight: bold; text-decoration: none;">César Díaz-Celis</del>, <del style="font-weight: bold; text-decoration: none;">Bibiana Onoa, Cristhian Cañari-Chumpitaz</del>, <del style="font-weight: bold; text-decoration: none;">Katherinne I. Requejo</del>, <del style="font-weight: bold; text-decoration: none;">Jianfang Liu</del>, <del style="font-weight: bold; text-decoration: none;">Michael Vien</del>, <del style="font-weight: bold; text-decoration: none;">Eva Nogales</del>, Gang Ren, <del style="font-weight: bold; text-decoration: none;">and Carlos Bustamante, Molecular Cell</del>, (<del style="font-weight: bold; text-decoration: none;">2022</del>), <del style="font-weight: bold; text-decoration: none;">18;82(16)</del>:<del style="font-weight: bold; text-decoration: none;">3000-3014.e9; PMID: 35907400 </del>DOI: 10.<del style="font-weight: bold; text-decoration: none;">1016</del>/<del style="font-weight: bold; text-decoration: none;">j.molcel.2022.06.032</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">3D Structural Dynamics </ins>of <ins style="font-weight: bold; text-decoration: none;">DNA Origami Mechanisms and Machines Using Individual</ins>-<ins style="font-weight: bold; text-decoration: none;">Particle </ins>Electron Tomography, <ins style="font-weight: bold; text-decoration: none;">Dongsheng Lei</ins>, <ins style="font-weight: bold; text-decoration: none;">Alex Marras</ins>, <ins style="font-weight: bold; text-decoration: none;">Jianfang Liu</ins>, <ins style="font-weight: bold; text-decoration: none;">Chaomin Huang</ins>, <ins style="font-weight: bold; text-decoration: none;">Lifeng Zhou</ins>, <ins style="font-weight: bold; text-decoration: none;">Carlos Castro</ins>, <ins style="font-weight: bold; text-decoration: none;">Hai-Jun Su</ins>, Gang Ren, <ins style="font-weight: bold; text-decoration: none;">Nature Communications</ins>, (<ins style="font-weight: bold; text-decoration: none;">2018</ins>), <ins style="font-weight: bold; text-decoration: none;">9</ins>:<ins style="font-weight: bold; text-decoration: none;">592, </ins>DOI: 10.<ins style="font-weight: bold; text-decoration: none;">1038</ins>/<ins style="font-weight: bold; text-decoration: none;">s41467-018-03018-0</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Abstract ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Abstract ==</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">It </del>has <del style="font-weight: bold; text-decoration: none;">been proposed that </del>the <del style="font-weight: bold; text-decoration: none;">intrinsic property </del>of <del style="font-weight: bold; text-decoration: none;">nucleosome arrays </del>to <del style="font-weight: bold; text-decoration: none;">undergo liquid</del>-<del style="font-weight: bold; text-decoration: none;">liquid phase separation </del>(<del style="font-weight: bold; text-decoration: none;">LLPS</del>) in <del style="font-weight: bold; text-decoration: none;">vitro is responsible for chromatin domain organization in vivo. However</del>, <del style="font-weight: bold; text-decoration: none;">understanding nucleosomal LLPS has been hindered by the challenge </del>to <del style="font-weight: bold; text-decoration: none;">characterize </del>the <del style="font-weight: bold; text-decoration: none;">structure of </del>the <del style="font-weight: bold; text-decoration: none;">resulting heterogeneous condensates. We used cryo</del>-electron tomography and <del style="font-weight: bold; text-decoration: none;">deep-learning-based 3D reconstruction/segmentation </del>to <del style="font-weight: bold; text-decoration: none;">determine </del>the <del style="font-weight: bold; text-decoration: none;">molecular organization of condensates at various stages </del>of <del style="font-weight: bold; text-decoration: none;">LLPS</del>. <del style="font-weight: bold; text-decoration: none;">We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates</del>, <del style="font-weight: bold; text-decoration: none;">followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion </del>of <del style="font-weight: bold; text-decoration: none;">spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure </del>of <del style="font-weight: bold; text-decoration: none;">nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by </del>which <del style="font-weight: bold; text-decoration: none;">chromatin may transition from interphase </del>to <del style="font-weight: bold; text-decoration: none;">metaphase structures</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Scaffolded DNA origami </ins>has <ins style="font-weight: bold; text-decoration: none;">proven to be a powerful and efficient technique to fabricate functional nanomachines by programming </ins>the <ins style="font-weight: bold; text-decoration: none;">folding </ins>of <ins style="font-weight: bold; text-decoration: none;">a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed </ins>to <ins style="font-weight: bold; text-decoration: none;">be precisely motion</ins>-<ins style="font-weight: bold; text-decoration: none;">controlled. Although two-dimensional </ins>(<ins style="font-weight: bold; text-decoration: none;">2D</ins>) <ins style="font-weight: bold; text-decoration: none;">imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic </ins>in <ins style="font-weight: bold; text-decoration: none;">3D</ins>, <ins style="font-weight: bold; text-decoration: none;">geometric analysis based on 2D imaging was insufficient </ins>to <ins style="font-weight: bold; text-decoration: none;">uncover </ins>the <ins style="font-weight: bold; text-decoration: none;">exact motion in 3D. Here we use </ins>the <ins style="font-weight: bold; text-decoration: none;">individual</ins>-<ins style="font-weight: bold; text-decoration: none;">particle </ins>electron tomography <ins style="font-weight: bold; text-decoration: none;">method </ins>and <ins style="font-weight: bold; text-decoration: none;">reconstruct 129 density maps from 129 individual DNA origami Bennett linkage mechanisms at ~ 6–14 nm resolution. The statistical analyses of these conformations lead </ins>to <ins style="font-weight: bold; text-decoration: none;">understanding </ins>the <ins style="font-weight: bold; text-decoration: none;">3D structural dynamics </ins>of <ins style="font-weight: bold; text-decoration: none;">Bennett linkage mechanisms</ins>. <ins style="font-weight: bold; text-decoration: none;">Moreover</ins>, <ins style="font-weight: bold; text-decoration: none;">our effort provides experimental verification </ins>of <ins style="font-weight: bold; text-decoration: none;">a theoretical kinematics model </ins>of <ins style="font-weight: bold; text-decoration: none;">DNA origami, </ins>which <ins style="font-weight: bold; text-decoration: none;">can be used as feedback </ins>to <ins style="font-weight: bold; text-decoration: none;">improve the design and control of motion via optimized DNA sequences and routing</ins>.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Keywords ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Keywords ==</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Cryo-ET, single molecule structure, individual-particle cryo-electron tomography, IPET, <del style="font-weight: bold; text-decoration: none;">nucleosome array</del>, <del style="font-weight: bold; text-decoration: none;">phase transition, aggregation</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Cryo-ET, single molecule structure, individual-particle cryo-electron tomography, IPET, <ins style="font-weight: bold; text-decoration: none;">DNA origami Bennett linkages</ins>, <ins style="font-weight: bold; text-decoration: none;">structural flexibility</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Paper links ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Paper links ==</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>https://<del style="font-weight: bold; text-decoration: none;">pubmed</del>.<del style="font-weight: bold; text-decoration: none;">ncbi</del>.<del style="font-weight: bold; text-decoration: none;">nlm.nih.gov</del>/<del style="font-weight: bold; text-decoration: none;">35907400</del>/</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>https://<ins style="font-weight: bold; text-decoration: none;">www</ins>.<ins style="font-weight: bold; text-decoration: none;">nature</ins>.<ins style="font-weight: bold; text-decoration: none;">com</ins>/<ins style="font-weight: bold; text-decoration: none;">articles</ins>/<ins style="font-weight: bold; text-decoration: none;">s41467-018-03018-0</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Related video ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Related video ==</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>https://www.<del style="font-weight: bold; text-decoration: none;">cell</del>.com/<del style="font-weight: bold; text-decoration: none;">cms/10.1016/j.molcel.2022.06.032/attachment/530f75ed-d615-46af-bdf6-255b34acf813/mmc2.mp4</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>https://www.<ins style="font-weight: bold; text-decoration: none;">youtube</ins>.com/<ins style="font-weight: bold; text-decoration: none;">watch?v=2Cjaxv9</ins>-<ins style="font-weight: bold; text-decoration: none;">btU</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">https://www.cell.com/cms/10.1016/j.molcel.2022.06.032/attachment/d2ae50b4-cafd-40f1-95c6-355322774031/mmc3.mp4</del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">https://www.cell.com/cms/10.1016/j.molcel.2022.06.032/attachment/bc9def6c-803f</del>-<del style="font-weight: bold; text-decoration: none;">4938-83d7-c4fd72610fc8/mmc4.mp4</del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Comments ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Comments ==</div></td></tr> </table>

Garygangren https://3demmethods.i2pc.es/index.php?title=2018Lei_DNABennet&diff=4849&oldid=prev 2024-11-12T09:23:43Z

<p>Created page with &quot;== Citation == Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography, Meng Zhang, César Díaz-Celis, Bibiana Onoa, Cristhian Cañari-Chumpitaz, Katherinne I. Requejo, Jianfang Liu, Michael Vien, Eva Nogales, Gang Ren, and Carlos Bustamante, Molecular Cell, (2022), 18;82(16):3000-3014.e9; PMID: 35907400 DOI: 10.1016/j.molcel.2022.06.032 == Abstract == It has been proposed that the intrinsic property of nucleosom...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography, Meng Zhang, César Díaz-Celis, Bibiana Onoa, Cristhian Cañari-Chumpitaz, Katherinne I. Requejo, Jianfang Liu, Michael Vien, Eva Nogales, Gang Ren, and Carlos Bustamante, Molecular Cell, (2022), 18;82(16):3000-3014.e9; PMID: 35907400 DOI: 10.1016/j.molcel.2022.06.032<br /> <br /> == Abstract ==<br /> It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of the resulting heterogeneous condensates. We used cryo-electron tomography and deep-learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.<br /> <br /> == Keywords ==<br /> Cryo-ET, single molecule structure, individual-particle cryo-electron tomography, IPET, nucleosome array, phase transition, aggregation<br /> <br /> == Paper links ==<br /> https://pubmed.ncbi.nlm.nih.gov/35907400/<br /> <br /> == Related video ==<br /> https://www.cell.com/cms/10.1016/j.molcel.2022.06.032/attachment/530f75ed-d615-46af-bdf6-255b34acf813/mmc2.mp4<br /> https://www.cell.com/cms/10.1016/j.molcel.2022.06.032/attachment/d2ae50b4-cafd-40f1-95c6-355322774031/mmc3.mp4<br /> https://www.cell.com/cms/10.1016/j.molcel.2022.06.032/attachment/bc9def6c-803f-4938-83d7-c4fd72610fc8/mmc4.mp4<br /> <br /> == Comments ==</div>

Garygangren