• December 2020

• November 2020

• October 2020

• September 2020

• August 2020

• July 2020

• June 2020

• May 2020

• April 2020

• 4DN Publications: Please add your preprints into the bioRxiv 4DN channel by contacting nils@hms.harvard.edu or leonid@mit.edu. Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome.
  • Recent new preprints added to bioRxiv 4DN channel:
    • SPIN reveals genome-wide landscape of nuclear compartmentalization. Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Peric-Hupkes, D., Chen, Y., Gilbert, D. M., van Steensel, B., Belmont, A. S., Ma, J. https://doi.org/10.1101/2020.03.09.982967 — Posted: 2020-03-10
    • Single-Cell Analysis of the 3D Topologies of Genomic Loci Using Genome Architecture Mapping. Welch, L. R., Baugher, C., Zhang, Y., Davis, T., Marzluff, W. F., Welch, J. D., Pombo, A. https://doi.org/10.1101/2020.02.10.941047 — Posted: 2020-02-12
    • An Improved 4'-Aminomethyltroxsalen-Based DNA Crosslinker for Biotinylation of DNA. Wielenberg, K., Wang, M., Yang, M., Ozer, A., Lis, J., Lin, H. https://doi.org/10.1101/2020.02.29.971317 — Posted: 2020-02-29
    • Detecting chromatin interactions along and between sister chromatids with SisterC. Marlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, Job Dekker. https://doi.org/10.1101/2020.03.10.986208 — Posted: 2020-03-11
    • Subtype-specific epigenomic landscape and 3D genome structure in bladder cancer. Tejaswi Iyyanki, Baozhen Zhang, Qiushi Jin, Hongbo Yang, Tingting Liu, Xiaotao Wang, Jie Xu, Fan Song, Yu Luan, Hironobu Yamashita, Lu Wang, Joshua Warrick, Jay Raman, Joshua J. Meeks, David Degraff, Feng Yue. https://doi.org/10.1101/2020.02.26.966697. — Posted: 2020-02-29
  • Recent new publications:
    • Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding. Tsung-Han S. Hsieh, Elena Slobodyanyuk, Anders S. Hansen, Claudia Cattoglio, Oliver J. Rando, Robert Tjian, Xavier Darzacq. Molecular Cell, available online 25 March 2020. https://doi.org/10.1016/j.molcel.2020.03.002
    • High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. Peiyao A. Zhao, Takayo Sasaki & David M. Gilbert. Genome Biology, 21, Article number: 76 (2020). https://doi.org/10.1186/s13059-020-01983-8

• Six 4DN RFAs (Phase 2) have been published. The announcement can be seen on the NIH Common Fund Website (https://commonfund.nih.gov/4Dnucleome/funding_opportunities).
  • Slides from 4DN phase 2 information webinar can be viewed here: Link to the PDF file
• Outreach
  • Higher-Order Chromatin Architecture in Time and Space: click here to register
    • The 2020 Keystone meeting is meant to highlight new frontiers across disciplines in tackling the dynamics and functional roles of the 3D genome in cellular functions across time and space in development and disease. The conference program will also include workshops on: (1) Leading computational methods to identify biologically relevant patterns in Hi-C data, (2) New genome mapping and imaging technologies, and (3) New data resources available through the 4D Nucleome consortium. Finally, it will conclude with a session devoted to novel tools for imaging and engineering the 3D genome.
    • When and where: March 15 - 19, 2020. Whistler Conference Centre, Whistler, BC, Canada
    • Scientific Organizers: Jennifer E. Phillips-Cremins, Job Dekker and Stavros Lomvardas
  • The Four-Dimensional Genome symposium: Click here to register
    • This symposium will bring together the latest advances in the fields of genomics, microscopy, and modeling to foster their integration towards a comprehensive spatial and temporal understanding of the functional four-dimensional organization of the eukaryotic genome.
    • When and where: Mar 29 - Apr 1, 2020. EMBL Heidelberg, Germany
    • Organizers: Wendy Bickmore, Jan Ellenberg, Susan M. Gasser, Christian Haring, Bas van Steensel, Tim Nurnberger.
• 4DN Publications: Please add your preprints into the bioRxiv 4DN channel by contacting nils@hms.harvard.edu or leonid@mit.edu. Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome.
  • Recent new preprints added to bioRxiv 4DN channel:
    • Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia. Yang, H., Zhang, H., Luan, Y., Liu, T., Roberts, K. G., Qian, M., Zhang, B., Yang, W., Perez-Andreu, V., Xu, J., Iyyanki, S., Kuang, D., Reshmi, S. C., Gastier-Foster, J., Smith, C., Pui, C., Evans, W. E., Hunger, S. P., Platanias, L. C., Relling, M. V., Mullighan, C. G., Loh, M. L., Yue, F., Yang, J. J. https://doi.org/10.1101/2020.02.23.961672 — Posted: 2020-02-25
    • GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. Markowski, J., Kempfer, R., Kukalev, A., Irastorza-Azcarate, I., Loof, G., Pombo, A., Schwarz, R. F. https://doi.org/10.1101/2020.01.30.927061 — Posted: 2020-01-31
• Scientific Webinar Series: February 28, 2020
  • Presenter: Brian Glenn St Hilaire (Baylor College of Medicine) - “ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL” (Link to presenter slides)
  • Presenter: Lisa Bashkirova (Columbia University) - “Nuclear architecture regulates the anatomic pattern of olfactory receptor expression in the olfactory epithelium” (Link to presenter slides)

• Six 4DN RFAs (Phase 2) have been published. The announcement can be seen on the NIH Common Fund Website (https://commonfund.nih.gov/4Dnucleome/funding_opportunities).
  • Slides from 4DN phase 2 information webinar can be viewed here: Link to the PDF file
• 4DN Directory system: Please update your email and profile on people.4dnucleome * After the launch of people.4dnucleome, we have consolidated all the email addresses of members.
  • If 4DN announcements are going to email address(es) that you didn't use before, or you cannot send 4DN announcements to working groups anymore, please consider updating your email address to your preferred one.
  • Your email address can be updated by:
    • Login to people.4dnucleome (https://people.4dnucleome.org/);
    • Click “My profile” on the left;
    • Update your email address (see this Google Slides for reference);
    • Click “UPDATE” to save.
    • This email address will be used for delivery of all 4DN-related messages and shall be used to send all 4DN-related group emails.
    • If you have any questions, please let us know at oh@4dnucleome.org
• Outreach
  • Higher-Order Chromatin Architecture in Time and Space: click here to register
    • The 2020 Keystone meeting is meant to highlight new frontiers across disciplines in tackling the dynamics and functional roles of the 3D genome in cellular functions across time and space in development and disease. The conference program will also include workshops on: (1) Leading computational methods to identify biologically relevant patterns in Hi-C data, (2) New genome mapping and imaging technologies, and (3) New data resources available through the 4D Nucleome consortium. Finally, it will conclude with a session devoted to novel tools for imaging and engineering the 3D genome.
    • When and where: March 15 - 19, 2020. Whistler Conference Centre, Whistler, BC, Canada
    • Scientific Organizers: Jennifer E. Phillips-Cremins, Job Dekker and Stavros Lomvardas
  • The Four-Dimensional Genome symposium: Click here to register
    • This symposium will bring together the latest advances in the fields of genomics, microscopy, and modeling to foster their integration towards a comprehensive spatial and temporal understanding of the functional four-dimensional organization of the eukaryotic genome.
    • When and where: Mar 29 - Apr 1, 2020. EMBL Heidelberg, Germany
    • Organizers: Wendy Bickmore, Jan Ellenberg, Susan M. Gasser, Christian Haring, Bas van Steensel, Tim Nurnberger.
• 4DN Publications: Please add your preprints into the bioRxiv 4DN channel by contacting nils@hms.harvard.edu or leonid@mit.edu. Please also feel free to notify us of your new publications through email: OH@4dnucleome.org or twitter @4DNucleome.
  • Recent new publications:
    • MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. Dechao Tian, Ruochi Zhang, Yang Zhang, Xiaopeng Zhu and Jian Ma. Genome Res. January 6, 2020, doi: https://doi.org/10.1101/gr.250316.119
    • Co-opted transposons help perpetuate conserved higher-order chromosomal structures. Mayank NK Choudhary, Ryan Z. Friedman, Julia T. Wang, Hyo Sik Jang, Xiaoyu Zhuo & Ting Wang. Genome Biology. Volume 21, Article number: 16 (2020). https://doi.org/10.1186/s13059-019-1916-8
    • Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Elizabeth H. Finn, Gianluca Pegoraro, Hugo B. Brandão, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny and Tom Misteli. Cell. Volume 176, Issue 6, 7 March 2019, Pages 1502-1515.e10. https://doi.org/10.1016/j.cell.2019.01.020
  • Recent new preprints added to bioRxiv 4DN channel:
    • Cell cycle dynamics of lamina associated DNA. van Schaik, T., Vos, M., Peric-Hupkes, D., van Steensel, B. https://doi.org/10.1101/2019.12.19.881979 — Posted: 2019-12-19
    • Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traits. Giusti-Rodriguez, P. M., Sullivan, P. F. https://doi.org/10.1101/406330 — Posted: 2019-01-30
    • Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild. Humble, E., Dobrynin, P., Senn, H., Chuven, J., Scott, A. F., Mohr, D. W., Dudchenko, O., Omer, A. D., Colaric, Z., Lieberman Aiden, E., Wildt, D., Oliagi, S., Tamazian, G., Pukazhenthi, B., Ogden, R., Koepfli, K.-P. https://doi.org/10.1101/867341 — Posted: 2019-12-08
    • Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus. Ma, J., Do, M., Le Gros, M. A., Peskin, C. S., Larabell, C. A., Mori, Y., Isaacson, S. A. https://doi.org/10.1101/2020.01.16.909333 — Posted: 2020-01-17
    • High-Resolution 3D Fluorescent Imaging of Intact Tissues. El-Nachef, D., Martinson, A. M., Yang, X., Murry, C. E., MacLellan, W. R. https://doi.org/10.1101/855254 — Posted: 2019-11-26
    • Probing multi-way chromatin interaction with hypergraph representation learning. Zhang, R., Ma, J. https://doi.org/10.1101/2020.01.22.916171 — Posted: 2020-01-23
• Scientific Webinar Series: January 24, 2020
  • Presenter: Leo Barinov (Princeton University) - “Interplay between chromatin organization and transcriptional activity”
  • Presenter: Mathias Hammer (University of Massachusetts medical school) - “A study on effects of fixation with Formaldehyde and Paraformaldehyde”

Newsletter Archive: 2019

Newsletter Archive: 2018

Newsletter Archive: 2017