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Newsletter Archive: 2019

December 2019

  • Happy new year 2020!
  • 2019 4DN Annual Meeting and 4DN-ASCB Satellite Meeting successfully concluded!
  • 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).
    • The 4DN program will be hosting a webinar to provide information on and answer questions about the phase two funding initiatives.
      • Date: January 21, 2020
      • Click the WebEx link to join
      • Audio connection: 1-650-479-3207 Call-in toll number (US/Canada), Access code: 733 412 130
  • 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
    • The Four-Dimensional Genome symposium
      • 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. Click here to register.
      • When and where: 29 Mar - 1 Apr 2020. EMBL Heidelberg, Germany
      • Organizers: Wendy Bickmore, Jan Ellenberg, Susan M. Gasser, Christian Haring, Bas van Steensel, Tim Nurnberger.
  • 4DN YouTube channel https://www.youtube.com/c/4DNucleome
    • Stats by Dec 31, 2019
      • Video released by 4DN: 25
      • Subscribers: 158
      • View: 5K+
      • Watch time: 3300 hours
    • 2 new outreach videos have been released.
      • Presenter: Ting Wang (Washington University): WashU Epigenome Browser: Engaging ENCODE, Roadmap Epigenomics, and 4DN. Link to YouTube
      • Presenter: Ting Wang (Washington University): WashU Epigenome Browser: Hands on demo. Link to YouTube
  • 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.
    • Stats by Dec 31, 2019:
      • Preprints: 224
      • Publications: 185
    • Recent new publications:
      • Common DNA sequence variation influences 3-dimensional conformation of the human genome. David U. Gorkin, Yunjiang Qiu, Ming Hu, Kipper Fletez-Brant, Tristin Liu, Anthony D. Schmitt, Amina Noor, Joshua Chiou, Kyle J. Gaulton, Jonathan Sebat, Yun Li, Kasper D. Hansen & Bing Ren. Genome Biology, volume 20, Article number: 255 (2019). https://doi.org/10.1186/s13059-019-1855-4
      • Gene expression amplification by nuclear speckle association. Jiah Kim, Neha Chivukula Venkata, Gabriela Andrea Hernandez Gonzalez, Nimish Khanna, Andrew S. Belmont. Journal of Cell Biology, (2020) 219 (1): e201904046. https://doi.org/10.1083/jcb.201904046
    • Recent new preprints added to bioRxiv 4DN channel:
      • Memory sequencing reveals heritable single cell gene expression programs associated with distinct cellular behaviors. Shaffer, S. M., Emert, B. L., Reyes-Hueros, R., Cote, C., Harmange, G., Sizemore, A. E., Gupte, R., Torre, E., Singh, A., Bassett, D. S., Raj, A. https://doi.org/10.1101/379016 — Posted: 2019-12-21
      • Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning. Lekschas, F., Peterson, B., Haehn, D., Ma, E., Gehlenborg, N., Pfister, H. https://doi.org/10.1101/597518 — Posted: 2019-12-12

November 2019

  • 2019 4DN Annual Meeting: December 4-6, 2019, Washington, D.C., Capital Hilton Hotel
  • Four new 4DN RFAs (Phase 2) have been published. The announcement can be seen on the NIH Common Fund Website (https://commonfund.nih.gov/4dnucleome).
  • 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
    • The Four-Dimensional Genome symposium
      • 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. Click here to register.
      • When and where: 29 Mar - 1 Apr 2020. EMBL Heidelberg, Germany
      • Organizers: Wendy Bickmore, Jan Ellenberg, Susan M. Gasser, Christian Haring, Bas van Steensel, Tim Nurnberger.
  • Job Opportunities
  • 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:
      • Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. Anders S. Hansen, Tsung-Han S. Hsieh, Claudia Cattoglio, Danny Reinberg, Xavier Darzacq, Robert Tjian. Mol Cell. 2019 Nov 7;76(3):395-411.e13. doi: 10.1016/j.molcel.2019.07.039. Epub 2019 Sep 12.
      • Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. Kyle Xiong & Jian Ma. Nat Commun. 2019 Nov 7;10(1):5069. doi: 10.1038/s41467-019-12954-4.
    • Recent new preprints added to bioRxiv 4DN channel:
      • ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL. Wutz, G., St. Hilaire, B. T. G., Ladurner, R., Stocsits, R., Nagasaka, K., Pignard, B., Sanborn, A., Tang, W., Varnai, C., Ivanov, M., Schoenfelder, S., van der Lelij, P., Huang, X., Duernberger, G., Roitinger, E., Mechtler, K., Davidson, I. F., Fraser, P., Aiden, E. L., Peters, J. M. 10.1101/779058 — Posted: 2019-09-23
      • Direct, sensitive and specific detection of individual single- or double-strand DNA breaks by fluorescence microscopy. Kordon, M., Zarebski, M., Solarczyk, K., Ma, H., Pederson, T., Dobrucki, J. W. 10.1101/772269 — Posted: 2019-09-18
      • Chromatin is frequently unknotted at the megabase scale. Goundaroulis, D., Aiden, E. L., Stasiak, A. 10.1101/762872 — Posted: 2019-09-09
      • Cohesin depleted cells pass through mitosis and reconstitute a functional nuclear architecture. Cremer, M., Brandstetter, K., Maiser, A., Rao, S. S., Schmid, V., Mitra, N., Mamberti, S., Klein, K. N., Gilbert, D. M., Leonhardt, H., Cardoso, M. C., Lieberman Aiden, E., Harz, H., Cremer, T. 10.1101/816611 — Posted: 2019-10-24
      • A cost-efficient open source laser engine for microscopy. Schroeder, D., Deschamps, J., Dasgupta, A., Matti, U., Ries, J. 10.1101/796482 — Posted: 2019-10-15
      • Genetic screening for single-cell variability modulators driving therapy resistance. Torre, E. A., Arai, E., Bayatpour, S., Beck, L. E., Emert, B. L., Shaffer, S. M., Mellis, I. A., Fane, M., Alicea, G., Budinich, K. A., Weeraratna, A., Shi, J., Raj, A. 10.1101/638809 — Posted: 2019-11-10
      • Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data. Kim, H.-J., Yardimici, G. G., Bonora, G., Ramani, V., Liu, J., Qiu, R., Lee, C., Hesson, J., Ware, C. B., Shendure, J., Duan, Z., Noble, W. S. 10.1101/534800 — Posted: 2019-11-18
      • MS2-TRIBE evaluates protein-RNA interactions and nuclear organization of transcription by RNA editing. Biswas, J., Rahman, R., Gupta, V., Rosbash, M., Singer, R. 10.1101/829606 — Posted: 2019-11-04

October 2019

  • 2019 4DN Annual Meeting: December 4-6, 2019, Washington, D.C., Capital Hilton Hotel
    • LATE REGISTRATION DEADLINE (NO ABSTRACT SUBMISSION): NOVEMBER 1, 2019, 11:59 pm PST
    • HOTEL BOOKING DEADLINE: NOVEMBER 1, 2019 (click here to book)
  • 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
    • The Four-Dimensional Genome symposium
      • 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. Click here to register.
      • When and where: 29 Mar - 1 Apr 2020. EMBL Heidelberg, Germany
      • Organizers: Wendy Bickmore, Jan Ellenberg, Susan M. Gasser, Christian Haring, Bas van Steensel, Tim Nurnberger.
  • Job Opportunities
  • 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:
      • TSA-Seq 2.0 reveals both conserved and variable chromosomal distances to nuclear speckles. Liguo Zhang, Yang Zhang, Yu Chen, Omid Gholamalamdari, Jian Ma, Andrew S. Belmont. https://doi.org/10.1101/824433 — Posted: 2019-10-30
      • Chromosome organization by one-sided and two-sided loop extrusion. Edward J. Banigan, Aafke A. van den Berg, Hugo B. Brandão, John F. Marko, Leonid A. Mirny. https://doi.org/10.1101/815340 — Posted: 2019-10-22
      • Architectural RNA is required for heterochromatin organization. Jitendra Thakur, He Fang, Trizia Llagas, Christine M. Disteche, Steven Henikoff. https://doi.org/10.1101/815340 — Posted: 2019-09-27
  • Scientific Webinar Series: October 25, 2019
    • Presenter: Nimrod Rappoport (Weizman Institute of Science) - “Single cell Hi-C and dissection of replication landscapes and chromosomal organization in mouse embryonic lineages” (Link to presenter slides)
    • Presenter: Kanishk Abhinav (The University of Edinburgh) - “Local environment of inner nuclear membrane proteins analyzed by proximity labeling and mass spectrometry” (Link to presenter slides)

September 2019

  • 2019 4DN Annual Meeting: December 4-6, 2019, Washington, D.C., Capital Hilton Hotel
    • REGISTRATION DEADLINE: OCTOBER 15, 2019, 11:59 pm PST
    • Registration Link: http://4dn-annual-meetings.smapply.io/
    • Talks of the first day (consortium only day) will be invited by session chairs in late October - early November
    • Many abstract selected talk slots are available. It is likely that more than 40 talks will be selected from abstracts.
  • 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
  • Job Opportunities
  • 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:
      • A supervised learning framework for chromatin loop detection in genome-wide contact maps. Salameh, T., Wang X., Song F., Zhang B., Wright S., Khunsriraksakul C., Yue F. https://doi.org/10.1101/739698 — Posted: 2019-08-20
      • High Resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. Zhao, P., Sasaki, T., Gilbert, D. https://doi.org/10.1101/755629 — Posted: 2019-09-05
  • Scientific Webinar Series: September 27, 2019
    • Presenter: Joshua Riback (Princeton University) - “Composition dependent phase separation underlies directional flux through the nucleolus”
    • Presenter: Jian Ma (School of Computer Science at Carnegie Mellon University) - “Multimodal, interactive data visualization and exploration for the 4D Nucleome” (Link to presenter slides)

August 2019

  • 2019 4DN Annual Meeting registration:
  • Outreach:
    • Dr. Zhen Chen from City of Hope and part of 4DN OH gave a talk on Cold Spring Harbor Meeting of Mechanisms of Eukaryotic Transcription titled “Dynamic changes in RNA-chromatin interactome promotes endothelial dysfunction”. She introduced to the audience 4DN resources including 4DN protocols, datasets, and papers that are potentially useful to their research.
  • 4DN Directory system launched: 4DN OH has developed and deployed 4DN Directory (https://people.4dnucleome.org/, also linked from the 4DN Web Portal), a centralized and integrated system for all 4DN personnel information where members can access the information of all 4DN members.
    • Resources directly managed by OH are accessible via one account (4DN Wiki and 4DN Directory).
    • Resetting login credential has been streamlined to make the entire process easier.
    • 4DN Directory also serves as a personnel management system. Once you are logged in, you will be able to update information that is accessible. If you are a PI, you will be able to add, update or inactivate your lab members;
    • You may search the entire consortium for any member, get their up-to-date information and/or contact them via email in the directory directly.
    • Details and some guides can be seen in the following Google Slides: https://docs.google.com/presentation/d/1NwSuF2Eew7NnYIddgK4Zc1F8DgBK8-g--VahBzFMZyE/edit?usp=sharing
  • Job Opportunities
  • 4DN YouTube channel
    • Thanks to all our subscribers. As we have got 130 subscribers, YouTube allowed us to create a customized short URL. Now you can access 4DN YouTube Channel directly using https://www.youtube.com/c/4DNucleome
    • 7 new videos of Scientific Webinar Series (April to July 2019) have been released.
      • Presenter: Soohyun Lee (Harvard Medical School) - “Reproducible Data Processing at the 4DN Data Coordination and Integration Center” Link to YouTube
      • Presenter: Jonas Ries (EMBL) - “Nuclear pores as versatile reference standards for quantitative microscopy” Link to YouTube
      • Presenter: Molly Gasperini (University of Washington) - “Pairing enhancers with their target genes via multiplexed cellular genetic screens” Link to YouTube
      • Presenter: Mayank NK Choudhary (Washington Univeristy) - “Co-opted transposons help perpetuate conserved higher-order chromosomal structures” Link to YouTube
      • Presenter: Anastassiia Vertii (University of Massachusetts Medical School) - “The composition and regulation of nucleolus-associated domains” Link to YouTube
      • Presenter: Mary Arrastia (California Institute of Technology) - “Studying the structural organization of subnuclear chromatin compartments through genome structure modeling” Link to YouTube
      • Presenter: Yanxiao Zhang (Ludwig Institute for Cancer Research San Diego) - “Transcriptionally Active HERV-H Retrotransposons Demarcate TADs in Human ESCs” Link to YouTube
  • 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:
      • Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy. Bertero, A., Fields, P.A., Smith, A.S.T., Leonard, A., Beussman, K., Sniadecki, N.J., Kim, D.-H., Tse, H.-F., Pabon, L., Shendure, J., Noble, W., and Murry, C. J Cell Biol (2019). https://doi.org/10.1083/jcb.201902117.
    • Recent new preprints added to bioRxiv 4DN channel:
      • Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C. Belaghzal, H., Borrman, T., Stephens, A. D., Lafontaine, D. L., Venev, S. V., Marko, J. F., Weng, Z., Dekker, J. https://doi.org/10.1101/704957 — Posted: 2019-07-16
      • A chromosome folding intermediate at the condensin-to-cohesin transition during telophase. Abramo, K., Valton, A.-L., Venev, S. V., Ozadam, H., Fox, A. N., Dekker, J. https://doi.org/10.1101/678474 — Posted: 2019-06-21
      • Measuring significant changes in chromatin conformation with ACCOST. Cook, K. B., Le Roch, K. G., Vert, J.-P., Noble, W. https://doi.org/10.1101/727768 — Posted: 2019-08-06
  • Scientific Webinar Series: August 23, 2019
    • Presenter: Andrew Stephens (Northwestern University) - Heterochromatin and HP1alpha provide different nuclear mechanical contributions to maintain nuclear shape and function (Link to presenter slides)
    • Presenter: Yodai Takei (California Institute of Technology) - Intron seqFISH enables spatial analysis of the nascent transcriptome in single cells (Link to presenter slides)

July 2019

  • 2019 4DN Annual Meeting registration:
  • Outreach:
  • 4DN Publications: Please add your preprints into 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:
      • Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin. Anastassiia Vertii, Jianhong Ou, Jun Yu, Aimin Yan1, Hervé Pagès, Haibo Liu, Lihua Julie Zhu and Paul D. Kaufman. Genome Research, June 14, 2019. https://doi.org/10.1101/gr.247072.118.
      • WashU Epigenome Browser update 2019. Daofeng Li, Silas Hsu, Deepak Purushotham, Renee L Sears, Ting Wang. Nucleic Acids Research, 47 (W1): W158–W165 (2019). https://doi.org/10.1093/nar/gkz348
    • Recent new preprints added to bioRxiv 4DN channel:
      • Trans- and cis-acting effects of the lncRNA Firre on epigenetic and structural features of the inactive X chromosome. FANG, H., Bonora, G., Lewandowski, J., Thakur, J., Filippova, G. N., Henikoff, S., Shendure, J., Duan, Z., Rinn, J., Deng, X., Noble, W. S., Disteche, C. M. https://doi.org/10.1101/687236 — Posted: 2019-06-30
      • Photoactivation of silicon rhodamines via a light-induced protonation. Frei, M. S., Hoess, P., Lampe, M., Nijmeijer, B., Kueblbeck, M., Ellenberg, J., Ries, J., Pitsch, S., Reymond, L., Johnsson, K. https://doi.org/10.1101/626853 — Posted: 2019-05-04
      • Chemogenetic control of nanobodies. Farrants, H., Tarnawski, M., Müller, T. G., Otsuka, S., Hiblot, J., Koch, B., Kueblbeck, M., Kräusslich, H.-G., Ellenberg, J., Johnsson, K. https://doi.org/10.1101/683557 — Posted: 2019-06-27
      • Versatile multi-transgene expression using improved BAC TG-EMBED toolkit, novel BAC episomes, and BAC-MAGIC. Zhao, B., Chaturvedi, P., Zimmerman, D. L., Belmont, A. S. https://doi.org/10.1101/708024 — Posted: 2019-07-23
      • Dynamic changes in RNA-chromatin interactome promote endothelial dysfunction. Calandrelli, R., Xu, L., Luo, Y., Wu, W., Fan, X., Nguyen, T., Chen, C., Sriram, K., Natarajan, R., Chen, Z., Zhong, S. https://doi.org/10.1101/712950 — Posted: 2019-07-24
  • Scientific Webinar Series
    • Presenter: Mary Arrastia (California Institute of Technology) - Studying the structural organization of subnuclear chromatin compartments through genome structure modeling (Link to presenter slides)
    • Presenter: Yanxiao Zhang (Ludwig Institute for Cancer Research San Diego) - Transcriptionally Active HERV-H Retrotransposons Demarcate TADs in Human ESCs (Link to presenter slides)

June 2019

  • 2019 4DN Annual Meeting registration:
  • Outreach:
    • Long-Read Sequencing Workshop. September 17-20, 2019 The Jackson Laboratory for Genomic Medicine, Farmington, CT. Registration Webpage Link
  • 4DN Publications: Please add your preprints into 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:
      • Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma. Cell System, VOLUME 8, ISSUE 6, P494-505.E14, JUNE 26, 2019. https://doi.org/10.1016/j.cels.2019.05.011
      • Two major mechanisms of chromosome organization. Leonid AMirny, Maxim Imakaev, Nezar Abdennur. Current Opinion in Cell Biology, 58: 142-152 (2019). https://doi.org/10.1016/j.ceb.2019.05.001
      • Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions. Nimish Khanna, Yaojun Zhang, Joseph S. Lucas, Olga K. Dudko & Cornelis Murre. Nature Communications, 10: 2771 (2019). https://doi.org/10.1038/s41467-019-10628-9
    • Recent new preprints added to bioRxiv 4DN channel:
      • HiNT: a computational method for detecting copy number variations and translocations from Hi-C data. Wang, S., Lee, S., Chu, C., Jain, D., Nelson, G., Walsh, J. M., Alver, B. H., Park, P. J. https://doi.org/10.1101/657080 — Posted: 2019-06-03
      • Inferring diploid 3D chromatin structures from Hi-C data. Cauer, A., Yardimci, G. G., Vert, J.-P., Varoquaux, N., Noble, W. https://doi.org/10.1101/644294 — Posted: 2019-05-21
      • Jointly embedding multiple single-cell omics measurements. Liu, J., Huang, Y., Singh, R., Vert, J.-P., Noble, W. https://doi.org/10.1101/644310 — Posted: 2019-05-21
  • Scientific Webinar Series
    • Presenter: Asli Yildirim (University of California, Los Angeles) - “Studying the structural organization of subnuclear chromatin compartments through genome structure modeling” (Link to presenter slides)
    • Presenter: Anastassiia Vertii (University of Massachusetts Medical School) - “The composition and regulation of nucleolus-associated domains” (Link to presenter slides)

May 2019

  • 2019 4DN Annual Meeting registration started:
    • Registration Link:
    • 2019 4D Nucleome Annual Meeting: December 4-6, 2019, Washington, D.C., Capital Hilton Hotel
  • 4DN Outreach:
    • A 4DN tutorial was given by Sheng Zhong at Southwestern Bioinformatics Conference, San Diego, May 31, 2019.
  • 4DN Publications: Please add your preprints into 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:
      • Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells. Cheng, L.-C., Baboo, S., Lindsay, C., Brusman, L. E., Martinez-Bartolome, S., Tapia, O., Zhang, X., Yates, J. R., Gerace, L. https://doi.org/10.1101/486415 — Posted: 2018-12-03
      • Spring Model - chromatin modeling tool based on OpenMM. Kadlof, M., Rozycka, J., Plewczynski, D. https://doi.org/10.1101/642322 — Posted: 2019-05-20
      • Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cells. Ruan, Y., Plewczynski, D., Zhu, J. J., Parteka, Z., Lee, B., Szalaj, P., Wang, P., Jodkowska, K., Arron, J., Chew, T. L. https://doi.org/10.1101/621920 — Posted: 2019-04-29
  • Scientific Webinar Series
    • Presenter: Molly Gasperini (University of Washington) - “Pairing enhancers with their target genes via multiplexed cellular genetic screens” (Link to presenter slides)
    • Presenter: Mayank NK Choudhary (Washington University) - “Co-opted transposons help perpetuate conserved higher-order chromosomal structures” (Link to presenter slides)

April 2019

  • Save the date:
    • 2019 4D Nucleome Annual Meeting: December 4-6, 2019, Washington, D.C., Capital Hilton Hotel
    • Registration and Hotel booking will open on June 1, 2019.
  • 4DN Outreach material: Full list of material can be found on the 4DN Outreach wiki page
    • New banners for webpages with the 4DN logo and a QR code directing to the 4DN portal are now available on the Outreach wiki page. Click here to get the HTML code * Long banner:
4D Nucleome Consortium https://www.4dnucleome.org/
  • Shortbanner:
  • 4DN Publications: Please add your preprints into 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:
      • Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning. Lekschas, F., Peterson, B., Haehn, D., Ma, E., Gehlenborg, N., Pfister, H. https://doi.org/10.1101/597518 — Posted: 2019-04-04
      • Common DNA sequence variation influences 3-dimensional conformation of the human genome. Gorkin, D., Qiu, Y., Hu, M., Fletez-Brant, K., Liu, T., Schmitt, A., Noor, A., Chiou, J., Gaulton, K., Sebat, J., Li, Y., Hansen, K., Ren, B. https://doi.org/10.1101/592741 — Posted: 2019-03-30
      • Nuclear pores as versatile reference standards for quantitative superresolution microscopy. Thevathasan, J. V., Kahnwald, M., Cieslinski, K., Hoess, P., Peneti, S. K., Reitberger, M., Heid, D., Kasuba, K. C., Hoerner, S. J., Li, Y., Wu, Y.-L., Mund, M., Matti, U., Pereira, P. M., Henriques, R., Nijmeijer-Winter, B., Kueblbeck, M., Jimenez Sabinina, V., Ellenberg, J., Ries, J. https://doi.org/10.1101/582668 — Posted: 2019-03-20
      • Direct visualization of single nuclear pore complex proteins using genetically-encoded probes for DNA-PAINT. Schlichthaerle, T., Strauss, M. T., Schueder, F., Auer, A., Nijmeijer, B., Kueblbeck, M., Jimenez Sabinina, V., Thevatasan, J. V., Ries, J., Ellenberg, J., Jungmann, R. https://doi.org/10.1101/579961 — Posted: 2019-03-23
      • Transcription amplification by nuclear speckle association. Kim, J., Khanna, N., Belmont, A. S. https://doi.org/10.1101/604298 — Posted: 2019-04-09
      • RNA polymerases as moving barriers to condensin loop extrusion. Brandao, H. B., Wang, X., Paul, P., van den Berg, A., Rudner, D. Z., Mirny, L. A. https://doi.org/10.1101/604280 — Posted: 2019-04-10
      • ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions. Tian, S. Z., Capurso, D., Kim, M., Lee, B., Zheng, M., Ruan, Y. https://doi.org/10.1101/613034 — Posted: 2019-04-18
      • iMARGI: Mapping RNA-chromatin interactome by sequencing. Weixin Wu, Zhangming Yan, Zhen Chen, Shu Chien, Sheng Zhong. https://www.protocols.io/view/imargi-protocol-w75fhq6
    • Recent new publications:
      • Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Alessandro Bertero, Paul A. Fields, Vijay Ramani, Giancarlo Bonora, Galip G. Yardimci, Hans Reinecke, Lil Pabon, William S. Noble, Jay Shendure & Charles E. Murry. Nature Communications, 10:1538 (2019). https://doi.org/10.1038/s41467-019-09483-5
      • MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. Ivan Juric, Miao Yu, Armen Abnousi, Ramya Raviram, Rongxin Fang, Yuan Zhao, Yanxiao Zhang, Yunjiang Qiu, Yuchen Yang, Yun Li, Bing Ren, Ming Hu. PLoS Comput Biol 15(4): e1006982. https://doi.org/10.1371/journal.pcbi.1006982

March 2019

  • 4DN Outreach activities:
    • A 4DN workshop was held in March 2019 at Keystone Symposium of 3D Genome: Gene Regulation and Disease at Banff, Canada. Organizers and speakers included Sheng Zhong, Bing Ren, Judy Mietz, Olivier Blondel, Feng Yue, Burak Alver, Nick Gilbert, Rieke Kemfer, Zhen Chen.
    • A 4DN workshop was given by Ting Wang and organized by Zhen Chen at City of Hope, Los Angeles, March 2019.
    • The 4DN Twitter account is gaining 80 followers and making 5-7,000 impression per month. Please contact Kara at kljohnso@ucsd.edu if you have material you would like to be distributed via Twitter
  • 4DN Outreach material: Full list of material can be found on the 4DN Outreach wiki page
    • New banners for webpages with the 4DN logo and a QR code directing to the 4DN portal is now available on the Outreach wiki page. Click here to get the HTML code * Long banner:
4D Nucleome Consortium https://www.4dnucleome.org/
  • Shortbanner:
  • A 4DN business card and a 4DN brochure have been created and posted on the outreach wiki page. Click here to get *
  • Feel free to modify-and-use all these outreach materials in your future presentation slides, posters, or websites! You can also personalize and print some 4DN business cards and hand them out.
  • 4DN Publications: Please add your preprints into 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:
    • Absolute quantification of cohesin, CTCF and their regulators in human cells. Holzmann, J., Politi, A. Z., Nagasaka, K., Hantsche-Grininger, M., Walther, N., Koch, B., Fuchs, J., Dürnberger, G., Tang, W., Ladurner, R., Stocsits, R. R., Busslinger, G. A., Novak, B., Mechtler, K., Davidson, I. F., Ellenberg, J., Peters, J.-M. https://doi.org/10.1101/560425 — Posted: 2019-02-27
    • Determining cellular CTCF and cohesin abundances to constrain 3D genome models. Cattoglio, C., Pustova, I., Walther, N., Ho, J. J., Hantsche-Grininger, M., Inouye, C. J., Hossain, M. J., Dailey, G. M., Ellenberg, J., Darzacq, X., Tjian, R., Hansen, A. S. https://doi.org/10.1101/370650 — Posted: 2019-02-24
  • Recent new publications:

February 2019

  • New 4D Nucleome internal Wiki! https://wiki.4dnucleome.org/.
  • Slides of 2018 annual meeting have been released (internal). Here is the link:
  • Outreach
    • Starting from March 2019, Education and Outreach meetings will take place once a month with Joint Analysis meetings. The first meeting will be on Mar 7. (see the wiki page of Outreach Working Group).
    • If you want to participate in the Outreach effort, send an email to oh@4dnucleome.org.
    • Registration is now open for the 2019 Gordon Research Conference on Genome Architecture in Hong Kong, August 4 - 9, 2019! Click here to the conference website!
    • François Jacob Conference: Evolution, Structure and Function of Chromosomes High Order Structure. Paris, June 4-7, 2019. Click here to the conference website!
  • 4DN YouTube channel released 4 new videos of Scientific Webinar.
    • Presenter: Matthew Denholtz (University of California, San Diego) - “Neutrophil genome dynamics in development and pathogen encounter” Link to Youtube
    • Presenter: Adrien Senecal (Albert Einstein College of Medicine) - “The p53 transcription factor regulates transcriptional burst frequency and multiple steps of formation and disruption of chromatin on the p21 gene locus” Link to Youtube
    • Presenter: Martin Falk (Massachusetts Institute of Technology) - “Heterochromatin drives organization of conventional and inverted nuclei” Link to Youtube
    • Presenter: John Rinn (University of Minnesota) - “Crispr Live Cell imaging (CLING) and HiC data: insights into CTCF, RNA and TAD Boundaries” Link to Youtube
  • Job Opportunities: Please check all the 8 open positions in the 4DN Job Advertisement Page for detailed information
  • 4DN Publications: Please add your preprints into 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:
      • MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. Tian, D., Zhang, R., Zhang, Y., Zhu, X., Ma, J. https://doi.org/10.1101/542092 — Posted: 2019-02-07
      • Comparing 3D genome organization in multiple species using Phylo-HMRF. Yang, Y., Zhang, Y., Ren, B., Dixon, J., Ma, J. https://doi.org/10.1101/552505 — Posted: 2019-02-19
      • Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy. Bertero, A., Fields, P. A., Smith, A. S., Leonard, A., Beussman, K., Sniadecki, N. J., Kim, D.-H., Tse, H.-F., Pabon, L., Shendure, J., Noble, W. S., Murry, C. E. https://doi.org/10.1101/555250 — Posted: 2019-02-19
      • Localization microscopy at doubled precision with patterned illumination. Cnossen, J., Hinsdale, T., Thorsen, R., Schueder, F., Jungmann, R., Smith, C. S., Rieger, B., Stallinga, S. https://doi.org/10.1101/554337 — Posted: 2019-02-20
      • Cooler: scalable storage for Hi-C data andother genomically-labeled arrays. Abdennur, N., Mirny, L. https://doi.org/10.1101/557660 — Posted: 2019-02-22
    • Recent new publications:
      • Multiplex chromatin interactions with single-molecule precision. Meizhen Zheng, Simon Zhongyuan Tian, Daniel Capurso, Minji Kim, Rahul Maurya, Byoungkoo Lee, Emaly Piecuch, Liang Gong, Jacqueline Jufen Zhu, Zhihui Li, Chee Hong Wong, Chew Yee Ngan, Ping Wang, Xiaoan Ruan, Chia-Lin Wei & Yijun Ruan. Nature 566, 558–562 (2019). https://doi.org/10.1038/s41586-019-0949-1
      • Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs. Zhangming Yan, Norman Huang, Weixin Wu, Weizhong Chen, Yiqun Jiang, Jingyao Chen, Xuerui Huang, Xingzhao Wen, Jie Xu, Qiushi Jin, Kang Zhang, Zhen Chen, Shu Chien, and Sheng Zhong. PNAS February 19, 2019 116 (8) 3328-3337. https://doi.org/10.1073/pnas.1819788116
  • Scientific Webinar Series this Month: February 22, 2019
    • Presenter: Haoyue (Adam) Zhang (Children's Hospital of Philadelphia) - “Re-configuration of Chromatin Structure During the Mitosis-G1 Phase Transition”
    • Presenter: Bas van Steensel (Netherlands Cancer Institute) - “Rewiring LADs by transcription” (Link to presenter slides)

January 2019

  • Post-doctoral Fellow at Stanford University: study chromatin-associated RNAs and their regulation of genome organization. Contact Aaron Straight astraigh@stanford.edu
  • 4DN Publications: Please add your preprints into 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.
  • Stats by Jan 31, 2019
  • Preprints (bioRxiv 4DN channel): 139 in total
  • Publications (Pubmed): 173 in total.
  • Recent new preprints added to bioRxiv 4DN channel:
  • Revealing Hi-C subcompartments by imputing high-resolution inter-chromosomal chromatin interactions. Xiong, K., Ma, J. https://doi.org/10.1101/505503 — Posted: 2018-12-23
  • An RNA-binding region regulates CTCF clustering and chromatin looping. Hansen, A. S., Hsieh, T.-H. S., Cattoglio, C., Pustova, I., Darzacq, X., Tjian, R. https://doi.org/10.1101/495432 — Posted: 2018-12-16
  • Guided nuclear exploration increases CTCF target search efficiency. Hansen, A. S., Amitai, A., Cattoglio, C., Tjian, R., Darzacq, X. https://doi.org/10.1101/495457 — Posted: 2018-12-13
  • Transient DNA Binding Induces RNA Polymerase II Compartmentalization During Herpesviral Infection Distinct From Phase Separation McSwiggen, D. T., Hansen, A. S., Marie-Nelly, H., Teves, S., Heckert, A., Dugast-Darzacq, C., Hao, Y., Umemoto, K. K., Tjian, R., Darzacq, X. https://doi.org/10.1101/375071 — Posted: 2018-07-30
  • Recent new publications:
  • Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Cell. 2018 Dec 21. pii: S0092-8674(18)31561-7. doi: https://doi.org/10.1016/j.cell.2018.11.036.
  • GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. Calandrelli R, Wu Q, Guan J, Zhong S. Genomics Proteomics Bioinformatics. 2018 Dec 13. pii: S1672-0229(18)30433-9. doi: https://doi.org/10.1016/j.gpb.2018.06.006.
  • CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization. Wang H, Xu X, Nguyen CM, Liu Y, Gao Y, Lin X, Daley T, Kipniss NH, La Russa M, Qi LS. Cell. 2018 Nov 15;175(5):1405-1417.e14. doi: https://doi.org/10.1016/j.cell.2018.09.013. Epub 2018 Oct 11.
  • Scientific Webinar Series this Month: January 25, 2019
  • Presenter: John Rinn (University of Minnesota) - “Crispr Live Cell imaging (CLING) and HiC data: insights into CTCF, RNA and TAD Boundaries”
  • Presenter: Daniel Capurso (The Jackson Laboratory for Genomic Medicine) - “ChIA-PIPE: a robust computational pipeline for ChIA-PET and related 3D genome mapping data”
4dn/phase1/newsletter_archive/newsletter_2019.txt · Last modified: 2025/04/22 16:21 (external edit)

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