Table of Contents

Newsletter Archive: 2019

December 2019

November 2019

October 2019

September 2019

August 2019

July 2019

June 2019

May 2019

April 2019

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”