4DN NEWSLETTER
October 2020

4DN News

4DN Phase II Funded Research Announcements
The first phase of the 4DN program was very successful, but there is still a need to deliver data and tools to the broader biomedical research community to address the role of nuclear organization in health and disease. A second stage of funding for the 4DN program is beginning and funded research groups have now all be announced.

4DN Phase II kick-off meeting
The kick-off meeting for Phase II of 4D Nucleome will be held virtually on Zoom on December 2-4, 2020. Additional information and registration will come soon, stay tuned on the Web Portal!

4DN Wiki Update
OH began updating the 4DN Wiki to move forward to the Phase II of 4DN. Please avoid using any previously saved bookmark to access any page, given that the Wiki structure is changing and old links will no longer work. During the transition, you should be able to navigate the Wiki as usual using the sidebar.

4DN Publications

Please notify 4DN OH at oh@4dnucleome.org of your new publications and tweet it by tagging us with @4DNucleome.

Your publication will be added to the 4DN Publication Repository accessible from the 4D Nucleome Web Portal.

Stress-induced RNA–chromatin interactions promote endothelial dysfunction
Riccardo Calandrelli, Lixia Xu, Yingjun Luo, Weixin Wu, Xiaochen Fan, Tri Nguyen, Chien-Ju Chen, Kiran Sriram, Xiaofang Tang, Andrew B. Burns, Rama Natarajan, Zhen Bouman Chen, Sheng Zhong
 
Chromatin-associated RNA (caRNA) has been proposed as a type of epigenomic modifier. Here, we test whether environmental stress can induce cellular dysfunction through modulating RNA-chromatin interactions. We induce endothelial cell (EC) dysfunction with high glucose and TNFα (H + T), that mimic the common stress in diabetes mellitus. We characterize the H + T-induced changes in gene expression by single cell (sc)RNA-seq, DNA interactions by Hi-C, and RNA-chromatin interactions by iMARGI. H + T induce inter-chromosomal RNA-chromatin interactions, particularly among the super enhancers. To test the causal relationship between H + T-induced RNA-chromatin interactions and the expression of EC dysfunction-related genes, we suppress the LINC00607 RNA. This suppression attenuates the expression of SERPINE1, a critical pro-inflammatory and pro-fibrotic gene. Furthermore, the changes of the co-expression gene network between diabetic and healthy donor-derived ECs corroborate the H + T-induced RNA-chromatin interactions. Taken together, caRNA-mediated dysregulation of gene expression modulates EC dysfunction, a crucial mechanism underlying numerous diseases.

4DN Pre-prints

Please notify OH (oh@4dnucleome.org) and Riccardo Calandrelli (rcalandrelli@eng.ucsd.edu) to add your pre-print into the 4DN bioRxiv channel and tweet it by tagging us with @4DNucleome.

Your pre-print will be added also to the 4DN Pre-print Repository accessible from the 4D Nucleome Web Portal.

HiCRep.py: Fast comparison of Hi-C contact matrices in Python
Lin, D., Sanders, J., Noble, W. S.
 
10.1101/2020.10.27.357756 - Posted: 2020-10-28

DNA-loop extruding SMC complexes can traverse one another in vivo
Brandão, H. B., Ren, Z., Karaboja, X., Mirny, L. A., Wang, X.
 
10.1101/2020.10.26.356329 - Posted: 2020-10-27

Deep learning enables fast and dense single-molecule localization with high accuracy
Speiser, A., Müller, L.-R., Matti, U., Obara, C. J., Legant, W. R., Kreshuk, A., Macke, J. H., Ries, J., Turaga, S. C.
 
10.1101/2020.10.26.355164 - Posted: 2020-10-26

MCM complexes are barriers that restrict cohesin-mediated loop extrusion
Dequeker, B. J. H., Brandao, H. B., Scherr, M. J., Gassler, J., Powell, S., Gaspar, I., Flyamer, I. M., Tang, W., Stocsits, R., Davidson, I. F., Peters, J.-M., Duderstadt, K. E., Mirny, L. A., Tachibana, K.
 
10.1101/2020.10.15.340356 - Posted: 2020-10-15

HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics
Strom, A. R., Biggs, R. J., Banigan, E. J., Wang, X., Chiu, K., Herman, C., Collado, J., Yue, F., Ritland Politz, J. C., Tait, L. J., Scalzo, D., Telling, A., Groudine, M., Brangwynne, C. P., Marko, J., Stephens, A. D.

10.1101/2020.10.09.331900 - Posted: 2020-10-09

Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia
Janssens, D., Meers, M. P., Wu, S. J., Babaeva, E., Meshinchi, S., Sarthy, J. F., Ahmad, K., Henikoff, S.

10.1101/2020.10.06.328948 - Posted: 2020-10-08

Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches
Desai, P. R., Brahmachari, S., Marko, J. F., Das, S., Neuman, K. C.

10.1101/2019.12.20.885533 - Posted: 2020-10-04

PYMEVisualize: an open-source tool for exploring 3D super-resolution data
Marin, Z., Graff, M., Barentine, A. E. S., Soeller, C., Chung, K. K. H., Fuentes, L. A., Baddeley, D.

10.1101/2020.09.29.315671 - Posted: 2020-09-30

Scientific Webinar Series

We have concluded the Scientific Webinar Series sessions for the first phase of 4D Nucleome. Thank you to all who have presented and joined over the past 5 years!
 
You can find Scientific Webinar presentation slides on the 4DN Wiki. 

Upcoming 4DN meetings (November 2020)

  • November 12 (10am PT, 1pm ET) JAWG
  • November 13 (9am PT, 12pm ET) NOFIC-AICS WG 

Working Group email lists

  • Policy WG - pubpol@4dnucleome.org
  • Policy WG - pubpol@4dnucleome.org
  • Omics WG - omics@4dnucleome.org
  • Imaging WG - image@4dnucleome.org
  • Data Analysis WG - analysis@4dnucleome.org
  • Outreach WG - outreach@4dnucleome.org
  • Cell Lines WG - cells@4dnucleome.org
  • Joint Analysis WG - meeting-4dn-dj@4dnucleome.org

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