4DN NEWSLETTER
November 2020

4DN News

4DN Phase II kick-off meeting
The kick-off meeting for Phase II members of 4D Nucleome will be held virtually on Zoom on December 2-4, 2020. Please check your emails for all the information (including the Zoom link) as well as  the 4DN Web Portal!
 
Please contact OH at oh@4dnucleome.org if you have any questions.

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.

A map of cis-regulatory elements and 3D genome structures in zebrafish
Hongbo Yang, Yu Luan, Tingting Liu, Hyung Joo Lee, Li Fang, Yanli Wang, Xiaotao Wang, Bo Zhang, Qiushi Jin, Khai Chung Ang, Xiaoyun Xing, Juan Wang, Jie Xu, Fan Song, Iyyanki Sriranga, Chachrit Khunsriraksakul, Tarik Salameh, Daofeng Li, Mayank N. K. Choudhary, Jacek Topczewski, Kai Wang, Glenn S. Gerhard, Ross C. Hardison, Ting Wang, Keith C. Cheng, Feng Yue
 
The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species1. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.

Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome
He Fang, Giancarlo Bonora, Jordan P. Lewandowski, Jitendra Thakur, Galina N. Filippova, Steven Henikoff, Jay Shendure, Zhijun Duan, John L. Rinn, Xinxian Deng, William S. Noble, Christine M. Disteche
 
Firre encodes a lncRNA involved in nuclear organization. Here, we show that Firre RNA expressed from the active X chromosome maintains histone H3K27me3 enrichment on the inactive X chromosome (Xi) in somatic cells. This trans-acting effect involves SUZ12, reflecting interactions between Firre RNA and components of the Polycomb repressive complexes. Without Firre RNA, H3K27me3 decreases on the Xi and the Xi-perinucleolar location is disrupted, possibly due to decreased CTCF binding on the Xi. We also observe widespread gene dysregulation, but not on the Xi. These effects are measurably rescued by ectopic expression of mouse or human Firre/FIRRE transgenes, supporting conserved trans-acting roles. We also find that the compact 3D structure of the Xi partly depends on the Firre locus and its RNA. In common lymphoid progenitors and T-cells Firre exerts a cis-acting effect on maintenance of H3K27me3 in a 26 Mb region around the locus, demonstrating cell type-specific trans- and cis-acting roles of this lncRNA.

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.

Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells
Swygert, S. G., Lin, D., Portillo-Ledesma, S., Lin, P.-Y., Hunt, D. R., Kao, C.-F., Schlick, T., Noble, W. S., Tsukiyama, T.
 
10.1101/2020.11.24.396713 - Posted: 2020-11-24

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation
Bonora, G., Ramani, V., Singh, R., Fang, H., Jackson, D., Srivatsan, S., Qiu, R., Lee, C., Trapnell, C., Shendure, J., Duan, Z., Deng, X., Noble, W. S., Disteche, C. M.
 
10.1101/2020.11.20.390765 - Posted: 2020-11-20

Transcriptional Network Orchestrating Regional Patterning of Cortical Progenitors
Ypsilanti, A. R., Pattabiraman, K., Catta-Preta, R., Golonzhka, O., Lindtner, S., Tang, K., Jones, I., Abnousi, A., Juric, I., Hu, M., Shen, Y., Dickel, D. E., Visel, A., Pennachio, L. A., Hawrylycz, M., Thompson, C., Zeng, H., Barozzi, I., Nord, A. S., Rubenstein, J. L. R.
 
10.1101/2020.11.03.366914 - Posted: 2020-11-04

HiC-ACT: Improved Detection of Chromatin Interactions from Hi-C Data via Aggregated Cauchy Test
Lagler, T. M., Yang, Y., Abnousi, A., Hu, M., Li, Y.
 
10.1101/2020.10.28.359869 - Posted: 2020-10-29

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 (December 2020)

  • December 10 (10am PT, 1pm ET) JAWG
  • December 18 (9am PT, 12pm ET) NOFIC-AICS WG 

Working Group email lists

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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