4DN NEWSLETTER
June 2020

4DN News

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.

Recent new publications

Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression
Jonathan A. Beagan, Elissa D. Pastuzyn, Lindsey R. Fernandez, Michael H. Guo, Kelly Feng, Katelyn R. Titus, Harshini Chandrashekar, Jason D. Shepherd, Jennifer E. Phillips-Cremins

Neuronal activation induces rapid transcription of immediate early genes (IEGs) and longer-term chromatin remodeling around secondary response genes (SRGs). Here, we use high-resolution chromosome-conformation-capture carbon-copy sequencing (5C-seq) to elucidate the extent to which long-range chromatin loops are altered during short- and long-term changes in neural activity. [...]

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.

Unsupervised manifold alignment for single-cell multi-omics data
Singh, R., Demetci, P., Bonora, G., Ramani, V., Lee, C., Fang, H., Duan, Z., Deng, X., Shendure, J., Disteche, C., Noble, W. S.

10.1101/2020.06.13.149195 - Posted: 2020-06-15

Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity
Mellis, I. A., Edelstein, H. I., Truitt, R., Beck, L. E., Symmons, O., Goyal, Y., Dunagin, M. C., Linares Saldana, R. A., Shah, P. P., Yang, W., Jain, R., Raj, A.

10.1101/2020.06.11.147207 - Posted: 2020-06-12

Chromatin Mechanics Dictates Subdiffusion and Coarsening Dynamics of Embedded Condensates
Lee, D. S. W., Wingreen, N. S., Brangwynne, C. P.

10.1101/2020.06.03.128561 - Posted: 2020-06-04

Gromov-Wasserstein optimal transport to align single-cell multi-omics data
Demetci, P., Santorella, R., Sandstede, B., Noble, W. S., Singh, R.
 
10.1101/2020.04.28.066787 - Posted: 2020-04-29

Scientific Webinar Series: June 26, 2020

A Structure-Function Analysis of Cajal Body Assembly
 
Karla Neugebauer - Yale University
 
Karla Neugebauer holds a BS in Biology from Cornell University, a PhD in Neuroscience from UCSF. She switched gears to RNA biology as a postdoc with Mark Roth at Fred Hutchinson Cancer Research Center. There she participated in the initial description of the SR protein family of splicing regulators and was inspired to study RNA metabolism in vivo by combining imaging, genomics, and sequencing strategies. She studied splicing in relation to nuclear speckles and discovered that most introns are removed during the process, or co-transcriptionally. Her lab has shown that snRNP assembly occurs in membraneless organelles called Cajal bodies (CBs) and that depletion of the CB scaffolding protein coilin is lethal in zebrafish embryos, due to a deficit in splicing. She is currently Professor of Molecular Biophysics and Biochemistry and of Cell Biology at Yale University, where she is also Director of the Yale Center for RNA Science and Biomedicine.

Focal enhancer-promoter loops: Fact or Fiction
 
Charles Danko - Cornell University
 
Charles Danko is the Robert N. Noyce Assistant Professor at Cornell University. His primary research interest is to understand how DNA sequence encodes complex programs of gene expression. Danko played a vital role in developing assays that map the location of RNA polymerase (PRO-seq, ChRO-seq), and has led the development of computational tools which leverage this information to identify active functional elements (dREG). Danko has a long-standing interest in integrating maps of chromatin architecture and transcription to understand the dynamic interactions that encode the timing and levels of gene transcription.

Upcoming 4DN meetings (July 2020)

  • July 9 (10am PT, 1pm ET) JAWG
  • July 10 (9am PT, 12pm ET) NOFIC-AICS WG
  • July 23 (10am PT, 1pm ET) JAWG
  • July 27 (11am PT, 2pm ET) Omics WG
  • July 30 (10am PT, 1pm ET) JAWG

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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