4D Nucleome Network Wiki

WORKSHOP

Integrated Approaches for Spatial and Temporal Mapping of Gene Activity in Cells and Tissues

SEPTEMBER 20, 2017

LOCATION: Bethesda North Marriott Hotel (Salon F-G)

1:00 Introductory statements; Rob Singer

The purpose of this workshop is to introduce expertise and technology to the consortium that would be important to help achieve the 4DN goals. The workshop will focus on spatial and temporal aspects of chromatin structure that lead to activation. The goal would be to: a) identify areas of collaboration for the 4DN network, 2) identify potential areas of collaboration with other programs, 3) provide an opportunity to have a dialog between 4DN investigators and other researchers working in this field.

1:05 Gary Karpen (Berkeley). “Phase transitions drive chromatin domain formation”

Gary has been assessing the role of chromatin in gene activation. His recent work demonstrates that chromatin domains undergo phase transitions. (Nature 2017, PMID:28636597)

1:30 Xiaowei Zhuang (Harvard). “Imaging the spatial organization of the chromosome and the transcriptome in single cells”.

Xiaowei has been developing superresolution methods for high resolution imaging of chromatin and their compartments over time (Science 2016, PMCID PMC4991974)

2:00 Michael Levine (Princeton) “Promoter-enhancer interactions as a model for gene activation”

Michael has been investigating the spatial and temporal events concerning promoters and enhancers in living embryos. They stand as a model for how 4D DNA folding can activate transcriptional bursting (Cell 2016, PMCID:PMC4970759)

2:30 break

3:00 Rifka Vlijm (Heidelberg) “Imaging nuclear structural changes using STED microscopy”.

Rifka has been working with Stefan Hell to develop dyes for superresolution STED microscopy for investigating nuclear events in living cells and embryos. (Chemistry, 2017, PMID 28370443)

3:30 Luke Lavis (Janelia Research Campus) “New dyes for imaging nuclear structures in real time”.

Luke is part of the senior leadership at Janelia. He is a leading organic chemist and responsible for generating the fluorogenic JF dyes that are now widely used for biological imaging. He is currently developing new variants that are brighter with lower phototoxicity. These dyes will eventually make it possible to image cells for longer times with less photodamage (Nature Methods 2016, PMID:27776112)

4:00 Discussion: Joan Ritland, Job Dekker, Andy Belmont, David Gilbert, Jan Liphardt, Rob Singer and Richard Conroy

The purpose of this session would be to discuss and come up with suggested Consortium activities for: 1) the temporal dynamics of nuclear architecture, 2) nuclear structure in primary cells in a 3D tissue environment.

5:00 Adjourn