4DN NEWSLETTER
April 2020

4DN News

Beginning May 1, 2020, please contact OH (oh@4dnucleome.org) and Riccardo Calandrelli (rcalandrelli@eng.ucsd.edu) for adding new preprints. Dr. Gehlenborg and Dr. Mirny will no longer be the responsible curators to the 4DN bioRxiv channel. We sincerely thank Hugo Brandao for the excellent job he has done for keeping the channel up to date!

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

Distinct features of nucleolus-associated domains in mouse embryonic stem cells
Aizhan Bizhanova, Aimin Yan, Jun Yu, Lihua Julie Zhu, Paul D. Kaufman

Heterochromatin in eukaryotic interphase cells frequently localizes to the nucleolar periphery (nucleolus-associated domains (NADs)) and the nuclear lamina (lamina-associated domains (LADs)). Gene expression in somatic cell NADs is generally low, but NADs have not been characterized in mammalian stem cells. Here, we generated the first genome-wide map of NADs in mouse embryonic stem cells (mESCs) via deep sequencing of chromatin associated with biochemically purified nucleoli. [...]

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.

HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data
Jain, D., Chu, C., Alver, B. H., Lee, S., Lee, E. A., Park, P. J.

10.1101/2020.04.27.060145 - Posted: 2020-04-28

Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin
Fiorillo, L., Musella, F., Kempfer, R., Chiariello, A. M., Bianco, S., Kukalev, A., Irastorza-Azcarate, I., Esposito, A., Conte, M., Prisco, A., Pombo, A., Nicodemi, M.

10.1101/2020.04.24.059915 - Posted: 2020-04-25

Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments
Chen, Z., Shaw, A., Wilson, H., Woringer, M., Darzacq, X., Marqusee, S., Wang, Q., Bustamante, C.

10.1101/2020.04.10.036442 - Posted: 2020-04-11

The spatial distributions of pre-mRNAs suggest post-transcriptional splicing of specific introns within endogenous genes
Cote, A. J., Cote, C. J., Bayatpour, S., Drexler, H. L., Alexander, K. A., Chen, F., Wassie, A. T., Boyden, E. S., Berger, S., Churchman, L. S., Raj, A.

10.1101/2020.04.06.028092 - Posted: 2020-04-07

Cell-type specialization in the brain is encoded by specific long-range chromatin topologies
Winick-Ng, W., Kukalev, A., Harabula, I., Zea Redondo, L., Meijer, M., Serebreni, L., Bianco, S., Szabo, D., Chiariello, A. M., Irastorza Azcarate, I., Fiorillo, L., Musella, F., Thieme, C., Irani, E., Torlai Triglia, E., Kolodziejczyk, A. A., Abentung, A., Apostolova, G., Paul, E. J., Franke, V., Kempfer, R., Akalin, A., Teichmann, S., Dechant, G., Ungless, M. A., Nicodemi, M., Castelo-Branco, G., Pombo, A.

10.1101/2020.04.02.020990  - Posted: 2020-04-02

CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells
Kubo N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J.D., Conte, M., Gorkin, D., Yu, M., Li, B., Dixon, J.R., Hu, M., Nicodemi, M., Zhao, H., Ren, B.

10.1101/2020.03.21.001693 - Posted: 2020-03-23

Scientific Webinar Series: April 24, 2020

CUT&RUN and CUT&Tag methods for profiling chromatin marks and chromatin structure

Kami Ahmad - Fred Hutchinson Cancer Research Center

Kami Ahmad is a principal investigator at the Fred Hutchinson Cancer Research Center working with Steven Henikoff's group. We work on technology development for chromatin profiling, including CUT&RUN and CUT&Tag methods. I apply these methods to deciphering the roles of chromatin silencing mechanisms in development.

Cryo-Milling TCC-Based Mapping of Genome-Wide Chromatin Contacts

Jiang Xu - University of Southern California

Jiang Xu is a PostDoc Researcher in Dr. Lin Chen's Research Group in University of Southern California. He got his degree in Clinical Medicine in 2004 and Ph.D. in Neurology in 2009 in China. Before jumping in the 3D nuclear structure field, he mainly focused on recombinant protein expression, purification and X-ray structural determination. He started to develop the cryo-milling based 3C method 4 years ago and have been doing so ever since.

Upcoming 4DN meetings (May 2020)

  • May 4 (12pm PT, 3pm ET) Imaging Workgroup
  • May 8 (9am PT, 12pm ET) NOFIC-AICS Workgroup
  • May 14 (10am PT, 1pm ET) JAWG
  • May 22 (8am PT, 11am ET) 4DN Scientific Webinar
  • May 22 (9am PT, 12pm ET) NOFIC-AICS Workgroup
  • May 25 (11am PT, 2pm ET) Omics Workgroup
  • May 28 (10am PT, 1pm ET) JAWG

Stay connected
created in Publicate