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Fluorescence Microscopy Journal Club

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

by Guy Nir1^, Irene Farabella2^, Cynthia Pérez Estrada1,3,4 ^, Carl G. Ebeling5^, Brian J. Beliveau1,6,7, Hiroshi M. Sasaki6,7, Soun H. Lee1, Son C. Nguyen1†, Ruth B. McCole1, Shyamtanu Chattoraj1, Jelena Erceg1, Jumana AlHaj Abed1, Nuno M. C. Martins1, Huy Q. Nguyen1, Mohammed Hannan1, Sheikh Russell3, Neva C. Durand3,8, Suhas S.P. Rao3,4,9, Jocelyn Y. Kishi6,7, Paula Soler-Vila2, Michele Di Pierro4, José N. Onuchic4, Steven Callahan10, John Schreiner10, Jeff Stuckey11*, Peng Yin6,7*, Erez Lieberman Aiden3,4,8,12*, Marc A. Marti- Renom2,13,14,15*, C.-ting Wu1,6*

PLoS 2018, Genet 14(12)

While progress has been made in understanding the organization and structure of chromosomes in situ, the size as well sequential and structural heterogeneity of chromosomal DNA within chromosomal regions make it a particularly challenging molecule to study. Understanding the organizational structure of chromosomes in situ would greatly benefit in understanding chromosomal function on both normal and pathological conditions.

The authors present a method for 3-D visualization of chromosomal DNA at the super resolution level through the use of OligoSTORM. Using a sequential labelling strategy with single molecule localization microscopy, the authors “walk” along 8.16 megabases (Mbs) of chromosome 19 of primary fibroblasts. The resulting images resolved structures of individual compartments within the chromosomal region imaged.

The authors also obtained Hi-C contact frequency data and integrated it with the localization microscopy data to produce 3-D models at 10 kilobase (kb) resolution.

Unknown patterns of chromosomal organization were observed in their results, as well as significant structural variability. The authors discuss the implications of their findings, and suggest that their methods could allow studies of chromosomes as single, fully integrated units of structure and function.