PMID- 29577183 OWN - NLM STAT- MEDLINE DCOM- 20190614 LR - 20190614 IS - 1573-6822 (Electronic) IS - 0742-2091 (Print) IS - 0742-2091 (Linking) VI - 34 IP - 5 DP - 2018 Oct TI - Developing novel methods to image and visualize 3D genomes. PG - 367-380 LID - 10.1007/s10565-018-9427-z [doi] AB - To investigate three-dimensional (3D) genome organization in prokaryotic and eukaryotic cells, three main strategies are employed, namely nuclear proximity ligation-based methods, imaging tools (such as fluorescence in situ hybridization (FISH) and its derivatives), and computational/visualization methods. Proximity ligation-based methods are based on digestion and re-ligation of physically proximal cross-linked chromatin fragments accompanied by massively parallel DNA sequencing to measure the relative spatial proximity between genomic loci. Imaging tools enable direct visualization and quantification of spatial distances between genomic loci, and advanced implementation of (super-resolution) microscopy helps to significantly improve the resolution of images. Computational methods are used to map global 3D genome structures at various scales driven by experimental data, and visualization methods are used to visualize genome 3D structures in virtual 3D space-based on algorithms. In this review, we focus on the introduction of novel imaging and visualization methods to study 3D genomes. First, we introduce the progress made recently in 3D genome imaging in both fixed cell and live cells based on long-probe labeling, short-probe labeling, RNA FISH, and the CRISPR system. As the fluorescence-capturing capability of a particular microscope is very important for the sensitivity of bioimaging experiments, we also introduce two novel super-resolution microscopy methods, SDOM and low-power super-resolution STED, which have potential for time-lapse super-resolution live-cell imaging of chromatin. Finally, we review some software tools developed recently to visualize proximity ligation-based data. The imaging and visualization methods are complementary to each other, and all three strategies are not mutually exclusive. These methods provide powerful tools to explore the mechanisms of gene regulation and transcription in cell nuclei. FAU - Ma, Tszshan AU - Ma T AD - School of Medicine, Tsinghua University, Beijing, 100084, China. FAU - Chen, Long AU - Chen L AD - MOE Key Laboratory of Bioinformatics; Bioinformatics Division, Center for Synthetic & Systems Biology, BNRist; Department of Automation, Tsinghua University, Beijing, 100084, China. AD - Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China. FAU - Shi, Maoxiang AU - Shi M AD - Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China. FAU - Niu, Jing AU - Niu J AD - School of Life Sciences, Tsinghua University, Beijing, 100084, China. FAU - Zhang, Xu AU - Zhang X AD - Department of Automation, Tsinghua University, Beijing, 100084, China. FAU - Yang, Xusan AU - Yang X AD - Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. FAU - Zhanghao, Karl AU - Zhanghao K AD - Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. FAU - Wang, Miaoyan AU - Wang M AD - Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. FAU - Xi, Peng AU - Xi P AD - Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. FAU - Jin, Dayong AU - Jin D AD - Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia. FAU - Zhang, Michael AU - Zhang M AD - MOE Key Laboratory of Bioinformatics; Bioinformatics Division, Center for Synthetic & Systems Biology, BNRist; Department of Automation, Tsinghua University, Beijing, 100084, China. AD - Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China. AD - Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China. AD - Department of Biological Sciences, Center for Systems Biology, the University of Texas at Dallas, Richardson, TX, 75080-3021, USA. FAU - Gao, Juntao AU - Gao J AD - MOE Key Laboratory of Bioinformatics; Bioinformatics Division, Center for Synthetic & Systems Biology, BNRist; Department of Automation, Tsinghua University, Beijing, 100084, China. jtgao@biomed.tsinghua.edu.cn. AD - Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China. jtgao@biomed.tsinghua.edu.cn. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20180326 PL - Switzerland TA - Cell Biol Toxicol JT - Cell biology and toxicology JID - 8506639 RN - 0 (Chromatin) RN - 9007-49-2 (DNA) SB - IM MH - Cell Nucleus MH - Chromatin/genetics/physiology MH - Chromosome Structures/*genetics/physiology/ultrastructure MH - Chromosomes/genetics MH - Computational Biology/*methods MH - DNA/metabolism MH - Genome/physiology MH - Humans MH - Imaging, Three-Dimensional/*methods MH - In Situ Hybridization, Fluorescence/methods MH - Sequence Analysis, DNA/methods PMC - PMC6133007 OTO - NOTNLM OT - 3D genomes OT - Chromatins OT - FISH method EDAT- 2018/03/27 06:00 MHDA- 2019/06/15 06:00 PMCR- 2018/03/26 CRDT- 2018/03/27 06:00 PHST- 2017/11/03 00:00 [received] PHST- 2018/03/11 00:00 [accepted] PHST- 2018/03/27 06:00 [pubmed] PHST- 2019/06/15 06:00 [medline] PHST- 2018/03/27 06:00 [entrez] PHST- 2018/03/26 00:00 [pmc-release] AID - 10.1007/s10565-018-9427-z [pii] AID - 9427 [pii] AID - 10.1007/s10565-018-9427-z [doi] PST - ppublish SO - Cell Biol Toxicol. 2018 Oct;34(5):367-380. doi: 10.1007/s10565-018-9427-z. Epub 2018 Mar 26.