Each human nucleus contains two meters of DNA that, amazingly, is packaged into an organelle a mere ~10 μm diameter. Yet, despite this dramatic difference in scale, the three-dimensional organization of the genome is non-random and plays a critical functional role in both health and disease. However, as much of our current view of nuclear organization is derived from ensemble techniques requiring populations of millions or more cells, much less is known about the organization of chromosomes in individual cells and many open questions remain about the mechanisms that shape and structure the genome. Our laboratory uses a combination of computational, molecular, and optical approaches to investigate the causes and consequences of 3D genome organization in single cells.
Imaging chromosome structure at the nanoscale
We use multiplexed DNA-PAINT and STORM single-molecule super-resolution microscopy in combination with programmable OIigopaint FISH probes to visualize the nanoscale structure of chromosomes. This approach provides a ~10-fold improvement in resolution compared to conventional microscopy and allows us to map the conformation and folding of chromosomes with exquisite detail.
Visualizing chromatin dynamics
We are interested in dynamic and structural properties of chromosomes in live cells. We will use advanced live-cell imaging approaches such as single-particle tracking, fluorescence correlation spectroscopy, and super-resolution imaging to investigate the behavior of chromosomes in vivo.
Genome mining and thermodynamic modeling
We build and use computational tools to find optimal sites for molecular reagents such as in situ hybridization probes on a genome-wide scale. We also use machine learning and analytical computing to predict the thermodynamic behavior of nucleic acid systems and to investigate the sequence and structural properties of the genome.
We are interested in deploying high-throughput approaches such as Hi-FISH and targeted mass spectrometry to identify the molecular factors that shape and structure the 3D genome.
Advanced microscopy and instrumentation
Multiplexed super-resolution imaging of chromosomes in their in situ context presents significant technical challenges. We design and build custom optical configurations and apply advanced optical methods to increase our ability to visualize genome organization in single cells.
Genomics technology development
We develop new enabling molecular technologies to allow researchers to investigate a broad range of questions involving genome organization and gene expression.
Kishi, J.Y.*, Beliveau, B.J.*, Lapan, S.W.*, West, E.R., Zhu, A., Sasaki, H.M., Saka, S.K., Wang, Y., Cepko, C.L.†, Yin, P.† SABER enables highly multiplexed and amplified detection of DNA and RNA in cells and tissues. [*Co-first authors] [†Co-corresponding authors] bioRxiv 2018
Nir, G.*, Farabella, I.*, Pérez Estrada, C.*, Ebeling, C.G.*, Beliveau, B.J., Sasaki, H.M., Lee, S.H., Nguyen, S., McCole, R.B., Chattoraj, S., Erceg, J., AlHaj Abed, J., Martins, N.C., Nguyen, H.Q., Hannan, M.A., Russell, S., Durand, N.C., Rao, S.P., Kishi, J.Y., Soler-Vila, P., Di Pierro, M., Onuchic, J.N., Callahan, S., Schreiner, J., Stuckey, J.†, Yin, P.†, Lieberman Aiden, E.†, Marti-Renom, M.A.†, Wu, C.T.† Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. [*Co-first authors] [†Co-corresponding authors] bioRxiv 2018
Beliveau, B.J.†, Kishi, J.Y., Nir, G., Sasaki, H.M., Saka, S.K., Nguyen, S.C., Wu, C.T., Yin, P†. OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. Proc. Natl. Acad. Sci. USA 115, E2183-E2192 (2018). [†Co-corresponding authors] Journal PDF bioRxiv
Schüder, F., Lara-Gutiérrez, J., Beliveau, B.J., Saka, S.K., Sasaki, H.M., Woehrstein, J.B., Strauss, M.T., Grabmayr, H., Yin, P., Jungmann, R. Multiplexed 3D super-resolution imaging of whole cells using Spinning Disc Confocal Microscopy and DNA-PAINT. Nat. Commun. 8, 2090 (2017). Journal PDF
Beliveau B.J., Boettiger A.B., Avendaño, M.S., Jungmann R., McCole R.B., Joyce E.F., Kim-Kiselak C., Bantignies F., Fonseka C.Y., Erceg J., Hannan M.A., Hoang, H.G., Colognori D., Lee J.T., Shih W.M., Yin P., Zhuang X., Wu C.-T. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat. Commun.6, 8147 (2015). Journal PDF
Beliveau B.J.*, Joyce E.F.*, Apostolopoulos N., Yilmaz F., Fonseka C.Y., McCole R.B., Chang Y., Li J.B., Senaratne T.N., Williams B.R., Rouillard J.M., Wu C.-T. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc. Natl. Acad. Sci. USA 109, 21301-06 (2012). [*Co-first authors] Journal PDF